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Detailed information for vg0807179141:

Variant ID: vg0807179141 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 7179141
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.94, C: 0.07, others allele: 0.00, population size: 62. )

Flanking Sequence (100 bp) in Reference Genome:

CCGGTGCAAAGCAAGAGTAAACCCTATTAAAGAAATGCAAACAATAATCAAAATTGGCATGTGGAATTTTTCTTGAGTTCTACATGTCGAAATTCACTAA[T/C]
AGGATTTTTAGTGGAATTTTCAGAGCTCTCGAAATAATTTTAACCATTTAAAATTGAGCTTGCAATATTTTAAATTCCAGGGAAATTCTTTTCCTCCTTT

Reverse complement sequence

AAAGGAGGAAAAGAATTTCCCTGGAATTTAAAATATTGCAAGCTCAATTTTAAATGGTTAAAATTATTTCGAGAGCTCTGAAAATTCCACTAAAAATCCT[A/G]
TTAGTGAATTTCGACATGTAGAACTCAAGAAAAATTCCACATGCCAATTTTGATTATTGTTTGCATTTCTTTAATAGGGTTTACTCTTGCTTTGCACCGG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	32.40%	1.00%	14.60%	52.05%	NA
All Indica	2759	2.10%	1.00%	15.88%	81.04%	NA
All Japonica	1512	94.60%	0.10%	0.99%	4.30%	NA
Aus	269	0.40%	3.00%	56.13%	40.52%	NA
Indica I	595	1.50%	0.00%	8.57%	89.92%	NA
Indica II	465	4.30%	0.90%	15.48%	79.35%	NA
Indica III	913	0.70%	1.20%	18.07%	80.07%	NA
Indica Intermediate	786	2.80%	1.70%	19.08%	76.46%	NA
Temperate Japonica	767	93.20%	0.00%	0.13%	6.65%	NA
Tropical Japonica	504	96.00%	0.20%	2.18%	1.59%	NA
Japonica Intermediate	241	96.30%	0.00%	1.24%	2.49%	NA
VI/Aromatic	96	4.20%	8.30%	77.08%	10.42%	NA
Intermediate	90	42.20%	0.00%	13.33%	44.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0807179141	T -> C	LOC_Os08g12190.1	downstream_gene_variant ; 1391.0bp to feature; MODIFIER	silent_mutation	Average:20.03; most accessible tissue: Minghui63 root, score: 31.271	N	N	N	N
vg0807179141	T -> C	LOC_Os08g12190-LOC_Os08g12210	intergenic_region ; MODIFIER	silent_mutation	Average:20.03; most accessible tissue: Minghui63 root, score: 31.271	N	N	N	N
vg0807179141	T -> DEL	N	N	silent_mutation	Average:20.03; most accessible tissue: Minghui63 root, score: 31.271	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0807179141	NA	4.82E-22	mr1122	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
vg0807179141	NA	9.38E-46	mr1194	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
vg0807179141	NA	9.28E-28	mr1223	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
vg0807179141	NA	7.86E-40	mr1480	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
vg0807179141	NA	2.21E-21	mr1588	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
vg0807179141	NA	7.77E-13	mr1641	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
vg0807179141	NA	2.19E-49	mr1692	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
vg0807179141	NA	1.22E-33	mr1780	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
vg0807179141	NA	3.58E-52	mr1935	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
vg0807179141	NA	1.84E-07	mr1004_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
vg0807179141	NA	2.63E-26	mr1588_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
vg0807179141	NA	3.19E-36	mr1780_2	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
vg0807179141	NA	7.48E-19	mr1945_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
vg0807179141	NA	2.55E-21	mr1968_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