RiceVarMap v3.0

Search for Variation by Gene

Search results

243 variations found. LOC_Os03g42230 (B3 DNA binding domain containing protein; expressed), ranging from 23,491,994 bp to 23,496,324 bp (including 0 kb upstream and 0 kb downstream of the gene).

Syntenic genes

MH63RS3: OsMH_03G0414000
ZS97RS3: OsZS_03G0418700
MSU: LOC_Os03g42230
RAP: Os03g0619600

Gene Structure

Five-point stars indicate variants annotated as snpEff HIGH impact or PolyPhen-2 damaging.

Chromatin accessibility landscape across tissues

Allele-specific chromatin accessibility effects predicted by Basenji are reported as the signed local sequence activity log-ratio (LSAR): log₂(P_ALT + 1) − log₂(P_REF + 1), using local predictions averaged across the central eight 128-bp output bins (1,024 bp total). Positive and negative values indicate increased and reduced predicted accessibility for the alternative allele, respectively. For Nipponbare SNP and non-SNP variants, a light-red five-point star (★) indicates an HEV and a red five-point star (★) indicates a strong HEV.

Tissue descriptions and sources

Population differentiation

Weighted FST is the VCFtools windowed Weir & Cockerham estimate. Windows are read directly from the precomputed 10 kb / 1 kb-step data.

Displayed region: gene ±500 kb

Weighted FST

Population 1 vs Population 2

Population comparison: -

Gene Peak FST

Local Peak FST

Genome-wide P95

Advanced information

Valid local windows 0 Mean FST NA Median FST NA Windows ≥ P95 NA

Nucleotide diversity (π)

Populations

Advanced information

Detailed Variation Information

Var ID	Chrom	Position	Primary Allele	Secondary Allele	Primary Allele Frequency	DEL Frequency	Var	GWAS Results	Effect
vg0323492012	chr03	23492012	C	T	61.90%	6.58%	T -> C	NA	LOC_Os03g42230.1 Alt: C\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492018	chr03	23492018	C	T	98.20%	1.33%	C -> T	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492022	chr03	23492022	CGCGACC GCTGCTA GGGTGG	C	91.30%	7.51%	CGCGACCGCT GCTAGGGTGG -> C,TGCGACCG CTGCTAGGGT GG,CATGGCG ACCGCTGCTA GGGTGG,CAT GGTGGTGGAT GCGACGGCGG TTGCTGTAGG GTGGATGCGA CAGTGGCCGG TGGCCGCGGC AGGATCGATG CGACCGCTGC TAGGGTGG,C AGGGTGG	NA	LOC_Os03g42230.1 Alt: C\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: CAGGGTGG\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: CAGGGTGG\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: CAGGGTGG\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: CAGGGTGG\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: CAGGGTGG\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42230.1 Alt: TGCGACCGCTGCTAGGGTGG\| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff) LOC_Os03g42230.1 Alt: TGCGACCGCTGCTAGGGTGG\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: TGCGACCGCTGCTAGGGTGG\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: TGCGACCGCTGCTAGGGTGG\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: TGCGACCGCTGCTAGGGTGG\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: TGCGACCGCTGCTAGGGTGG\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42230.1 Alt: CATGGTGGTGGATGCGACGGCGGTTGCTGTAGGGTGGATGCGACAGTGGCCGGTGGCCGCGGCAGGATCGATGCGACCGCTGCTAGGGTGG\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: CATGGTGGTGGATGCGACGGCGGTTGCTGTAGGGTGGATGCGACAGTGGCCGGTGGCCGCGGCAGGATCGATGCGACCGCTGCTAGGGTGG\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: CATGGTGGTGGATGCGACGGCGGTTGCTGTAGGGTGGATGCGACAGTGGCCGGTGGCCGCGGCAGGATCGATGCGACCGCTGCTAGGGTGG\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: CATGGTGGTGGATGCGACGGCGGTTGCTGTAGGGTGGATGCGACAGTGGCCGGTGGCCGCGGCAGGATCGATGCGACCGCTGCTAGGGTGG\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: CATGGTGGTGGATGCGACGGCGGTTGCTGTAGGGTGGATGCGACAGTGGCCGGTGGCCGCGGCAGGATCGATGCGACCGCTGCTAGGGTGG\| downstream_gene_variant MODIFIER(snpEff) N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: CATGGCGACCGCTGCTAGGGTGG\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: CATGGCGACCGCTGCTAGGGTGG\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: CATGGCGACCGCTGCTAGGGTGG\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: CATGGCGACCGCTGCTAGGGTGG\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: CATGGCGACCGCTGCTAGGGTGG\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323492026	chr03	23492026	ACCG	A	98.50%	1.10%	ACCG -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492028	chr03	23492028	C	T	99.80%	0.00%	C -> T	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff) LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)
vg0323492034	chr03	23492034	TAG	TG	98.60%	1.08%	TAG -> T,TG	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: TG\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: TG\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: TG\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: TG\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: TG\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323492035	chr03	23492035	A	G	70.60%	18.73%	A -> G	NA	N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: G\| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: G\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323492038	chr03	23492038	G	T	98.60%	1.10%	G -> T	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492041	chr03	23492041	GATGCGA CGGCGGC CGCGGT	Unkown	98.70%	1.12%	GATGCGACGG CGGCCGCGGT -> G	NA	LOC_Os03g42230.1 Alt: G\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: G\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: G\| downstream_gene_variant MODIFIER(snpEff)
vg0323492043	chr03	23492043	TGCGACG GCGGCCG C	T	91.60%	7.62%	TGCGACGGCG GCCGC -> T	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492057	chr03	23492057	CGG	TGG	95.30%	3.87%	CGG -> TGG,C	NA	LOC_Os03g42230.1 Alt: C\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: C\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: C\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: C\| downstream_gene_variant MODIFIER(snpEff) N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: TGG\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: TGG\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: TGG\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: TGG\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: TGG\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323492061	chr03	23492061	G	A	74.50%	18.96%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492074	chr03	23492074	G	Unkown	98.80%	0.83%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)
vg0323492078	chr03	23492078	C	T	91.70%	7.49%	C -> T	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492084	chr03	23492084	C	T	91.70%	7.45%	C -> T	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492086	chr03	23492086	G	Unkown	98.30%	1.38%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)
vg0323492099	chr03	23492099	G	A	93.70%	5.29%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492103	chr03	23492103	G	A	74.80%	20.57%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492105	chr03	23492105	C	T	52.90%	11.40%	C -> T	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492114	chr03	23492114	C	T	75.40%	20.78%	C -> T	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492128	chr03	23492128	C	T	95.20%	4.30%	C -> T	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492130	chr03	23492130	A	Unkown	99.10%	0.21%	A -> ATGGCGGCTG TGGCGGGAT	NA	LOC_Os03g42230.1 Alt: ATGGCGGCTGTGGCGGGAT\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: ATGGCGGCTGTGGCGGGAT\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: ATGGCGGCTGTGGCGGGAT\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: ATGGCGGCTGTGGCGGGAT\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: ATGGCGGCTGTGGCGGGAT\| downstream_gene_variant MODIFIER(snpEff)
vg0323492133	chr03	23492133	A	G	69.10%	26.60%	A -> G,ATGCGACG G,ATGTGACG G	NA	LOC_Os03g42230.1 Alt: ATGCGACGG\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: ATGCGACGG\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: ATGCGACGG\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: ATGCGACGG\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: ATGCGACGG\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42230.1 Alt: ATGTGACGG\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: ATGTGACGG\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: ATGTGACGG\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: ATGTGACGG\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: ATGTGACGG\| downstream_gene_variant MODIFIER(snpEff) N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: G\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323492140	chr03	23492140	C	T	98.60%	1.08%	C -> T	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492142	chr03	23492142	A	G	70.00%	26.75%	A -> G	NA	N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: G\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323492143	chr03	23492143	C	T	81.90%	14.83%	C -> T	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492144	chr03	23492144	A	G	91.60%	5.92%	A -> G	NA	N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: G\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323492150	chr03	23492150	G	A	93.90%	4.68%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492153	chr03	23492153	G	GCGACGA CGGCTGC GACAGGA TCGATA	40.90%	15.47%	G -> GCGACGACGG CTGCGACAGG ATCGATA,GC GACGACGGCT GCGACAGGAT TGATA,A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: GCGACGACGGCTGCGACAGGATTGATA\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: GCGACGACGGCTGCGACAGGATTGATA\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: GCGACGACGGCTGCGACAGGATTGATA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: GCGACGACGGCTGCGACAGGATTGATA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: GCGACGACGGCTGCGACAGGATTGATA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: GCGACGACGGCTGCGACAGGATCGATA\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: GCGACGACGGCTGCGACAGGATCGATA\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: GCGACGACGGCTGCGACAGGATCGATA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: GCGACGACGGCTGCGACAGGATCGATA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: GCGACGACGGCTGCGACAGGATCGATA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323492156	chr03	23492156	A	ACGACGG CTGCGAC AGGAT	99.70%	0.00%	A -> ACGACGGCTG CGACAGGAT	NA	LOC_Os03g42230.1 Alt: ACGACGGCTGCGACAGGAT\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: ACGACGGCTGCGACAGGAT\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: ACGACGGCTGCGACAGGAT\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: ACGACGGCTGCGACAGGAT\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: ACGACGGCTGCGACAGGAT\| downstream_gene_variant MODIFIER(snpEff)
vg0323492159	chr03	23492159	ATAGCCG	GTAGCCG	93.00%	6.01%	ATAGCCG -> GTAGCCG,A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff) N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: GTAGCCG\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: GTAGCCG\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: GTAGCCG\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: GTAGCCG\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: GTAGCCG\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323492160	chr03	23492160	T	C	99.70%	0.00%	T -> C	NA	LOC_Os03g42230.1 Alt: C\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: C\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: C\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: C\| downstream_gene_variant MODIFIER(snpEff)
vg0323492161	chr03	23492161	A	G	92.30%	5.82%	A -> G,ACGACGAT T,T	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: G\| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: G\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: ACGACGATT\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: ACGACGATT\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: ACGACGATT\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: ACGACGATT\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: ACGACGATT\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323492164	chr03	23492164	C	T	88.30%	10.24%	C -> T	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492165	chr03	23492165	G	Unkown	99.20%	0.66%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)
vg0323492168	chr03	23492168	GTAGGAT	ATAGGAT	99.80%	0.00%	GTAGGAT -> ATAGGAT,G	NA	LOC_Os03g42230.1 Alt: ATAGGAT\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: ATAGGAT\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: ATAGGAT\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: ATAGGAT\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: ATAGGAT\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42230.1 Alt: G\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: G\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: G\| downstream_gene_variant MODIFIER(snpEff)
vg0323492169	chr03	23492169	T	C	92.80%	6.20%	T -> C	NA	LOC_Os03g42230.1 Alt: C\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492170	chr03	23492170	AGGATCG ATGCGAC GGCAGCC GCGGTG	GGGATCG ATGCGAC GGCAGCC GCGGTG	72.80%	22.77%	AGGATCGATG CGACGGCAGC CGCGGTG -> GGGATCGATG CGACGGCAGC CGCGGTG,A	NA	LOC_Os03g42230.1 Alt: GGGATCGATGCGACGGCAGCCGCGGTG\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: GGGATCGATGCGACGGCAGCCGCGGTG\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: GGGATCGATGCGACGGCAGCCGCGGTG\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: GGGATCGATGCGACGGCAGCCGCGGTG\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: GGGATCGATGCGACGGCAGCCGCGGTG\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff) N Alt: DEL/silent_mutation(CooVar)
vg0323492179	chr03	23492179	G	A	99.80%	0.00%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)
vg0323492181	chr03	23492181	G	Unkown	98.80%	0.68%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)
vg0323492183	chr03	23492183	C	T	94.60%	2.29%	C -> T	mr1166 (All); LR P-value: 2.61E-13; mr1184 (All); LR P-value: 4.74E-06; mr1424 (All); LR P-value: 5.63E-06; mr1471 (All); LR P-value: 6.96E-11; mr1515 (All); LR P-value: 8.40E-19; mr1549 (All); LR P-value: 7.09E-38; mr1586 (All); LR P-value: 2.60E-24; mr1652 (All); LR P-value: 1.82E-06; mr1706 (All); LR P-value: 2.68E-07; mr1722 (All); LR P-value: 3.93E-09; mr1730 (All); LR P-value: 3.56E-10; mr1735 (All); LR P-value: 1.84E-06; mr1808 (All); LR P-value: 4.73E-06; mr1193_2 (All); LR P-value: 4.80E-11; mr1549_2 (All); LR P-value: 1.95E-31; mr1757_2 (All); LR P-value: 2.76E-26; mr1808_2 (All); LR P-value: 1.64E-09; mr1815_2 (All); LR P-value: 1.72E-06; mr1855_2 (All); LR P-value: 9.31E-22	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492184	chr03	23492184	G	Unkown	94.90%	4.38%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)
vg0323492185	chr03	23492185	G	T	68.50%	26.85%	G -> T,A	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492186	chr03	23492186	CAGCCGC GGTGGGA TCGATGC GACGAT	TAGCCGC GGTGGGA TCGATGC GACGAT	92.00%	7.32%	CAGCCGCGGT GGGATCGATG CGACGAT -> TAGCCGCGGT GGGATCGATG CGACGAT,C	NA	LOC_Os03g42230.1 Alt: TAGCCGCGGTGGGATCGATGCGACGAT\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: TAGCCGCGGTGGGATCGATGCGACGAT\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: TAGCCGCGGTGGGATCGATGCGACGAT\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: TAGCCGCGGTGGGATCGATGCGACGAT\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: TAGCCGCGGTGGGATCGATGCGACGAT\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: C\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: C\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: C\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: C\| downstream_gene_variant MODIFIER(snpEff)
vg0323492187	chr03	23492187	A	G	73.00%	23.09%	A -> G	NA	N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: G\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323492189	chr03	23492189	C	T	98.50%	1.12%	C -> T	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492190	chr03	23492190	C	T	92.90%	6.54%	C -> T	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492196	chr03	23492196	G	A	99.60%	0.02%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492198	chr03	23492198	G	T	94.90%	2.29%	G -> T	mr1058 (All); LR P-value: 3.32E-06; mr1101 (All); LR P-value: 5.11E-26; mr1166 (All); LR P-value: 3.45E-13; mr1184 (All); LR P-value: 4.93E-06; mr1207 (All); LR P-value: 4.75E-06; mr1230 (All); LR P-value: 5.79E-06; mr1424 (All); LR P-value: 2.74E-06; mr1471 (All); LR P-value: 2.53E-11; mr1515 (All); LR P-value: 8.77E-19; mr1549 (All); LR P-value: 9.11E-38; mr1586 (All); LR P-value: 3.14E-24; mr1652 (All); LR P-value: 1.21E-06; mr1706 (All); LR P-value: 1.06E-07; mr1722 (All); LR P-value: 1.91E-09; mr1730 (All); LR P-value: 1.12E-10; mr1735 (All); LR P-value: 2.26E-06; mr1787 (All); LR P-value: 3.34E-06; mr1808 (All); LR P-value: 5.00E-06; mr1939 (All); LR P-value: 8.64E-09; mr1193_2 (All); LR P-value: 2.79E-10; mr1549_2 (All); LR P-value: 1.26E-31; mr1808_2 (All); LR P-value: 1.79E-09; mr1815_2 (All); LR P-value: 1.33E-06	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492206	chr03	23492206	C	T	99.60%	0.00%	C -> T	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)
vg0323492207	chr03	23492207	G	A	50.30%	13.37%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492210	chr03	23492210	G	Unkown	94.80%	4.49%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)
vg0323492211	chr03	23492211	A	G	92.90%	6.43%	A -> G	NA	N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: G\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323492212	chr03	23492212	T	C	92.90%	6.43%	T -> C	NA	LOC_Os03g42230.1 Alt: C\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492220	chr03	23492220	C	A	73.10%	22.51%	C -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492221	chr03	23492221	G	A	92.30%	7.17%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492227	chr03	23492227	A	G	66.00%	28.04%	A -> G	NA	N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: G\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323492229	chr03	23492229	G	T	92.30%	7.15%	G -> T	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492237	chr03	23492237	T	C	43.90%	6.83%	C -> T	mr1038 (All); LR P-value: 3.46E-06; mr1038 (Ind_All); LR P-value: 4.85E-07; mr1045 (All); LR P-value: 1.01E-07; mr1053 (All); LR P-value: 6.07E-07; mr1058 (All); LR P-value: 5.03E-07; mr1236 (Ind_All); LR P-value: 2.39E-06; mr1329 (All); LR P-value: 3.78E-13; mr1389 (Ind_All); LR P-value: 3.54E-07; mr1524 (All); LR P-value: 8.13E-11; mr1637 (All); LR P-value: 6.46E-09; mr1663 (All); LR P-value: 2.22E-09; mr1671 (Ind_All); LR P-value: 7.76E-06; mr1716 (All); LR P-value: 2.71E-07; mr1045_2 (All); LR P-value: 1.79E-06; mr1322_2 (All); LR P-value: 2.75E-10; mr1325_2 (All); LR P-value: 5.52E-16; mr1326_2 (All); LR P-value: 1.04E-15; mr1498_2 (All); LR P-value: 6.96E-07; mr1527_2 (All); LR P-value: 8.92E-08; mr1623_2 (All); LR P-value: 1.79E-07; mr1671_2 (Ind_All); LR P-value: 4.09E-06; mr1925_2 (All); LR P-value: 5.93E-07	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492238	chr03	23492238	G	A	67.80%	27.08%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492242	chr03	23492242	G	A	92.30%	7.19%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492251	chr03	23492251	C	T	98.30%	0.97%	C -> T	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492274	chr03	23492274	A	AC	79.40%	14.77%	A -> AC	NA	N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: AC\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: AC\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: AC\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: AC\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: AC\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323492275	chr03	23492275	C	T	93.80%	3.51%	C -> T	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492276	chr03	23492276	G	T	39.20%	16.78%	G -> T	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492282	chr03	23492282	G	A	44.40%	17.05%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492292	chr03	23492292	C	T	65.00%	5.56%	T -> C	NA	LOC_Os03g42230.1 Alt: C\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492309	chr03	23492309	A	G	63.80%	27.11%	A -> G	NA	N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: G\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323492335	chr03	23492335	A	G	66.70%	24.71%	A -> G	NA	N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: G\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323492348	chr03	23492348	C	T	94.60%	4.36%	C -> T	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492350	chr03	23492350	G	T	96.10%	1.59%	G -> T	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492352	chr03	23492352	C	T	69.90%	24.57%	C -> T	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492357	chr03	23492357	G	A	91.20%	7.70%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492358	chr03	23492358	CGGCG	CGCG	78.30%	17.14%	CGGCG -> CGCG,TGGCG ,C	NA	LOC_Os03g42230.1 Alt: C\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: C\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: C\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: C\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42230.1 Alt: CGCG\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: CGCG\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: CGCG\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: CGCG\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: CGCG\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: TGGCG\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: TGGCG\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: TGGCG\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: TGGCG\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: TGGCG\| downstream_gene_variant MODIFIER(snpEff)
vg0323492361	chr03	23492361	CGG	C	79.50%	15.79%	CGG -> C,TGG	NA	LOC_Os03g42230.1 Alt: C\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: TGG\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: TGG\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: TGG\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: TGG\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: TGG\| downstream_gene_variant MODIFIER(snpEff)
vg0323492365	chr03	23492365	C	A	88.90%	9.39%	C -> A,G,CT	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: G\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: CT\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: CT\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: CT\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: CT\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: CT\| downstream_gene_variant MODIFIER(snpEff)
vg0323492376	chr03	23492376	T	C	66.50%	26.43%	T -> C	NA	LOC_Os03g42230.1 Alt: C\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492378	chr03	23492378	G	A	86.30%	10.60%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492390	chr03	23492390	CCGG	C	99.80%	0.00%	CCGG -> C	NA	LOC_Os03g42230.1 Alt: C\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: C\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: C\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: C\| downstream_gene_variant MODIFIER(snpEff)
vg0323492398	chr03	23492398	G	A	73.00%	20.00%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492400	chr03	23492400	C	T	91.30%	7.77%	C -> T	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492401	chr03	23492401	G	A	85.30%	10.16%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492404	chr03	23492404	C	T	84.70%	10.41%	C -> T	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492409	chr03	23492409	G	T	73.80%	19.91%	G -> T	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492414	chr03	23492414	T	A	98.00%	1.48%	T -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492425	chr03	23492425	C	T	98.10%	1.38%	C -> T	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492428	chr03	23492428	C	T	91.90%	6.37%	C -> T	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492431	chr03	23492431	TGAACTC CTTGTGG TCATGGA CGATGAG CCGC	T	95.10%	2.01%	TGAACTCCTT GTGGTCATGG ACGATGAGCC GC -> T,TAACTCCT TGTGGTCATG GACGATGAGC CGC	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: TAACTCCTTGTGGTCATGGACGATGAGCCGC\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: TAACTCCTTGTGGTCATGGACGATGAGCCGC\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: TAACTCCTTGTGGTCATGGACGATGAGCCGC\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: TAACTCCTTGTGGTCATGGACGATGAGCCGC\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: TAACTCCTTGTGGTCATGGACGATGAGCCGC\| downstream_gene_variant MODIFIER(snpEff)
vg0323492440	chr03	23492440	TGTG	T	94.40%	4.51%	TGTG -> T	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492443	chr03	23492443	GGTCATG GACGATG AGCCGCG AACTCCT TGTC	Unkown	98.20%	1.42%	GGTCATGGAC GATGAGCCGC GAACTCCTTG TC -> G,CGTCATGG ACGATGAGCC GCGAACTCCT TGTC	Spikelet_length (Ind_All); LR P-value: 7.07E-08; mr1038 (All); LR P-value: 7.35E-07; mr1038 (Ind_All); LR P-value: 5.17E-07; mr1106 (All); LR P-value: 1.38E-07; mr1106 (Ind_All); LR P-value: 2.29E-06; mr1221 (Ind_All); LR P-value: 3.68E-07; mr1236 (All); LR P-value: 1.14E-07; mr1236 (Ind_All); LR P-value: 3.63E-07; mr1389 (All); LR P-value: 4.37E-07; mr1389 (Ind_All); LR P-value: 7.40E-07; mr1653 (Ind_All); LR P-value: 3.18E-06; mr1816 (All); LR P-value: 3.57E-07; mr1816 (Ind_All); LR P-value: 5.37E-06; mr1844 (Ind_All); LR P-value: 9.76E-06; mr1886 (All); LR P-value: 7.61E-07; mr1038_2 (All); LR P-value: 9.45E-07	LOC_Os03g42230.1 Alt: CGTCATGGACGATGAGCCGCGAACTCCTTGTC\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: CGTCATGGACGATGAGCCGCGAACTCCTTGTC\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: CGTCATGGACGATGAGCCGCGAACTCCTTGTC\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: CGTCATGGACGATGAGCCGCGAACTCCTTGTC\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: CGTCATGGACGATGAGCCGCGAACTCCTTGTC\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42230.1 Alt: G\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: G\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: G\| downstream_gene_variant MODIFIER(snpEff)
vg0323492447	chr03	23492447	GTGGACG ATGAGCC GCGAACT CCTTGTC G	ATGGACG ATGAGCC GCGAACT CCTTGTC G	50.70%	13.63%	ATGGACGATG AGCCGCGAAC TCCTTGTCG -> GTGGACGATG AGCCGCGAAC TCCTTGTCG, A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff) N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: GTGGACGATGAGCCGCGAACTCCTTGTCG\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: GTGGACGATGAGCCGCGAACTCCTTGTCG\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: GTGGACGATGAGCCGCGAACTCCTTGTCG\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: GTGGACGATGAGCCGCGAACTCCTTGTCG\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: GTGGACGATGAGCCGCGAACTCCTTGTCG\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323492448	chr03	23492448	T	G	99.60%	0.00%	T -> G	NA	LOC_Os03g42230.1 Alt: G\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: G\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: G\| downstream_gene_variant MODIFIER(snpEff)
vg0323492449	chr03	23492449	GGAC	G	99.60%	0.00%	GGAC -> G	NA	LOC_Os03g42230.1 Alt: G\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: G\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: G\| downstream_gene_variant MODIFIER(snpEff)
vg0323492452	chr03	23492452	CGATG	C	99.60%	0.00%	CGATG -> C	NA	LOC_Os03g42230.1 Alt: C\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: C\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: C\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: C\| downstream_gene_variant MODIFIER(snpEff)
vg0323492454	chr03	23492454	A	G	92.50%	6.16%	A -> G	NA	N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: G\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323492455	chr03	23492455	C	T	50.40%	13.06%	T -> C	NA	LOC_Os03g42230.1 Alt: C\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492459	chr03	23492459	C	CGACA	99.60%	0.00%	C -> CGACA	NA	LOC_Os03g42230.1 Alt: CGACA\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: CGACA\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: CGACA\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: CGACA\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: CGACA\| downstream_gene_variant MODIFIER(snpEff)
vg0323492460	chr03	23492460	C	T	99.60%	0.00%	C -> T	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff) LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)
vg0323492461	chr03	23492461	G	A	85.50%	12.84%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492462	chr03	23492462	C	T	99.90%	0.00%	C -> T	Spikelet_length (Ind_All); LR P-value: 8.00E-08; mr1038 (All); LR P-value: 2.65E-06; mr1038 (Ind_All); LR P-value: 1.60E-06; mr1106 (All); LR P-value: 6.26E-07; mr1106 (Ind_All); LR P-value: 9.58E-06; mr1221 (Ind_All); LR P-value: 1.47E-06; mr1236 (All); LR P-value: 2.87E-07; mr1236 (Ind_All); LR P-value: 8.92E-07; mr1389 (All); LR P-value: 1.11E-06; mr1389 (Ind_All); LR P-value: 1.60E-06; mr1816 (All); LR P-value: 1.24E-06; mr1928 (Ind_All); LR P-value: 6.25E-06	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)
vg0323492466	chr03	23492466	C	G	91.20%	7.58%	C -> G	NA	N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: G\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323492474	chr03	23492474	C	T	94.40%	4.51%	C -> T,G	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: G\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: G\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: G\| downstream_gene_variant MODIFIER(snpEff)
vg0323492475	chr03	23492475	G	A	75.70%	16.91%	G -> A,C	NA	LOC_Os03g42230.1 Alt: C\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: C\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: C\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: C\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492484	chr03	23492484	G	A	69.10%	24.59%	G -> A,T	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff) LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492487	chr03	23492487	G	Unkown	99.30%	0.59%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)
vg0323492488	chr03	23492488	A	G	97.50%	1.97%	A -> G	NA	N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: G\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323492489	chr03	23492489	CGGCGCA	Unkown	98.30%	1.10%	CGGCGCA -> TGGCGCA,C	NA	LOC_Os03g42230.1 Alt: TGGCGCA\| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff) LOC_Os03g42230.1 Alt: TGGCGCA\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: TGGCGCA\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: TGGCGCA\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: TGGCGCA\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: TGGCGCA\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42230.1 Alt: C\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: C\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: C\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: C\| downstream_gene_variant MODIFIER(snpEff)
vg0323492494	chr03	23492494	G	C	63.10%	6.86%	C -> G,A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff) N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: G\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323492495	chr03	23492495	C	A	64.90%	5.90%	A -> C,AT	NA	LOC_Os03g42230.1 Alt: C\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: AT\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: AT\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: AT\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: AT\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: AT\| downstream_gene_variant MODIFIER(snpEff)
vg0323492497	chr03	23492497	C	T	99.80%	0.00%	C -> T	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff) LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)
vg0323492498	chr03	23492498	G	A	62.40%	30.70%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492508	chr03	23492508	CTGG	CGG	61.50%	32.04%	CTGG -> CGG,C	NA	LOC_Os03g42230.1 Alt: C\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: C\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: C\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: C\| downstream_gene_variant MODIFIER(snpEff) N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: CGG\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: CGG\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: CGG\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: CGG\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: CGG\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323492510	chr03	23492510	G	C	61.50%	32.06%	G -> C	NA	LOC_Os03g42230.1 Alt: C\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492522	chr03	23492522	G	A	61.20%	31.76%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492531	chr03	23492531	G	A	75.10%	14.90%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492535	chr03	23492535	C	T	48.90%	17.29%	C -> T	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492540	chr03	23492540	C	T	99.80%	0.00%	C -> T	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)
vg0323492552	chr03	23492552	G	A	95.70%	3.03%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492557	chr03	23492557	ATTTTTC CT	A	99.70%	0.00%	ATTTTTCCT -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)
vg0323492559	chr03	23492559	A	T	38.80%	9.46%	T -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492560	chr03	23492560	T	C	75.50%	14.18%	T -> C	NA	LOC_Os03g42230.1 Alt: C\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492564	chr03	23492564	C	A	75.50%	14.18%	C -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492567	chr03	23492567	G	A	99.70%	0.00%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)
vg0323492571	chr03	23492571	G	A	72.30%	10.33%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492572	chr03	23492572	AT	A	48.50%	5.12%	A -> AT	NA	N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: AT\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: AT\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: AT\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: AT\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: AT\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323492579	chr03	23492579	A	T	97.20%	2.45%	A -> T	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492584	chr03	23492584	G	Unkown	97.10%	2.45%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)
vg0323492588	chr03	23492588	A	G	99.70%	0.00%	A -> G	NA	LOC_Os03g42230.1 Alt: G\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: G\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: G\| downstream_gene_variant MODIFIER(snpEff)
vg0323492592	chr03	23492592	C	Unkown	97.10%	2.45%	C -> T	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)
vg0323492595	chr03	23492595	T	TC	84.40%	5.71%	T -> TC	NA	LOC_Os03g42230.1 Alt: TC\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: TC\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: TC\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: TC\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: TC\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492601	chr03	23492601	C	T	99.70%	0.00%	C -> T,G	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: G\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: G\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: G\| downstream_gene_variant MODIFIER(snpEff)
vg0323492605	chr03	23492605	C	T	64.50%	0.00%	T -> C	NA	LOC_Os03g42230.1 Alt: C\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323492618	chr03	23492618	T	Unkown	99.70%	0.00%	T -> G	NA	LOC_Os03g42230.1 Alt: G\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: G\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: G\| downstream_gene_variant MODIFIER(snpEff)
vg0323492621	chr03	23492621	A	G	64.30%	0.00%	G -> A,C,T	NA	LOC_Os03g42230.1 Alt: C\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: C\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: C\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: C\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)
vg0323492627	chr03	23492627	C	Unkown	99.70%	0.00%	C -> T	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)
vg0323492628	chr03	23492628	A	G	99.70%	0.00%	A -> G	NA	LOC_Os03g42230.1 Alt: G\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323492629	chr03	23492629	T	TG	99.70%	0.00%	T -> TG,TGTG	NA	LOC_Os03g42230.1 Alt: TG\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: TG\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: TG\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: TG\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: TG\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: TGTG\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: TGTG\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: TGTG\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: TGTG\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: TGTG\| downstream_gene_variant MODIFIER(snpEff)
vg0323492630	chr03	23492630	G	Unkown	99.70%	0.00%	G -> GA	NA	LOC_Os03g42230.1 Alt: GA\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: GA\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: GA\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: GA\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: GA\| downstream_gene_variant MODIFIER(snpEff)
vg0323492633	chr03	23492633	C	T	99.30%	0.00%	C -> T	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)
vg0323492640	chr03	23492640	C	T	99.80%	0.00%	C -> T	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323492644	chr03	23492644	A	G	99.70%	0.00%	A -> G	NA	LOC_Os03g42230.1 Alt: G\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: G\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: G\| downstream_gene_variant MODIFIER(snpEff)
vg0323492646	chr03	23492646	A	G	62.70%	0.00%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323492647	chr03	23492647	A	G	62.70%	0.00%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323492654	chr03	23492654	T	C	63.60%	0.11%	C -> T,A	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492656	chr03	23492656	T	C	63.10%	0.15%	C -> T,CCTCAAAG ATGGAAAAAA TGCTTGATAC CTCATGTACC TCGTACCTCA TAATACCTCT TT,CCTCAAA GATGGAAAAA ATGCTCTTGA TACCTCATGT ACCTCGTACC TCATAATACC TCTTT,CCTC AAAGATGGAA AAAATGATAC CTCATGTACC TCGTACCTCA TAATACCTCT TT,CCTCAAA GATGGAAAAA ATGCTCTAAC TTGATACCTC ATGTACCTCG TACCTCATAA TACCTCTTT, CCTCAAAGAT GGAAAAAATG CTCTAACTCG ATATGGGGCG ATACCTCATG TACCTCGTAC CTCGTAATAC CTCTTT	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: CCTCAAAGATGGAAAAAATGCTTGATACCTCATGTACCTCGTACCTCATAATACCTCTTT\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: CCTCAAAGATGGAAAAAATGCTTGATACCTCATGTACCTCGTACCTCATAATACCTCTTT\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: CCTCAAAGATGGAAAAAATGCTTGATACCTCATGTACCTCGTACCTCATAATACCTCTTT\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: CCTCAAAGATGGAAAAAATGCTTGATACCTCATGTACCTCGTACCTCATAATACCTCTTT\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: CCTCAAAGATGGAAAAAATGCTTGATACCTCATGTACCTCGTACCTCATAATACCTCTTT\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42230.1 Alt: CCTCAAAGATGGAAAAAATGCTCTAACTTGATACCTCATGTACCTCGTACCTCATAATACCTCTTT\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: CCTCAAAGATGGAAAAAATGCTCTAACTTGATACCTCATGTACCTCGTACCTCATAATACCTCTTT\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: CCTCAAAGATGGAAAAAATGCTCTAACTTGATACCTCATGTACCTCGTACCTCATAATACCTCTTT\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: CCTCAAAGATGGAAAAAATGCTCTAACTTGATACCTCATGTACCTCGTACCTCATAATACCTCTTT\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: CCTCAAAGATGGAAAAAATGCTCTAACTTGATACCTCATGTACCTCGTACCTCATAATACCTCTTT\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42230.1 Alt: CCTCAAAGATGGAAAAAATGATACCTCATGTACCTCGTACCTCATAATACCTCTTT\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: CCTCAAAGATGGAAAAAATGATACCTCATGTACCTCGTACCTCATAATACCTCTTT\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: CCTCAAAGATGGAAAAAATGATACCTCATGTACCTCGTACCTCATAATACCTCTTT\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: CCTCAAAGATGGAAAAAATGATACCTCATGTACCTCGTACCTCATAATACCTCTTT\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: CCTCAAAGATGGAAAAAATGATACCTCATGTACCTCGTACCTCATAATACCTCTTT\| downstream_gene_variant MODIFIER(snpEff) N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: CCTCAAAGATGGAAAAAATGCTCTAACTCGATATGGGGCGATACCTCATGTACCTCGTACCTCGTAATACCTCTTT\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: CCTCAAAGATGGAAAAAATGCTCTAACTCGATATGGGGCGATACCTCATGTACCTCGTACCTCGTAATACCTCTTT\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: CCTCAAAGATGGAAAAAATGCTCTAACTCGATATGGGGCGATACCTCATGTACCTCGTACCTCGTAATACCTCTTT\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: CCTCAAAGATGGAAAAAATGCTCTAACTCGATATGGGGCGATACCTCATGTACCTCGTACCTCGTAATACCTCTTT\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: CCTCAAAGATGGAAAAAATGCTCTAACTCGATATGGGGCGATACCTCATGTACCTCGTACCTCGTAATACCTCTTT\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42230.1 Alt: CCTCAAAGATGGAAAAAATGCTCTTGATACCTCATGTACCTCGTACCTCATAATACCTCTTT\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: CCTCAAAGATGGAAAAAATGCTCTTGATACCTCATGTACCTCGTACCTCATAATACCTCTTT\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: CCTCAAAGATGGAAAAAATGCTCTTGATACCTCATGTACCTCGTACCTCATAATACCTCTTT\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: CCTCAAAGATGGAAAAAATGCTCTTGATACCTCATGTACCTCGTACCTCATAATACCTCTTT\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: CCTCAAAGATGGAAAAAATGCTCTTGATACCTCATGTACCTCGTACCTCATAATACCTCTTT\| downstream_gene_variant MODIFIER(snpEff)
vg0323492659	chr03	23492659	G	Unkown	94.80%	2.69%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)
vg0323492660	chr03	23492660	G	A	94.50%	3.03%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492664	chr03	23492664	G	A	93.90%	3.00%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492665	chr03	23492665	A	G	51.60%	0.02%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492671	chr03	23492671	T	Unkown	99.70%	0.00%	T -> TGCTCTA	NA	LOC_Os03g42230.1 Alt: TGCTCTA\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: TGCTCTA\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: TGCTCTA\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: TGCTCTA\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: TGCTCTA\| downstream_gene_variant MODIFIER(snpEff)
vg0323492672	chr03	23492672	G	A	64.40%	0.04%	A -> G	NA	N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: G\| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: G\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323492675	chr03	23492675	A	C	64.20%	0.28%	C -> A,CGATATGA TACCTCATGT ACCTCGTACC TCATAATACC TCTTTAAGGA TGGAAAAAAT GCTA,CGATA TGGGGCGCTA AGTGGATGAA GATACCTCAT GTACCTCGTA CCTCATAATA CCTCTTTAAG GATGGAAAAA ATGCTA,CGA TATGGGGCGC TAAGTGGATA CCTCATGTAC CTCGTACCTC ATAATACCTC TTTAAGGATG GAAAAAATGC TA	NA	LOC_Os03g42230.1 Alt: CGATATGGGGCGCTAAGTGGATGAAGATACCTCATGTACCTCGTACCTCATAATACCTCTTTAAGGATGGAAAAAATGCTA\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: CGATATGGGGCGCTAAGTGGATGAAGATACCTCATGTACCTCGTACCTCATAATACCTCTTTAAGGATGGAAAAAATGCTA\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: CGATATGGGGCGCTAAGTGGATGAAGATACCTCATGTACCTCGTACCTCATAATACCTCTTTAAGGATGGAAAAAATGCTA\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: CGATATGGGGCGCTAAGTGGATGAAGATACCTCATGTACCTCGTACCTCATAATACCTCTTTAAGGATGGAAAAAATGCTA\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: CGATATGGGGCGCTAAGTGGATGAAGATACCTCATGTACCTCGTACCTCATAATACCTCTTTAAGGATGGAAAAAATGCTA\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42230.1 Alt: CGATATGATACCTCATGTACCTCGTACCTCATAATACCTCTTTAAGGATGGAAAAAATGCTA\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: CGATATGATACCTCATGTACCTCGTACCTCATAATACCTCTTTAAGGATGGAAAAAATGCTA\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: CGATATGATACCTCATGTACCTCGTACCTCATAATACCTCTTTAAGGATGGAAAAAATGCTA\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: CGATATGATACCTCATGTACCTCGTACCTCATAATACCTCTTTAAGGATGGAAAAAATGCTA\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: CGATATGATACCTCATGTACCTCGTACCTCATAATACCTCTTTAAGGATGGAAAAAATGCTA\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42230.1 Alt: CGATATGGGGCGCTAAGTGGATACCTCATGTACCTCGTACCTCATAATACCTCTTTAAGGATGGAAAAAATGCTA\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: CGATATGGGGCGCTAAGTGGATACCTCATGTACCTCGTACCTCATAATACCTCTTTAAGGATGGAAAAAATGCTA\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: CGATATGGGGCGCTAAGTGGATACCTCATGTACCTCGTACCTCATAATACCTCTTTAAGGATGGAAAAAATGCTA\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: CGATATGGGGCGCTAAGTGGATACCTCATGTACCTCGTACCTCATAATACCTCTTTAAGGATGGAAAAAATGCTA\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: CGATATGGGGCGCTAAGTGGATACCTCATGTACCTCGTACCTCATAATACCTCTTTAAGGATGGAAAAAATGCTA\| downstream_gene_variant MODIFIER(snpEff) N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323492687	chr03	23492687	T	C	87.80%	1.71%	T -> C,A	NA	LOC_Os03g42230.1 Alt: C\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492692	chr03	23492692	GATTTTG ATAGTTT GGTCAAC CTATCTA TA	G	63.40%	0.04%	G -> GATTTTGATA GTTTGGTCAA CCTATCTATA ,GATTTTGAT AGTTTGGTCT ACCTATCTAT A,GACTTTGA TAGTTTGGTC AACCTATCTA TA	NA	LOC_Os03g42230.1 Alt: GATTTTGATAGTTTGGTCAACCTATCTATA\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: GATTTTGATAGTTTGGTCAACCTATCTATA\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: GATTTTGATAGTTTGGTCAACCTATCTATA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: GATTTTGATAGTTTGGTCAACCTATCTATA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: GATTTTGATAGTTTGGTCAACCTATCTATA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: GATTTTGATAGTTTGGTCTACCTATCTATA\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: GATTTTGATAGTTTGGTCTACCTATCTATA\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: GATTTTGATAGTTTGGTCTACCTATCTATA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: GATTTTGATAGTTTGGTCTACCTATCTATA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: GATTTTGATAGTTTGGTCTACCTATCTATA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: GACTTTGATAGTTTGGTCAACCTATCTATA\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: GACTTTGATAGTTTGGTCAACCTATCTATA\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: GACTTTGATAGTTTGGTCAACCTATCTATA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: GACTTTGATAGTTTGGTCAACCTATCTATA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: GACTTTGATAGTTTGGTCAACCTATCTATA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323492698	chr03	23492698	GTGAA	GATAGTT TGAA	98.80%	0.02%	GTGAA -> GATAGTTTGA A,GATAGTTT GGTCAACCTG AA,GATAGTT TGGTCAACCT ATGAA,G	NA	LOC_Os03g42230.1 Alt: GATAGTTTGAA\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: GATAGTTTGAA\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: GATAGTTTGAA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: GATAGTTTGAA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: GATAGTTTGAA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: GATAGTTTGGTCAACCTATGAA\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: GATAGTTTGGTCAACCTATGAA\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: GATAGTTTGGTCAACCTATGAA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: GATAGTTTGGTCAACCTATGAA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: GATAGTTTGGTCAACCTATGAA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: G\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: GATAGTTTGGTCAACCTGAA\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: GATAGTTTGGTCAACCTGAA\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: GATAGTTTGGTCAACCTGAA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: GATAGTTTGGTCAACCTGAA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: GATAGTTTGGTCAACCTGAA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323492700	chr03	23492700	G	GGTC	95.90%	2.29%	G -> GGTC	NA	N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: GGTC\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: GGTC\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: GGTC\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: GGTC\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: GGTC\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323492709	chr03	23492709	G	A	93.80%	0.00%	G -> A,T	mr1166 (All); LR P-value: 2.61E-13; mr1184 (All); LR P-value: 4.74E-06; mr1424 (All); LR P-value: 5.63E-06; mr1471 (All); LR P-value: 6.96E-11; mr1515 (All); LR P-value: 8.40E-19; mr1549 (All); LR P-value: 7.09E-38; mr1586 (All); LR P-value: 2.60E-24; mr1652 (All); LR P-value: 1.82E-06; mr1706 (All); LR P-value: 2.68E-07; mr1722 (All); LR P-value: 3.93E-09; mr1730 (All); LR P-value: 3.56E-10; mr1735 (All); LR P-value: 1.84E-06; mr1808 (All); LR P-value: 4.73E-06; mr1193_2 (All); LR P-value: 4.80E-11; mr1549_2 (All); LR P-value: 1.95E-31; mr1757_2 (All); LR P-value: 2.76E-26; mr1808_2 (All); LR P-value: 1.64E-09; mr1815_2 (All); LR P-value: 1.72E-06; mr1855_2 (All); LR P-value: 9.31E-22	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323492718	chr03	23492718	G	A	64.30%	0.06%	A -> G	NA	N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: G\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323492745	chr03	23492745	A	C	89.80%	1.04%	A -> C	NA	LOC_Os03g42230.1 Alt: C\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492752	chr03	23492752	G	C	84.00%	6.05%	G -> C	NA	LOC_Os03g42230.1 Alt: C\| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: C\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492754	chr03	23492754	G	GCGTTCT TTTCAGG CTAGTCG TCCTCGT TT	98.40%	0.08%	G -> GCGTTCTTTT CAGGCTAGTC GTCC,GCGTT CTT,GCGTTC TTTTCAGGC, GCGTTCTTTT CAGGCTAGTC GTCCTCGTTT ,GCGTTCT,G CGTTCTTT	NA	LOC_Os03g42230.1 Alt: GCGTTCTTTTCAGGC\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: GCGTTCTTTTCAGGC\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: GCGTTCTTTTCAGGC\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: GCGTTCTTTTCAGGC\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: GCGTTCTTTTCAGGC\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42230.1 Alt: GCGTTCTTTTCAGGCTAGTCGTCCTCGTTT\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: GCGTTCTTTTCAGGCTAGTCGTCCTCGTTT\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: GCGTTCTTTTCAGGCTAGTCGTCCTCGTTT\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: GCGTTCTTTTCAGGCTAGTCGTCCTCGTTT\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: GCGTTCTTTTCAGGCTAGTCGTCCTCGTTT\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42230.1 Alt: GCGTTCTTTTCAGGCTAGTCGTCC\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: GCGTTCTTTTCAGGCTAGTCGTCC\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: GCGTTCTTTTCAGGCTAGTCGTCC\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: GCGTTCTTTTCAGGCTAGTCGTCC\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: GCGTTCTTTTCAGGCTAGTCGTCC\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42230.1 Alt: GCGTTCT\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: GCGTTCT\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: GCGTTCT\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: GCGTTCT\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: GCGTTCT\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42230.1 Alt: GCGTTCTTT\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: GCGTTCTTT\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: GCGTTCTTT\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: GCGTTCTTT\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: GCGTTCTTT\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42230.1 Alt: GCGTTCTT\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: GCGTTCTT\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: GCGTTCTT\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: GCGTTCTT\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: GCGTTCTT\| downstream_gene_variant MODIFIER(snpEff)
vg0323492755	chr03	23492755	T	C	86.50%	5.37%	T -> C	NA	LOC_Os03g42230.1 Alt: C\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323492757	chr03	23492757	T	TTCTTTT CAGGCTA GTCGTCC TC	90.30%	2.75%	T -> TTCTTTTCAG GCTAGTCGTC CTC,TTCTTT TCAGGCTAGT C,TTCTTTTC A,TTCTTTTC AGGCTA,TTC TTTTCAG,TT CTTTTCAGGC TAGTCGTCCT CGTTTTCC	NA	LOC_Os03g42230.1 Alt: TTCTTTTCAGGCTA\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: TTCTTTTCAGGCTA\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: TTCTTTTCAGGCTA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: TTCTTTTCAGGCTA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: TTCTTTTCAGGCTA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: TTCTTTTCAGGCTAGTCGTCCTC\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: TTCTTTTCAGGCTAGTCGTCCTC\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: TTCTTTTCAGGCTAGTCGTCCTC\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: TTCTTTTCAGGCTAGTCGTCCTC\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: TTCTTTTCAGGCTAGTCGTCCTC\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: TTCTTTTCAGGCTAGTC\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: TTCTTTTCAGGCTAGTC\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: TTCTTTTCAGGCTAGTC\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: TTCTTTTCAGGCTAGTC\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: TTCTTTTCAGGCTAGTC\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: TTCTTTTCA\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: TTCTTTTCA\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: TTCTTTTCA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: TTCTTTTCA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: TTCTTTTCA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: TTCTTTTCAG\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: TTCTTTTCAG\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: TTCTTTTCAG\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: TTCTTTTCAG\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: TTCTTTTCAG\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: TTCTTTTCAGGCTAGTCGTCCTCGTTTTCC\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: TTCTTTTCAGGCTAGTCGTCCTCGTTTTCC\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: TTCTTTTCAGGCTAGTCGTCCTCGTTTTCC\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: TTCTTTTCAGGCTAGTCGTCCTCGTTTTCC\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: TTCTTTTCAGGCTAGTCGTCCTCGTTTTCC\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323492759	chr03	23492759	T	G	97.50%	1.02%	T -> G	NA	N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: G\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323492760	chr03	23492760	G	T	96.90%	1.02%	G -> T,C	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: C\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323492794	chr03	23492794	T	C	99.60%	0.00%	T -> C	NA	LOC_Os03g42230.1 Alt: C\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323492800	chr03	23492800	C	T	99.60%	0.00%	C -> T	NA	LOC_Os03g42230.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323492833	chr03	23492833	C	A	99.60%	0.00%	C -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323492901	chr03	23492901	C	T	99.60%	0.00%	C -> T	NA	LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: T\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323493017	chr03	23493017	T	C	99.60%	0.00%	T -> C	NA	LOC_Os03g42235.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: C\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323493099	chr03	23493099	T	TCACCTA GCTCTTT CTTACCA GTGGCAA TAAAATG ACAATCA AAAG	99.60%	0.00%	T -> TCACCTAGCT CTTTCTTACC AGTGGCAATA AAATGACAAT CAAAAG	NA	LOC_Os03g42235.1 Alt: TCACCTAGCTCTTTCTTACCAGTGGCAATAAAATGACAATCAAAAG\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: TCACCTAGCTCTTTCTTACCAGTGGCAATAAAATGACAATCAAAAG\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: TCACCTAGCTCTTTCTTACCAGTGGCAATAAAATGACAATCAAAAG\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: TCACCTAGCTCTTTCTTACCAGTGGCAATAAAATGACAATCAAAAG\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: TCACCTAGCTCTTTCTTACCAGTGGCAATAAAATGACAATCAAAAG\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323493120	chr03	23493120	T	G	99.60%	0.00%	T -> G	NA	LOC_Os03g42235.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: G\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323493134	chr03	23493134	A	C	99.60%	0.00%	A -> C	NA	LOC_Os03g42235.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: C\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323493186	chr03	23493186	T	C	99.30%	0.00%	T -> C	NA	LOC_Os03g42235.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: C\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: C\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: C\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42230.1 Alt: C\| intron_variant MODIFIER(snpEff)
vg0323493188	chr03	23493188	TG	T	99.60%	0.00%	TG -> T	NA	LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: T\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323493198	chr03	23493198	T	C	99.60%	0.00%	T -> C	NA	LOC_Os03g42235.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: C\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323493204	chr03	23493204	G	A	94.10%	0.00%	G -> A	Spikelet_length (Ind_All); LR P-value: 1.40E-07; mr1038 (All); LR P-value: 4.83E-06; mr1038 (Ind_All); LR P-value: 5.00E-06; mr1106 (All); LR P-value: 7.91E-07; mr1221 (Ind_All); LR P-value: 7.62E-07; mr1236 (All); LR P-value: 3.48E-08; mr1236 (Ind_All); LR P-value: 2.11E-07; mr1389 (All); LR P-value: 1.52E-06; mr1389 (Ind_All); LR P-value: 2.10E-06; mr1408 (Ind_All); LR P-value: 8.58E-06; mr1418 (All); LR P-value: 9.85E-06; mr1816 (All); LR P-value: 5.95E-07; mr1886 (All); LR P-value: 1.58E-06; mr1928 (Ind_All); LR P-value: 9.73E-06; mr1038_2 (All); LR P-value: 2.20E-06	LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: A\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323493210	chr03	23493210	C	T	94.40%	0.00%	C -> T	mr1166 (All); LR P-value: 2.61E-13; mr1184 (All); LR P-value: 4.74E-06; mr1424 (All); LR P-value: 5.63E-06; mr1471 (All); LR P-value: 6.96E-11; mr1515 (All); LR P-value: 8.40E-19; mr1549 (All); LR P-value: 7.09E-38; mr1586 (All); LR P-value: 2.60E-24; mr1652 (All); LR P-value: 1.82E-06; mr1706 (All); LR P-value: 2.68E-07; mr1722 (All); LR P-value: 3.93E-09; mr1730 (All); LR P-value: 3.56E-10; mr1735 (All); LR P-value: 1.84E-06; mr1808 (All); LR P-value: 4.73E-06; mr1193_2 (All); LR P-value: 4.80E-11; mr1549_2 (All); LR P-value: 1.95E-31; mr1757_2 (All); LR P-value: 2.76E-26; mr1808_2 (All); LR P-value: 1.64E-09; mr1815_2 (All); LR P-value: 1.72E-06; mr1855_2 (All); LR P-value: 9.31E-22	LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: T\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323493212	chr03	23493212	A	G	99.10%	0.00%	A -> G	NA	LOC_Os03g42235.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: G\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323493214	chr03	23493214	G	A	99.60%	0.00%	G -> A	NA	LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: A\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323493215	chr03	23493215	T	A	99.60%	0.00%	T -> A	NA	LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: A\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323493227	chr03	23493227	G	A	99.60%	0.00%	G -> A	NA	LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: A\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323493241	chr03	23493241	T	C	99.60%	0.00%	T -> C	NA	LOC_Os03g42235.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: C\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323493260	chr03	23493260	C	T	64.90%	0.40%	T -> C	NA	LOC_Os03g42235.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: C\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323493468	chr03	23493468	T	A	99.30%	0.00%	T -> A	NA	LOC_Os03g42230.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)
vg0323493487	chr03	23493487	G	A	99.60%	0.00%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
vg0323493526	chr03	23493526	A	G	99.60%	0.00%	A -> G	NA	LOC_Os03g42230.1 Alt: G\| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
vg0323493536	chr03	23493536	G	A	99.60%	0.00%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
vg0323493544	chr03	23493544	A	G	99.60%	0.00%	A -> G	NA	LOC_Os03g42230.1 Alt: G\| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
vg0323493659	chr03	23493659	T	C	99.60%	0.00%	T -> C	NA	LOC_Os03g42235.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: C\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323493729	chr03	23493729	CT	C	99.60%	0.00%	CT -> C,CTT	NA	LOC_Os03g42235.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: C\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: CTT\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: CTT\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: CTT\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: CTT\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: CTT\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323493781	chr03	23493781	A	T	99.60%	0.00%	A -> T	NA	LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: T\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323493803	chr03	23493803	A	T	99.60%	0.00%	A -> T	NA	LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: T\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323493833	chr03	23493833	G	T	99.60%	0.00%	G -> T	NA	LOC_Os03g42230.1 Alt: T\| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
vg0323493927	chr03	23493927	A	G	99.60%	0.00%	A -> G	NA	LOC_Os03g42230.1 Alt: G\| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
vg0323494010	chr03	23494010	A	G	64.50%	0.40%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os03g42230.1 Alt: DEL/frameshift_variant(CooVar)
vg0323494017	chr03	23494017	C	T	64.90%	0.40%	T -> C	NA	LOC_Os03g42230.1 Alt: C\| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) LOC_Os03g42230.1 Alt: DEL/frameshift_variant(CooVar)
vg0323494067	chr03	23494067	T	C	99.60%	0.00%	T -> C	NA	LOC_Os03g42230.1 Alt: C\| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
vg0323494214	chr03	23494214	A	G	65.00%	0.38%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os03g42230.1 Alt: DEL/frameshift_variant(CooVar)
vg0323494233	chr03	23494233	T	C	99.70%	0.00%	T -> C	NA	LOC_Os03g42230.1 Alt: C\| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
vg0323494306	chr03	23494306	G	A	64.40%	0.38%	A -> G	NA	N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: G\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323494322	chr03	23494322	T	A	99.60%	0.00%	T -> A	NA	LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: A\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323494325	chr03	23494325	A	T	99.60%	0.00%	A -> T	NA	LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: T\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323494606	chr03	23494606	A	T	64.90%	0.19%	T -> A	NA	LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42240.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: A\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323494622	chr03	23494622	C	T	99.70%	0.00%	C -> T	NA	LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42240.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: T\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323494693	chr03	23494693	T	G	99.70%	0.00%	T -> G	NA	LOC_Os03g42235.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42240.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: G\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: G\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42230.1 Alt: G\| intron_variant MODIFIER(snpEff)
vg0323494710	chr03	23494710	G	A	99.60%	0.00%	G -> A	NA	LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42240.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: A\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323494981	chr03	23494981	A	G	99.60%	0.00%	A -> G	NA	LOC_Os03g42230.1 Alt: G\| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
vg0323495107	chr03	23495107	T	C	98.00%	0.00%	T -> C	NA	LOC_Os03g42230.1 Alt: C\| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
vg0323495139	chr03	23495139	C	T	64.90%	0.00%	T -> C	NA	LOC_Os03g42230.1 Alt: C\| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
vg0323495166	chr03	23495166	G	A	99.60%	0.00%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
vg0323495189	chr03	23495189	T	G	99.60%	0.00%	T -> G	NA	LOC_Os03g42230.1 Alt: G\| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
vg0323495232	chr03	23495232	G	T	99.30%	0.00%	G -> T	NA	LOC_Os03g42230.1 Alt: T\| missense_variant MODERATE(snpEff) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42240.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)
vg0323495248	chr03	23495248	C	CA	58.20%	0.00%	CA -> C,CAA,CAAA AAA,CAAAAA	NA	LOC_Os03g42235.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42240.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: C\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: CAAAAAA\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42240.1 Alt: CAAAAAA\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: CAAAAAA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: CAAAAAA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: CAAAAAA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: CAAAAAA\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: CAA\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42240.1 Alt: CAA\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: CAA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: CAA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: CAA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: CAA\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: CAAAAA\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42240.1 Alt: CAAAAA\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: CAAAAA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: CAAAAA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: CAAAAA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: CAAAAA\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323495274	chr03	23495274	T	TCAAA	99.70%	0.00%	T -> TCAAA,TCAA ACAAA	NA	LOC_Os03g42235.1 Alt: TCAAA\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42240.1 Alt: TCAAA\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: TCAAA\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: TCAAA\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: TCAAA\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42230.1 Alt: TCAAA\| intron_variant MODIFIER(snpEff) LOC_Os03g42235.1 Alt: TCAAACAAA\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42240.1 Alt: TCAAACAAA\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.1 Alt: TCAAACAAA\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.2 Alt: TCAAACAAA\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42220.3 Alt: TCAAACAAA\| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g42230.1 Alt: TCAAACAAA\| intron_variant MODIFIER(snpEff)
vg0323495328	chr03	23495328	C	T	99.60%	0.00%	C -> T	NA	LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42240.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: T\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323495345	chr03	23495345	A	G	51.90%	0.00%	G -> A	mr1045 (All); LR P-value: 4.81E-08; mr1058 (All); LR P-value: 3.04E-07; mr1236 (Ind_All); LR P-value: 3.32E-07; mr1329 (All); LR P-value: 1.36E-12; mr1408 (All); LR P-value: 1.51E-06; mr1524 (All); LR P-value: 3.56E-10; mr1595 (All); LR P-value: 1.68E-08; mr1637 (All); LR P-value: 4.67E-09; mr1657 (All); LR P-value: 2.32E-11; mr1663 (All); LR P-value: 1.37E-09; mr1716 (All); LR P-value: 9.46E-08; mr1727 (All); LR P-value: 7.58E-06; mr1756 (All); LR P-value: 8.98E-07; mr1785 (All); LR P-value: 9.24E-07; mr1804 (All); LR P-value: 3.27E-07; mr1322_2 (All); LR P-value: 4.13E-09; mr1325_2 (All); LR P-value: 4.06E-15; mr1326_2 (All); LR P-value: 7.96E-15; mr1498_2 (All); LR P-value: 5.23E-07; mr1623_2 (All); LR P-value: 2.44E-07; mr1925_2 (All); LR P-value: 4.46E-07	LOC_Os03g42230.1 Alt: A\| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
vg0323495355	chr03	23495355	G	A	99.60%	0.00%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
vg0323495363	chr03	23495363	T	A	64.40%	0.00%	A -> T	NA	LOC_Os03g42230.1 Alt: T\| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
vg0323495377	chr03	23495377	C	A	99.60%	0.00%	C -> A	NA	LOC_Os03g42230.1 Alt: A\| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
vg0323495445	chr03	23495445	G	A	64.90%	0.34%	A -> G	NA	LOC_Os03g42230.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os03g42230.1 Alt: G\| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
vg0323495492	chr03	23495492	A	T	64.90%	0.04%	T -> A	NA	LOC_Os03g42230.1 Alt: A\| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os03g42230.1 Alt: DEL/frameshift_variant(CooVar)
vg0323495555	chr03	23495555	G	T	51.80%	0.06%	T -> G	mr1045 (All); LR P-value: 1.06E-07; mr1058 (All); LR P-value: 7.06E-07; mr1236 (Ind_All); LR P-value: 3.46E-06; mr1329 (All); LR P-value: 2.13E-12; mr1408 (All); LR P-value: 2.13E-06; mr1524 (All); LR P-value: 3.75E-10; mr1637 (All); LR P-value: 7.18E-09; mr1657 (All); LR P-value: 4.11E-11; mr1716 (All); LR P-value: 8.40E-08; mr1785 (All); LR P-value: 9.33E-07; mr1322_2 (All); LR P-value: 1.73E-08; mr1325_2 (All); LR P-value: 3.33E-14; mr1326_2 (All); LR P-value: 5.33E-14; mr1623_2 (All); LR P-value: 4.17E-07; mr1671_2 (Ind_All); LR P-value: 5.63E-06; mr1925_2 (All); LR P-value: 1.38E-06	LOC_Os03g42230.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os03g42230.1 Alt: G\| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
vg0323495587	chr03	23495587	A	T	51.80%	0.02%	T -> A	mr1045 (All); LR P-value: 2.38E-08; mr1058 (All); LR P-value: 2.68E-07; mr1236 (Ind_All); LR P-value: 2.94E-06; mr1329 (All); LR P-value: 7.86E-13; mr1408 (All); LR P-value: 1.32E-06; mr1524 (All); LR P-value: 2.85E-10; mr1637 (All); LR P-value: 4.11E-09; mr1663 (All); LR P-value: 1.50E-09; mr1669 (All); LR P-value: 3.57E-07; mr1716 (All); LR P-value: 5.33E-08; mr1727 (All); LR P-value: 6.41E-06; mr1748 (All); LR P-value: 2.66E-06; mr1756 (All); LR P-value: 1.45E-06; mr1785 (All); LR P-value: 5.52E-07; mr1804 (All); LR P-value: 2.65E-07; mr1937 (All); LR P-value: 9.43E-06; mr1322_2 (All); LR P-value: 1.21E-08; mr1325_2 (All); LR P-value: 1.63E-14; mr1326_2 (All); LR P-value: 3.63E-14; mr1623_2 (All); LR P-value: 7.50E-07; mr1925_2 (All); LR P-value: 1.19E-06	LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42240.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: A\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323495724	chr03	23495724	A	G	64.20%	0.08%	G -> A	NA	LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42240.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42220.3 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: A\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323495795	chr03	23495795	T	A	99.60%	0.00%	T -> A	NA	LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42240.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: A\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323495797	chr03	23495797	C	T	64.90%	0.11%	T -> C	NA	LOC_Os03g42235.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42240.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: C\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323495806	chr03	23495806	G	A	64.10%	0.11%	A -> G	NA	N Alt: DEL/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42240.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: G\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323495816	chr03	23495816	C	CT	65.00%	0.23%	CT -> C	NA	LOC_Os03g42235.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42240.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: C\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323495830	chr03	23495830	A	G	51.90%	0.25%	G -> A	mr1045 (All); LR P-value: 4.81E-08; mr1058 (All); LR P-value: 3.04E-07; mr1236 (Ind_All); LR P-value: 3.32E-07; mr1329 (All); LR P-value: 1.36E-12; mr1408 (All); LR P-value: 1.51E-06; mr1524 (All); LR P-value: 3.56E-10; mr1595 (All); LR P-value: 1.68E-08; mr1637 (All); LR P-value: 4.67E-09; mr1657 (All); LR P-value: 2.32E-11; mr1663 (All); LR P-value: 1.37E-09; mr1716 (All); LR P-value: 9.46E-08; mr1727 (All); LR P-value: 7.58E-06; mr1756 (All); LR P-value: 8.98E-07; mr1785 (All); LR P-value: 9.24E-07; mr1804 (All); LR P-value: 3.27E-07; mr1322_2 (All); LR P-value: 4.13E-09; mr1325_2 (All); LR P-value: 4.06E-15; mr1326_2 (All); LR P-value: 7.96E-15; mr1498_2 (All); LR P-value: 5.23E-07; mr1623_2 (All); LR P-value: 2.44E-07; mr1925_2 (All); LR P-value: 4.46E-07	LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42240.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: A\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323495860	chr03	23495860	G	A	99.60%	0.00%	G -> A	NA	LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42240.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42230.1 Alt: A\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323495908	chr03	23495908	A	G	99.70%	0.00%	A -> G	NA	LOC_Os03g42235.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42240.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42230.1 Alt: G\| intron_variant MODIFIER(snpEff)
vg0323495949	chr03	23495949	C	G	99.60%	0.00%	C -> G	NA	LOC_Os03g42230.1 Alt: G\| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
vg0323496018	chr03	23496018	C	A	99.50%	0.00%	C -> A	NA	LOC_Os03g42230.1 Alt: A\| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
vg0323496117	chr03	23496117	T	C	99.60%	0.00%	T -> C	NA	LOC_Os03g42230.1 Alt: C\| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
vg0323496121	chr03	23496121	T	C	99.60%	0.00%	T -> C	NA	LOC_Os03g42230.1 Alt: C\| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
vg0323496125	chr03	23496125	A	G	99.60%	0.00%	A -> G	NA	LOC_Os03g42230.1 Alt: G\| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
vg0323496138	chr03	23496138	G	C	99.60%	0.00%	G -> C	NA	LOC_Os03g42230.1 Alt: C\| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
vg0323496163	chr03	23496163	G	C	99.70%	0.00%	G -> C	NA	LOC_Os03g42230.1 Alt: C\| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
vg0323496229	chr03	23496229	T	A	94.10%	0.00%	T -> A	Spikelet_length (Ind_All); LR P-value: 9.33E-08; mr1038 (All); LR P-value: 1.39E-06; mr1038 (Ind_All); LR P-value: 1.63E-06; mr1106 (All); LR P-value: 3.05E-07; mr1215 (All); LR P-value: 9.63E-06; mr1221 (Ind_All); LR P-value: 1.15E-06; mr1236 (All); LR P-value: 9.50E-09; mr1236 (Ind_All); LR P-value: 5.65E-08; mr1389 (All); LR P-value: 6.44E-07; mr1389 (Ind_All); LR P-value: 9.97E-07; mr1418 (All); LR P-value: 9.40E-06; mr1653 (Ind_All); LR P-value: 8.59E-06; mr1816 (All); LR P-value: 5.17E-07; mr1886 (All); LR P-value: 8.65E-07; mr1038_2 (All); LR P-value: 5.34E-07; mr1038_2 (Ind_All); LR P-value: 1.11E-06	LOC_Os03g42230.1 Alt: A\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42240.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
vg0323496278	chr03	23496278	A	G	64.60%	0.36%	G -> A	NA	LOC_Os03g42230.1 Alt: A\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42240.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323496286	chr03	23496286	C	T	64.20%	0.38%	T -> C	NA	LOC_Os03g42230.1 Alt: C\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42240.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)
vg0323496292	chr03	23496292	G	T	98.90%	0.32%	G -> T	NA	LOC_Os03g42230.1 Alt: T\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42235.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42240.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar)

Information

This module provides a gene-centered integrative view of genetic variation and regulatory features in rice. It summarizes local genetic variants, functional and phenotypic annotations, chromatin accessibility, model-predicted regulatory effects of non-coding variants, and population genetic statistics within the genomic neighborhood of a queried gene. Quantitative chromatin accessibility and transcriptome profiles across multiple tissues, developmental stages, and three reference varieties are jointly presented to support functional, regulatory, and evolutionary interpretation.

Gene Expression Profiles: Quantitative gene expression levels across multiple tissues and developmental stages are shown where available. These profiles enable direct comparison between transcriptional output and local regulatory activity, facilitating interpretation of tissue-specific gene regulation.

Chromatin Accessibility Landscape: Tissue-resolved chromatin accessibility profiles are visualized across the queried genomic region using ATAC-seq data. Accessibility signals are quantified from Tn5 insertion events aggregated into fixed genomic windows of 250 bp with a sliding step of 100 bp. Heatmap-style visualization highlights spatial and tissue-specific patterns of chromatin openness, revealing putative cis-regulatory elements and their tissue specificity.

Regulatory Effect Predictions for Non-coding Variants: Allele-specific chromatin accessibility effects are predicted using Basenji (Kelley et al., 2018), a deep learning sequence-to-signal model trained to predict chromatin accessibility from genomic sequence. The signed local sequence activity log-ratio is LSAR = log₂(P_ALT + 1) − log₂(P_REF + 1), where P_ALT and P_REF are local predictions averaged across the central eight 128-bp output bins (1,024 bp total). Positive values indicate that the alternative allele is predicted to increase chromatin accessibility, whereas negative values indicate reduced accessibility relative to the reference allele. These scores enable systematic prioritization of non-coding variants with potential regulatory impact.

High-impact regulatory variants (HEVs): HEV cutoffs depend on both the reference genome and the variant set used for calibration. A symbol is shown for a tissue-specific score only when its absolute unrounded value reaches the applicable cutoff. Both predicted increases and decreases can therefore be marked.

Nipponbare (IRGSP-1.0; vg) SNP and non-SNP variants: A light-red ★ denotes an HEV at 0.052 (exact value 0.051688551903), a cutoff calibrated from the SNP-only q90 and applied to both SNP and non-SNP scores. A red ★ denotes a strong HEV at the combined SNP and non-SNP q90 cutoff of 0.106 (exact value 0.10640232). Strong HEVs are displayed as ★ only.
MH63RS3 (vm) SNPs: a light-red ★ denotes an HEV at the SNP-only q90 cutoff of 0.052 (exact value 0.052074253559). No strong-HEV tier is used.
ZS97RS3 (vz) SNPs: a light-red ★ denotes an HEV at the SNP-only q90 cutoff of 0.047 (exact value 0.047439455986). No strong-HEV tier is used.

These model-derived HEVs are distinct from snpEff HIGH-impact or PolyPhen-2 damaging annotations. “Strong” describes the predicted effect magnitude relative to the combined calibration cutoff; it is not a confidence score.

Population differentiation and diversity statistics: Population genetic statistics are displayed across the gene neighborhood to provide evolutionary context. Genetic differentiation is quantified using F_ST, calculated in sliding windows of 10 kb with a step size of 1 kb between predefined rice populations. Nucleotide diversity (π) is computed using the same window and step size to measure local genetic variation within populations. Joint visualization of F_ST and π highlights genomic regions under potential selection and links regulatory variation with population-level evolutionary processes.

Genetic Variants in the Gene Neighborhood: All genetic variants located within the gene body and flanking regions are listed and visualized along the genomic coordinate system. Variants are annotated with sequence context, functional annotations, and population-level allele statistics, enabling detailed inspection of local genetic diversity and variant distribution.