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Detailed information for vg1126984434:

Variant ID: vg1126984434 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 26984434
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.61, C: 0.38, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

TCTATATACTACCAGCACAAAAATACTTCCGCATAGGAAAACTTGTCCTCTTTGTAATATATATGGATAATTTTATCATATTTGAGAAGGTATTGAGAGG[C/T]
ATCATATTTTCTAGTGTAAAACTTAATACCAAAATTTTTAGCGTAAAATCTTAGTATCAGCAGGCACTTTCTTAAAAACTGTAAAATTTTTCAATATATA

Reverse complement sequence

TATATATTGAAAAATTTTACAGTTTTTAAGAAAGTGCCTGCTGATACTAAGATTTTACGCTAAAAATTTTGGTATTAAGTTTTACACTAGAAAATATGAT[G/A]
CCTCTCAATACCTTCTCAAATATGATAAAATTATCCATATATATTACAAAGAGGACAAGTTTTCCTATGCGGAAGTATTTTTGTGCTGGTAGTATATAGA

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	67.50%	30.00%	0.28%	2.18%	NA
All Indica	2759	71.10%	25.40%	0.25%	3.19%	NA
All Japonica	1512	58.00%	41.40%	0.13%	0.46%	NA
Aus	269	78.80%	17.80%	0.74%	2.60%	NA
Indica I	595	91.40%	7.60%	0.17%	0.84%	NA
Indica II	465	38.50%	60.60%	0.86%	0.00%	NA
Indica III	913	79.30%	15.90%	0.00%	4.82%	NA
Indica Intermediate	786	65.60%	29.10%	0.25%	4.96%	NA
Temperate Japonica	767	45.50%	54.20%	0.13%	0.13%	NA
Tropical Japonica	504	71.40%	28.00%	0.00%	0.60%	NA
Japonica Intermediate	241	69.70%	28.60%	0.41%	1.24%	NA
VI/Aromatic	96	84.40%	15.60%	0.00%	0.00%	NA
Intermediate	90	64.40%	32.20%	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
vg1126984434	C -> T	LOC_Os11g44630.1	intron_variant ; MODIFIER	silent_mutation	Average:29.601; most accessible tissue: Callus, score: 75.786	N	N	N	N
vg1126984434	C -> DEL	N	N	silent_mutation	Average:29.601; most accessible tissue: Callus, score: 75.786	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1126984434	NA	3.25E-13	Grain_width	Ind_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
vg1126984434	NA	3.63E-06	mr1561	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
vg1126984434	NA	2.46E-10	mr1644	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
vg1126984434	NA	1.37E-09	mr1644	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
vg1126984434	NA	2.44E-13	mr1191_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
vg1126984434	NA	3.16E-11	mr1191_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
vg1126984434	NA	1.17E-06	mr1330_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
vg1126984434	NA	1.48E-07	mr1332_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
vg1126984434	NA	4.00E-13	mr1380_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
vg1126984434	NA	8.95E-10	mr1380_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
vg1126984434	NA	1.97E-12	mr1561_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
vg1126984434	NA	2.47E-09	mr1561_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
vg1126984434	NA	1.76E-09	mr1875_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
vg1126984434	NA	8.25E-09	mr1875_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
vg1126984434	NA	7.11E-10	mr1908_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
vg1126984434	NA	2.37E-08	mr1908_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
vg1126984434	NA	5.49E-07	mr1977_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
vg1126984434	NA	5.76E-11	mr1996_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
vg1126984434	NA	6.34E-09	mr1996_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