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Detailed information for vg0805155489:

Variant ID: vg0805155489 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 5155489
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.83, A: 0.17, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

TTCGATTGCACACAGCTATGGCACTTAGAACCTTTGACAATGGAAAACTTAGGAATTAAACACATGCTGGAAAGCCGAGACATCAAGCCAAAATTAATAT[A/G]
ACATAAACGTGAGTGCCAAACATTAGCCTCATCATCCACACTGCCACAAATATGGTTCACAGACTTATTGCAGAAATCAGAAAGGGAAAAGCGGAACAGG

Reverse complement sequence

CCTGTTCCGCTTTTCCCTTTCTGATTTCTGCAATAAGTCTGTGAACCATATTTGTGGCAGTGTGGATGATGAGGCTAATGTTTGGCACTCACGTTTATGT[T/C]
ATATTAATTTTGGCTTGATGTCTCGGCTTTCCAGCATGTGTTTAATTCCTAAGTTTTCCATTGTCAAAGGTTCTAAGTGCCATAGCTGTGTGCAATCGAA

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	23.30%	13.90%	45.41%	17.41%	NA
All Indica	2759	2.20%	18.80%	54.91%	24.07%	NA
All Japonica	1512	66.30%	6.10%	19.97%	7.61%	NA
Aus	269	1.90%	6.70%	82.16%	9.29%	NA
Indica I	595	0.70%	8.40%	55.13%	35.80%	NA
Indica II	465	3.90%	9.00%	58.92%	28.17%	NA
Indica III	913	1.50%	30.60%	53.56%	14.35%	NA
Indica Intermediate	786	3.30%	18.70%	53.94%	24.05%	NA
Temperate Japonica	767	83.30%	0.90%	7.69%	8.08%	NA
Tropical Japonica	504	44.40%	15.70%	37.70%	2.18%	NA
Japonica Intermediate	241	58.10%	2.50%	21.99%	17.43%	NA
VI/Aromatic	96	7.30%	10.40%	75.00%	7.29%	NA
Intermediate	90	27.80%	18.90%	40.00%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0805155489	A -> G	LOC_Os08g08870.1	missense_variant ; p.Tyr374His; MODERATE	nonsynonymous_codon ; Y374H	Average:20.036; most accessible tissue: Zhenshan97 panicle, score: 36.038	benign	-1.317	TOLERATED	1.00
vg0805155489	A -> DEL	LOC_Os08g08870.1	N	frameshift_variant	Average:20.036; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0805155489	NA	6.67E-29	mr1137	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
vg0805155489	NA	2.04E-07	mr1162	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
vg0805155489	NA	2.22E-07	mr1193	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
vg0805155489	NA	3.77E-06	mr1291	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
vg0805155489	NA	2.65E-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
vg0805155489	NA	1.32E-06	mr1588	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
vg0805155489	NA	4.45E-06	mr1619	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
vg0805155489	NA	3.77E-06	mr1708	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
vg0805155489	6.24E-07	6.24E-07	mr1828	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
vg0805155489	NA	5.89E-06	mr1091_2	Jap_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
vg0805155489	5.99E-07	5.98E-07	mr1440_2	Jap_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
vg0805155489	NA	3.86E-27	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
vg0805155489	NA	6.50E-07	mr1588_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
vg0805155489	NA	1.26E-06	mr1646_2	Jap_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
vg0805155489	NA	5.67E-06	mr1865_2	Jap_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