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Detailed information for vg0901967595:

Variant ID: vg0901967595 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 1967595
Reference Allele: A	Alternative Allele: T
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, A: 0.02, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:

CCAGGAAAATTTCAGAGAGTATAATTAACCATGGAGAAGTTAATGAAAATTAAATCCAGCCATGCTTTATATTTAGGAAATTTTATTTCCCACATTTAAC[A/T]
TCACTTGTAAATTAATGAACATTTAATATAAATTCTAATAATAATTTATTAAATAATTTATAAATCATAAGAAGAAAATCAAGATGTGACAATTTCATCC

Reverse complement sequence

GGATGAAATTGTCACATCTTGATTTTCTTCTTATGATTTATAAATTATTTAATAAATTATTATTAGAATTTATATTAAATGTTCATTAATTTACAAGTGA[T/A]
GTTAAATGTGGGAAATAAAATTTCCTAAATATAAAGCATGGCTGGATTTAATTTTCATTAACTTCTCCATGGTTAATTATACTCTCTGAAATTTTCCTGG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	71.20%	22.00%	4.87%	2.01%	NA
All Indica	2759	92.00%	1.80%	4.17%	1.99%	NA
All Japonica	1512	26.40%	64.20%	7.14%	2.31%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	92.80%	4.40%	2.35%	0.50%	NA
Indica II	465	90.10%	1.30%	6.02%	2.58%	NA
Indica III	913	92.60%	0.10%	4.38%	2.96%	NA
Indica Intermediate	786	92.00%	2.20%	4.20%	1.65%	NA
Temperate Japonica	767	2.20%	96.70%	0.39%	0.65%	NA
Tropical Japonica	504	57.30%	21.40%	16.47%	4.76%	NA
Japonica Intermediate	241	38.60%	49.80%	9.13%	2.49%	NA
VI/Aromatic	96	92.70%	1.00%	2.08%	4.17%	NA
Intermediate	90	74.40%	18.90%	5.56%	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
vg0901967595	A -> DEL	N	N	silent_mutation	Average:50.402; most accessible tissue: Zhenshan97 flag leaf, score: 72.387	N	N	N	N
vg0901967595	A -> T	LOC_Os09g03870.1	intron_variant ; MODIFIER	silent_mutation	Average:50.402; most accessible tissue: Zhenshan97 flag leaf, score: 72.387	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0901967595	NA	3.16E-14	Grain_thickness	Jap_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0901967595	NA	1.69E-12	Grain_width	Jap_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0901967595	2.13E-06	NA	mr1008	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
vg0901967595	2.34E-06	9.24E-11	mr1008	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
vg0901967595	4.06E-07	NA	mr1009	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
vg0901967595	4.30E-07	2.49E-11	mr1009	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
vg0901967595	NA	7.28E-06	mr1014	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
vg0901967595	8.89E-06	NA	mr1015	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
vg0901967595	6.09E-06	1.51E-07	mr1015	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
vg0901967595	NA	1.45E-07	mr1190	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
vg0901967595	NA	6.56E-06	mr1295	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
vg0901967595	NA	1.55E-09	mr1368	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
vg0901967595	NA	5.17E-06	mr1445	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
vg0901967595	NA	2.04E-07	mr1125_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
vg0901967595	NA	1.49E-10	mr1552_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
vg0901967595	NA	4.46E-08	mr1578_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