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Detailed information for vg0404474445:

Variant ID: vg0404474445 (JBrowse)	Variation Type: INDEL
Chromosome: chr04	Position: 4474445
Reference Allele: GGTATTGGTGGTGT	Alternative Allele: CGTATTGGTGGTGT,TGTATTGGTGGTGT,G
Primary Allele: GGTATTGGTGGTGT	Secondary Allele: CGTATTGGTGGTGT

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCTCGGTTCAATCCAGGTAACAGATCGAGATCATTAGGCACCGGTGCCGGATTATTAGGATTATTATATTCCTGCACGCACGATCAGAGTTCAATACTTA[GGTATTGGTGGTGT/CGTATTGGTGGTGT,TGTATTGGTGGTGT,G]
TATCTTAATTTTCTATTGTTGTTTTTACACTAGAAAAAATGCCTATGCGTTACAACGGGTGAAAGCTATTTTAATTTTATTATTGTTATATAGTTTAGTT

Reverse complement sequence

AACTAAACTATATAACAATAATAAAATTAAAATAGCTTTCACCCGTTGTAACGCATAGGCATTTTTTCTAGTGTAAAAACAACAATAGAAAATTAAGATA[ACACCACCAATACC/ACACCACCAATACG,ACACCACCAATACA,C]
TAAGTATTGAACTCTGATCGTGCGTGCAGGAATATAATAATCCTAATAATCCGGCACCGGTGCCTAATGATCTCGATCTGTTACCTGGATTGAACCGAGG

Allele Frequencies:

Populations	Population Size	Frequency of GGTATTGGTGGTGT(primary allele)	Frequency of CGTATTGGTGGTGT(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	69.90%	9.30%	7.87%	12.93%	TGTATTGGTGGTGT: 0.02%
All Indica	2759	71.40%	0.70%	12.00%	15.88%	TGTATTGGTGGTGT: 0.04%
All Japonica	1512	62.70%	24.70%	1.72%	10.85%	NA
Aus	269	94.40%	1.10%	3.35%	1.12%	NA
Indica I	595	23.20%	0.00%	38.66%	38.15%	NA
Indica II	465	93.30%	0.60%	1.72%	4.30%	NA
Indica III	913	85.30%	0.80%	3.07%	10.73%	TGTATTGGTGGTGT: 0.11%
Indica Intermediate	786	78.90%	1.00%	8.27%	11.83%	NA
Temperate Japonica	767	72.40%	6.60%	1.83%	19.17%	NA
Tropical Japonica	504	42.70%	54.80%	2.18%	0.40%	NA
Japonica Intermediate	241	73.90%	19.50%	0.41%	6.22%	NA
VI/Aromatic	96	57.30%	40.60%	2.08%	0.00%	NA
Intermediate	90	82.20%	6.70%	4.44%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0404474445	GGTATTGGTGGTGT -> DEL	N	N	silent_mutation	Average:37.424; most accessible tissue: Minghui63 flag leaf, score: 83.621	N	N	N	N
vg0404474445	GGTATTGGTGGTGT -> G	LOC_Os04g08370.1	upstream_gene_variant ; 934.0bp to feature; MODIFIER	N	Average:37.424; most accessible tissue: Minghui63 flag leaf, score: 83.621	N	N	N	N
vg0404474445	GGTATTGGTGGTGT -> G	LOC_Os04g08370-LOC_Os04g08390	intergenic_region ; MODIFIER	N	Average:37.424; most accessible tissue: Minghui63 flag leaf, score: 83.621	N	N	N	N
vg0404474445	GGTATTGGTGGTGT -> CGTATTGGTGGTGT	LOC_Os04g08370.1	upstream_gene_variant ; 933.0bp to feature; MODIFIER	silent_mutation	Average:37.424; most accessible tissue: Minghui63 flag leaf, score: 83.621	N	N	N	N
vg0404474445	GGTATTGGTGGTGT -> CGTATTGGTGGTGT	LOC_Os04g08370-LOC_Os04g08390	intergenic_region ; MODIFIER	silent_mutation	Average:37.424; most accessible tissue: Minghui63 flag leaf, score: 83.621	N	N	N	N
vg0404474445	GGTATTGGTGGTGT -> TGTATTGGTGGTGT	LOC_Os04g08370.1	upstream_gene_variant ; 933.0bp to feature; MODIFIER	silent_mutation	Average:37.424; most accessible tissue: Minghui63 flag leaf, score: 83.621	N	N	N	N
vg0404474445	GGTATTGGTGGTGT -> TGTATTGGTGGTGT	LOC_Os04g08370-LOC_Os04g08390	intergenic_region ; MODIFIER	silent_mutation	Average:37.424; most accessible tissue: Minghui63 flag leaf, score: 83.621	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0404474445	2.91E-06	5.68E-09	mr1364_2	All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0404474445	NA	1.52E-09	mr1364_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0404474445	3.31E-06	NA	mr1549_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251