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Detailed information for vg1121984717:

Variant ID: vg1121984717 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21984717
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.02, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

CCAACACCATACAAGATGCTTTTTCCCTCAAAAATACCATACAAAAGTGTTTGTTAAGCGGAATTCTCAATTTTGTTTTTTTTTTTTTGGACAACCTCTA[T/C]
AAGTTTTGCATGTAACTGTTGGAACTACATATTGTGTGCTGAATTTATTTTCAATTACTGTTTTCTTTCTTGTCTGTTGTATCATTTAGCCATCACATGT

Reverse complement sequence

ACATGTGATGGCTAAATGATACAACAGACAAGAAAGAAAACAGTAATTGAAAATAAATTCAGCACACAATATGTAGTTCCAACAGTTACATGCAAAACTT[A/G]
TAGAGGTTGTCCAAAAAAAAAAAAACAAAATTGAGAATTCCGCTTAACAAACACTTTTGTATGGTATTTTTGAGGGAAAAAGCATCTTGTATGGTGTTGG

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	73.00%	27.00%	0.02%	0.00%	NA
All Indica	2759	98.40%	1.60%	0.04%	0.00%	NA
All Japonica	1512	20.10%	79.90%	0.00%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	98.80%	1.20%	0.00%	0.00%	NA
Indica II	465	98.10%	1.90%	0.00%	0.00%	NA
Indica III	913	98.90%	1.10%	0.00%	0.00%	NA
Indica Intermediate	786	97.70%	2.20%	0.13%	0.00%	NA
Temperate Japonica	767	11.50%	88.50%	0.00%	0.00%	NA
Tropical Japonica	504	34.50%	65.50%	0.00%	0.00%	NA
Japonica Intermediate	241	17.40%	82.60%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	78.90%	21.10%	0.00%	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
vg1121984717	T -> C	LOC_Os11g37210.1	downstream_gene_variant ; 1931.0bp to feature; MODIFIER	silent_mutation	Average:58.093; most accessible tissue: Callus, score: 82.469	N	N	N	N
vg1121984717	T -> C	LOC_Os11g37200.1	intron_variant ; MODIFIER	silent_mutation	Average:58.093; most accessible tissue: Callus, score: 82.469	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121984717	NA	1.25E-55	Grain_width	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
vg1121984717	NA	1.51E-42	mr1136	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
vg1121984717	NA	4.32E-24	mr1698	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
vg1121984717	NA	3.28E-06	mr1698	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
vg1121984717	9.40E-07	NA	mr1745	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
vg1121984717	NA	1.03E-34	mr1780	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
vg1121984717	NA	9.23E-34	mr1448_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
vg1121984717	4.10E-06	NA	mr1517_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
vg1121984717	NA	1.38E-07	mr1517_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
vg1121984717	NA	6.14E-08	mr1576_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
vg1121984717	9.99E-07	7.00E-26	mr1698_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
vg1121984717	NA	2.18E-06	mr1698_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
vg1121984717	1.15E-07	NA	mr1745_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