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Detailed information for vg1117421514:

Variant ID: vg1117421514 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 17421514
Reference Allele: T	Alternative Allele: C
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: 107. )

Flanking Sequence (100 bp) in Reference Genome:

GTTTACCTCTAATCGAGTAATGTATATTCCTCGCAAAAAATAAAGAAGAACCATTGCGTCAAATACCAATGGATGGTTCAAGTATGGCCGAGTTTAGTTC[T/C]
AAACTTTTTCTTCAAACTTTTAACTTTTTTATCACATTAAAACTTTTCTACACACATAAACTTTCAACTTTTTCATCACATCGTTCCAATTTCAACCAAA

Reverse complement sequence

TTTGGTTGAAATTGGAACGATGTGATGAAAAAGTTGAAAGTTTATGTGTGTAGAAAAGTTTTAATGTGATAAAAAAGTTAAAAGTTTGAAGAAAAAGTTT[A/G]
GAACTAAACTCGGCCATACTTGAACCATCCATTGGTATTTGACGCAATGGTTCTTCTTTATTTTTTGCGAGGAATATACATTACTCGATTAGAGGTAAAC

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	73.60%	19.70%	1.71%	5.01%	NA
All Indica	2759	83.00%	6.90%	2.25%	7.87%	NA
All Japonica	1512	53.50%	45.00%	0.60%	0.93%	NA
Aus	269	92.90%	5.60%	1.49%	0.00%	NA
Indica I	595	82.20%	11.80%	1.51%	4.54%	NA
Indica II	465	70.10%	8.20%	1.51%	20.22%	NA
Indica III	913	89.80%	2.80%	3.50%	3.83%	NA
Indica Intermediate	786	83.50%	7.00%	1.78%	7.76%	NA
Temperate Japonica	767	34.60%	64.70%	0.00%	0.78%	NA
Tropical Japonica	504	73.20%	24.00%	1.59%	1.19%	NA
Japonica Intermediate	241	72.60%	26.10%	0.41%	0.83%	NA
VI/Aromatic	96	66.70%	32.30%	1.04%	0.00%	NA
Intermediate	90	68.90%	18.90%	5.56%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1117421514	T -> DEL	N	N	silent_mutation	Average:65.693; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N
vg1117421514	T -> C	LOC_Os11g29970.1	upstream_gene_variant ; 4033.0bp to feature; MODIFIER	silent_mutation	Average:65.693; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N
vg1117421514	T -> C	LOC_Os11g29980.1	downstream_gene_variant ; 4031.0bp to feature; MODIFIER	silent_mutation	Average:65.693; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N
vg1117421514	T -> C	LOC_Os11g29970-LOC_Os11g29980	intergenic_region ; MODIFIER	silent_mutation	Average:65.693; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1117421514	NA	2.00E-13	Plant_height	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
vg1117421514	NA	2.20E-06	mr1183	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
vg1117421514	NA	3.47E-06	mr1503	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
vg1117421514	3.01E-06	NA	mr1973	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
vg1117421514	NA	2.73E-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
vg1117421514	NA	8.05E-08	mr1805_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