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Detailed information for vg0117039557:

Variant ID: vg0117039557 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 17039557
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATATTTAATTGTATCTCACGATGGTTAATAGTGATTGGTTAATTAATTAATTTGCCAACTAAAACTTGATAATGGTGGGATGTGAGCACATGGTTTTGAT[A/G]
GTAGTGCTCATGACAATTAAGGACCGGTTCACGAGTTTCGGTTGTAAAACATTAGCCGTGCCAACCACAAGCCAGAATGCGCAACGGTTGGACACTTTGT

Reverse complement sequence

ACAAAGTGTCCAACCGTTGCGCATTCTGGCTTGTGGTTGGCACGGCTAATGTTTTACAACCGAAACTCGTGAACCGGTCCTTAATTGTCATGAGCACTAC[T/C]
ATCAAAACCATGTGCTCACATCCCACCATTATCAAGTTTTAGTTGGCAAATTAATTAATTAACCAATCACTATTAACCATCGTGAGATACAATTAAATAT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	38.50%	2.90%	2.92%	55.63%	NA
All Indica	2759	5.20%	3.30%	3.08%	88.47%	NA
All Japonica	1512	96.00%	1.50%	0.00%	2.51%	NA
Aus	269	32.00%	7.10%	18.96%	42.01%	NA
Indica I	595	4.40%	0.00%	1.68%	93.95%	NA
Indica II	465	5.60%	11.00%	1.72%	81.72%	NA
Indica III	913	2.80%	1.00%	4.60%	91.57%	NA
Indica Intermediate	786	8.30%	3.80%	3.18%	84.73%	NA
Temperate Japonica	767	98.80%	0.30%	0.00%	0.91%	NA
Tropical Japonica	504	94.60%	0.20%	0.00%	5.16%	NA
Japonica Intermediate	241	89.60%	8.30%	0.00%	2.07%	NA
VI/Aromatic	96	93.80%	0.00%	1.04%	5.21%	NA
Intermediate	90	56.70%	6.70%	1.11%	35.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0117039557	A -> G	LOC_Os01g31170.1	upstream_gene_variant ; 4310.0bp to feature; MODIFIER	silent_mutation	Average:12.704; most accessible tissue: Callus, score: 31.671	N	N	N	N
vg0117039557	A -> G	LOC_Os01g31150.1	downstream_gene_variant ; 2321.0bp to feature; MODIFIER	silent_mutation	Average:12.704; most accessible tissue: Callus, score: 31.671	N	N	N	N
vg0117039557	A -> G	LOC_Os01g31160.1	intron_variant ; MODIFIER	silent_mutation	Average:12.704; most accessible tissue: Callus, score: 31.671	N	N	N	N
vg0117039557	A -> DEL	N	N	silent_mutation	Average:12.704; most accessible tissue: Callus, score: 31.671	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0117039557	NA	1.45E-06	mr1761	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
vg0117039557	NA	2.65E-17	mr1281_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
vg0117039557	NA	7.07E-46	mr1519_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
vg0117039557	NA	8.66E-07	mr1568_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
vg0117039557	NA	2.95E-12	mr1666_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
vg0117039557	2.53E-06	NA	mr1707_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
vg0117039557	NA	8.01E-24	mr1708_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
vg0117039557	NA	1.03E-13	mr1770_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
vg0117039557	NA	7.78E-08	mr1783_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
vg0117039557	9.18E-06	NA	mr1860_2	Ind_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