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Detailed information for vg0812584594:

Variant ID: vg0812584594 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 12584594
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAAATGGATTTTAATTTGGAATGGATTTATCAGGACGTGACAATTACCACAAGGTGTCAATGCTCACTTTCAGCCCCAGCCATCAGTTGACAAGACAGAG[G/T]
CCAGTATCGGCATTGTACCTTTGGATGTTCCAGCACAGCAGCCAAGAAATCAAGTACCAGATGGAGAACCCGAGCATAAGAAAGTTATTGTCTGTTACAA

Reverse complement sequence

TTGTAACAGACAATAACTTTCTTATGCTCGGGTTCTCCATCTGGTACTTGATTTCTTGGCTGCTGTGCTGGAACATCCAAAGGTACAATGCCGATACTGG[C/A]
CTCTGTCTTGTCAACTGATGGCTGGGGCTGAAAGTGAGCATTGACACCTTGTGGTAATTGTCACGTCCTGATAAATCCATTCCAAATTAAAATCCATTTT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.00%	2.00%	3.62%	2.37%	NA
All Indica	2759	99.90%	0.00%	0.00%	0.04%	NA
All Japonica	1512	79.10%	6.00%	8.20%	6.75%	NA
Aus	269	84.00%	0.00%	13.38%	2.60%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.00%	0.00%	0.13%	NA
Temperate Japonica	767	94.40%	1.80%	3.65%	0.13%	NA
Tropical Japonica	504	65.90%	4.00%	11.90%	18.25%	NA
Japonica Intermediate	241	58.10%	23.20%	14.94%	3.73%	NA
VI/Aromatic	96	93.80%	1.00%	5.21%	0.00%	NA
Intermediate	90	90.00%	1.10%	6.67%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0812584594	G -> T	LOC_Os08g21030.1	upstream_gene_variant ; 4642.0bp to feature; MODIFIER	silent_mutation	Average:20.098; most accessible tissue: Zhenshan97 root, score: 30.989	N	N	N	N
vg0812584594	G -> T	LOC_Os08g21050.1	upstream_gene_variant ; 810.0bp to feature; MODIFIER	silent_mutation	Average:20.098; most accessible tissue: Zhenshan97 root, score: 30.989	N	N	N	N
vg0812584594	G -> T	LOC_Os08g21030-LOC_Os08g21050	intergenic_region ; MODIFIER	silent_mutation	Average:20.098; most accessible tissue: Zhenshan97 root, score: 30.989	N	N	N	N
vg0812584594	G -> DEL	N	N	silent_mutation	Average:20.098; most accessible tissue: Zhenshan97 root, score: 30.989	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0812584594	4.62E-06	4.62E-06	mr1973	Jap_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