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Detailed information for vg0309199102:

Variant ID: vg0309199102 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 9199102
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATGAGGAATTTTACCGTTCTTTAGAAAGTACCTTGAGATACATAATTTTTACATAAAAATTTTTAGTACTTTAAGATACTTAGTACCAAATTTTACACTA[G/A]
AAAATATGTTAGTATCTCTGAGTACTATCTTAAGGATGATAAAATTATCCAACATTTATAGTTGGCTTTCGTTTATTTGAACTGTGGTATGTGTTCCGTG

Reverse complement sequence

CACGGAACACATACCACAGTTCAAATAAACGAAAGCCAACTATAAATGTTGGATAATTTTATCATCCTTAAGATAGTACTCAGAGATACTAACATATTTT[C/T]
TAGTGTAAAATTTGGTACTAAGTATCTTAAAGTACTAAAAATTTTTATGTAAAAATTATGTATCTCAAGGTACTTTCTAAAGAACGGTAAAATTCCTCAT

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	62.90%	37.00%	0.11%	0.00%	NA
All Indica	2759	45.40%	54.40%	0.18%	0.00%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	20.40%	79.60%	0.00%	0.00%	NA
Indica I	595	75.50%	24.20%	0.34%	0.00%	NA
Indica II	465	67.50%	32.30%	0.22%	0.00%	NA
Indica III	913	18.60%	81.40%	0.00%	0.00%	NA
Indica Intermediate	786	40.70%	59.00%	0.25%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	87.50%	12.50%	0.00%	0.00%	NA
Intermediate	90	78.90%	21.10%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0309199102	G -> A	LOC_Os03g16670.1	upstream_gene_variant ; 3439.0bp to feature; MODIFIER	silent_mutation	Average:54.282; most accessible tissue: Zhenshan97 root, score: 74.04	N	N	N	N
vg0309199102	G -> A	LOC_Os03g16660.1	downstream_gene_variant ; 1875.0bp to feature; MODIFIER	silent_mutation	Average:54.282; most accessible tissue: Zhenshan97 root, score: 74.04	N	N	N	N
vg0309199102	G -> A	LOC_Os03g16660-LOC_Os03g16670	intergenic_region ; MODIFIER	silent_mutation	Average:54.282; most accessible tissue: Zhenshan97 root, score: 74.04	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0309199102	8.27E-07	NA	mr1671_2	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