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Detailed information for vg0811122646:

Variant ID: vg0811122646 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 11122646
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 354. )

Flanking Sequence (100 bp) in Reference Genome:

GTTGAGAGCTTGTGCACTTGACTTTGGCGGAGCTTGGGATAAAAGTCTACCATATGCTAAATTCTCTTACAATAACAGCTATCAGGCCAGTTTGCAAATG[G/A]
CACCGTTTGAAGCATTGTACGGACGGAAGTGCCGCACTCCGCTCTTCTGGGATCAAACTGGAGAACGCCAACTGTTCGGGACAGAGGTGCTAACCGAGGC

Reverse complement sequence

GCCTCGGTTAGCACCTCTGTCCCGAACAGTTGGCGTTCTCCAGTTTGATCCCAGAAGAGCGGAGTGCGGCACTTCCGTCCGTACAATGCTTCAAACGGTG[C/T]
CATTTGCAAACTGGCCTGATAGCTGTTATTGTAAGAGAATTTAGCATATGGTAGACTTTTATCCCAAGCTCCGCCAAAGTCAAGTGCACAAGCTCTCAAC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.10%	4.40%	2.62%	0.87%	NA
All Indica	2759	99.80%	0.10%	0.00%	0.04%	NA
All Japonica	1512	76.40%	13.60%	7.47%	2.58%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.80%	0.10%	0.00%	0.11%	NA
Indica Intermediate	786	99.70%	0.30%	0.00%	0.00%	NA
Temperate Japonica	767	95.60%	0.50%	2.74%	1.17%	NA
Tropical Japonica	504	48.20%	34.30%	14.48%	2.98%	NA
Japonica Intermediate	241	74.30%	11.60%	7.88%	6.22%	NA
VI/Aromatic	96	90.60%	0.00%	9.38%	0.00%	NA
Intermediate	90	95.60%	1.10%	2.22%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0811122646	G -> A	LOC_Os08g18140.1	missense_variant ; p.Ala635Thr; MODERATE	nonsynonymous_codon ; A635T	Average:44.161; most accessible tissue: Minghui63 young leaf, score: 71.839	benign	0.563	DELETERIOUS	0.01
vg0811122646	G -> DEL	LOC_Os08g18140.1	N	frameshift_variant	Average:44.161; most accessible tissue: Minghui63 young leaf, score: 71.839	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0811122646	1.47E-06	3.26E-07	mr1082	Jap_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
vg0811122646	2.80E-09	6.08E-10	mr1083	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
vg0811122646	2.05E-07	NA	mr1086	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
vg0811122646	6.73E-06	6.73E-06	mr1145	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
vg0811122646	9.33E-08	9.33E-08	mr1204	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
vg0811122646	4.08E-09	4.64E-09	mr1226	Jap_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
vg0811122646	5.73E-06	NA	mr1437	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
vg0811122646	2.40E-06	NA	mr1560	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
vg0811122646	2.08E-11	2.08E-11	mr1076_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
vg0811122646	NA	7.96E-06	mr1082_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
vg0811122646	NA	1.36E-10	mr1083_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
vg0811122646	NA	3.67E-06	mr1103_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
vg0811122646	NA	8.75E-08	mr1104_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
vg0811122646	3.10E-06	8.64E-08	mr1107_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
vg0811122646	NA	1.88E-09	mr1226_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
vg0811122646	2.44E-08	2.44E-08	mr1264_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
vg0811122646	NA	1.24E-07	mr1408_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
vg0811122646	NA	8.93E-07	mr1498_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