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Detailed information for vg0321855451:

Variant ID: vg0321855451 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 21855451
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAGGCAGTGGGCGATCCCCTCTTGCGCCGCGGTGAATCCGGCATCTGGACAACCGGACACCCCGGCCGACCCAACTCCATCACGCCCACCCTCGCCACCG[G/A]
TGCCTAGGAAAGGGTCGAGCTATACTTCAGATCAAGCAGTTACCCACTCCTGCTTGTGGTAAGCACGGTAAGTCTCCAAGGGTTTCCCGTGAACCGGTCC

Reverse complement sequence

GGACCGGTTCACGGGAAACCCTTGGAGACTTACCGTGCTTACCACAAGCAGGAGTGGGTAACTGCTTGATCTGAAGTATAGCTCGACCCTTTCCTAGGCA[C/T]
CGGTGGCGAGGGTGGGCGTGATGGAGTTGGGTCGGCCGGGGTGTCCGGTTGTCCAGATGCCGGATTCACCGCGGCGCAAGAGGGGATCGCCCACTGCCTT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	80.00%	0.40%	0.83%	18.79%	NA
All Indica	2759	72.90%	0.60%	0.76%	25.73%	NA
All Japonica	1512	93.70%	0.00%	0.99%	5.29%	NA
Aus	269	67.70%	0.00%	0.74%	31.60%	NA
Indica I	595	93.40%	0.50%	0.17%	5.88%	NA
Indica II	465	67.30%	1.50%	0.43%	30.75%	NA
Indica III	913	65.60%	0.10%	0.77%	33.52%	NA
Indica Intermediate	786	69.10%	0.80%	1.40%	28.75%	NA
Temperate Japonica	767	99.20%	0.00%	0.00%	0.78%	NA
Tropical Japonica	504	93.50%	0.00%	0.60%	5.95%	NA
Japonica Intermediate	241	76.80%	0.00%	4.98%	18.26%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	85.60%	0.00%	1.11%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0321855451	G -> A	LOC_Os03g39330.1	upstream_gene_variant ; 1669.0bp to feature; MODIFIER	silent_mutation	Average:32.678; most accessible tissue: Minghui63 root, score: 41.911	N	N	N	N
vg0321855451	G -> A	LOC_Os03g39330-LOC_Os03g39350	intergenic_region ; MODIFIER	silent_mutation	Average:32.678; most accessible tissue: Minghui63 root, score: 41.911	N	N	N	N
vg0321855451	G -> DEL	N	N	silent_mutation	Average:32.678; most accessible tissue: Minghui63 root, score: 41.911	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0321855451	1.39E-06	8.61E-06	mr1740	Ind_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