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Detailed information for vg0117362788:

Variant ID: vg0117362788 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 17362788
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACTTAGCTTCTGATTTCTTAAAAGCCTTTGTCAAGTCTTATTGAGCCTAAAACCCGCAAAAGCTATTAAAAACCTTTAGTCCTCATTGGCTAAGTCGAAA[G/T]
ACCAAACATGGCAATGATAAATCAAGTAAGCAAATTGAATTGATAAAAATCACACTCCATTATTATCATAGTAGCCCCCTGACTGAAAACTTCAAGGAAA

Reverse complement sequence

TTTCCTTGAAGTTTTCAGTCAGGGGGCTACTATGATAATAATGGAGTGTGATTTTTATCAATTCAATTTGCTTACTTGATTTATCATTGCCATGTTTGGT[C/A]
TTTCGACTTAGCCAATGAGGACTAAAGGTTTTTAATAGCTTTTGCGGGTTTTAGGCTCAATAAGACTTGACAAAGGCTTTTAAGAAATCAGAAGCTAAGT

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	53.30%	0.70%	35.93%	10.05%	NA
All Indica	2759	24.30%	1.20%	57.70%	16.82%	NA
All Japonica	1512	97.90%	0.00%	1.92%	0.20%	NA
Aus	269	79.60%	0.00%	18.96%	1.49%	NA
Indica I	595	26.70%	0.50%	43.70%	29.08%	NA
Indica II	465	24.10%	0.60%	62.58%	12.69%	NA
Indica III	913	20.60%	2.20%	62.87%	14.35%	NA
Indica Intermediate	786	27.00%	0.80%	59.41%	12.85%	NA
Temperate Japonica	767	99.20%	0.00%	0.78%	0.00%	NA
Tropical Japonica	504	95.40%	0.00%	4.17%	0.40%	NA
Japonica Intermediate	241	98.80%	0.00%	0.83%	0.41%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	67.80%	0.00%	27.78%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0117362788	G -> T	LOC_Os01g31714.1	downstream_gene_variant ; 185.0bp to feature; MODIFIER	silent_mutation	Average:12.212; most accessible tissue: Callus, score: 21.898	N	N	N	N
vg0117362788	G -> T	LOC_Os01g31730.1	downstream_gene_variant ; 655.0bp to feature; MODIFIER	silent_mutation	Average:12.212; most accessible tissue: Callus, score: 21.898	N	N	N	N
vg0117362788	G -> T	LOC_Os01g31714-LOC_Os01g31730	intergenic_region ; MODIFIER	silent_mutation	Average:12.212; most accessible tissue: Callus, score: 21.898	N	N	N	N
vg0117362788	G -> DEL	N	N	silent_mutation	Average:12.212; most accessible tissue: Callus, score: 21.898	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0117362788	2.26E-06	4.00E-06	mr1815	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