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Detailed information for vg0804837959:

Variant ID: vg0804837959 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 4837959
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.62, C: 0.38, others allele: 0.00, population size: 74. )

Flanking Sequence (100 bp) in Reference Genome:

CCAGGGCGCACTTAGCGACCAGCTCGGCAACAACGTCGAGGCATACGTCGACGACATCGTTGTCAAGACTAAGACAAGCGACTCATTGATTGACGATCTA[T/C]
GGGAAACGTTCGACAACCTCCGATGATATCGCCTTATGCTCAATCCAGAGAAGTGCACGTTCAGAGTACCGTCGGGCAAGCTGCTCGGTTTCCTCGTATC

Reverse complement sequence

GATACGAGGAAACCGAGCAGCTTGCCCGACGGTACTCTGAACGTGCACTTCTCTGGATTGAGCATAAGGCGATATCATCGGAGGTTGTCGAACGTTTCCC[A/G]
TAGATCGTCAATCAATGAGTCGCTTGTCTTAGTCTTGACAACGATGTCGTCGACGTATGCCTCGACGTTGTTGCCGAGCTGGTCGCTAAGTGCGCCCTGG

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	32.50%	3.10%	5.08%	59.35%	NA
All Indica	2759	5.30%	5.10%	5.40%	84.20%	NA
All Japonica	1512	88.00%	0.00%	0.20%	11.84%	NA
Aus	269	7.10%	0.00%	29.74%	63.20%	NA
Indica I	595	8.20%	0.00%	1.51%	90.25%	NA
Indica II	465	5.40%	24.70%	7.31%	62.58%	NA
Indica III	913	2.20%	0.70%	6.24%	90.91%	NA
Indica Intermediate	786	6.60%	2.50%	6.23%	84.61%	NA
Temperate Japonica	767	90.60%	0.00%	0.13%	9.26%	NA
Tropical Japonica	504	86.90%	0.00%	0.40%	12.70%	NA
Japonica Intermediate	241	81.70%	0.00%	0.00%	18.26%	NA
VI/Aromatic	96	7.30%	2.10%	1.04%	89.58%	NA
Intermediate	90	37.80%	2.20%	7.78%	52.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0804837959	T -> C	LOC_Os08g08390.1	missense_variant ; p.Trp774Arg; MODERATE	nonsynonymous_codon ; W774R	Average:19.588; most accessible tissue: Minghui63 root, score: 41.911	probably damaging	2.379	TOLERATED	1.00
vg0804837959	T -> DEL	LOC_Os08g08390.1	N	frameshift_variant	Average:19.588; most accessible tissue: Minghui63 root, score: 41.911	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0804837959	NA	1.21E-07	mr1089	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
vg0804837959	NA	8.77E-08	mr1093	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
vg0804837959	NA	1.42E-06	mr1243	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
vg0804837959	NA	2.52E-06	mr1251	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
vg0804837959	NA	1.45E-06	mr1257	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
vg0804837959	NA	9.57E-08	mr1423	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
vg0804837959	1.53E-06	NA	mr1435	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
vg0804837959	NA	8.41E-09	mr1435	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
vg0804837959	NA	1.37E-08	mr1546	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
vg0804837959	NA	4.43E-07	mr1599	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
vg0804837959	NA	4.17E-08	mr1089_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
vg0804837959	NA	2.01E-07	mr1235_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
vg0804837959	NA	9.15E-08	mr1993_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