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Detailed information for vg1100571681:

Variant ID: vg1100571681 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 571681
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:

CAAGTTTTTCTCACTTCTAAGTATCAAGTACTAACCTTCAGTATTCTGACAATGCAGGGTTGTGATGGATCGGTGCTGCTAGATGACACCCCAACCTTCA[C/T]
TGGAGAGAAGACCGCCGCCCCGAACAACAACTCTCTGCGTGGATTCGATGTTATAGACAACATCAAGGCACAGGTTGAGGGGATCTGTCCGCAGGTGGTG

Reverse complement sequence

CACCACCTGCGGACAGATCCCCTCAACCTGTGCCTTGATGTTGTCTATAACATCGAATCCACGCAGAGAGTTGTTGTTCGGGGCGGCGGTCTTCTCTCCA[G/A]
TGAAGGTTGGGGTGTCATCTAGCAGCACCGATCCATCACAACCCTGCATTGTCAGAATACTGAAGGTTAGTACTTGATACTTAGAAGTGAGAAAAACTTG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.60%	4.30%	2.09%	0.00%	NA
All Indica	2759	98.70%	0.10%	1.23%	0.00%	NA
All Japonica	1512	83.40%	12.50%	4.10%	0.00%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	96.30%	0.20%	3.53%	0.00%	NA
Indica II	465	98.50%	0.20%	1.29%	0.00%	NA
Indica III	913	99.80%	0.10%	0.11%	0.00%	NA
Indica Intermediate	786	99.20%	0.00%	0.76%	0.00%	NA
Temperate Japonica	767	92.00%	4.00%	3.91%	0.00%	NA
Tropical Japonica	504	77.60%	19.00%	3.37%	0.00%	NA
Japonica Intermediate	241	68.00%	25.70%	6.22%	0.00%	NA
VI/Aromatic	96	95.80%	3.10%	1.04%	0.00%	NA
Intermediate	90	91.10%	7.80%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1100571681	C -> T	LOC_Os11g02100.1	missense_variant ; p.Thr22Ile; MODERATE	nonsynonymous_codon ; T22I	Average:71.639; most accessible tissue: Minghui63 panicle, score: 77.956	benign	1.007	TOLERATED	0.09

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1100571681	NA	2.54E-14	Grain_weight	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
vg1100571681	NA	2.11E-06	Grain_weight	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
vg1100571681	NA	1.40E-06	mr1063	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
vg1100571681	1.31E-06	NA	mr1104	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
vg1100571681	NA	2.63E-06	mr1104	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
vg1100571681	3.44E-08	NA	mr1107	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
vg1100571681	NA	2.04E-06	mr1179	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
vg1100571681	NA	8.81E-06	mr1213	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
vg1100571681	NA	5.40E-07	mr1224	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
vg1100571681	1.60E-06	NA	mr1437	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
vg1100571681	NA	1.36E-06	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
vg1100571681	8.18E-06	8.17E-06	mr1663	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
vg1100571681	NA	1.35E-07	mr1729	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
vg1100571681	NA	9.82E-07	mr1729	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
vg1100571681	3.85E-06	8.77E-12	mr1751	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
vg1100571681	7.30E-06	3.19E-07	mr1751	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
vg1100571681	NA	2.29E-06	mr1906	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
vg1100571681	NA	3.13E-06	mr1906	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
vg1100571681	NA	5.92E-06	mr1960	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