Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1121751063:

Variant ID: vg1121751063 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21751063
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, C: 0.00, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

AAATTCTGTACTAAGAAACTGGGAGATGGCAAATGAACTTTATTCTGGGAGGACAATTGGATTGGAGGTAGGCCTTTAAATGAGCAATTCTCAGACCTGT[A/C]
CAGTATCACTAACACAAAGCACATCACAGTGGATAAGGTTCTGCAGGGGGGTTGGGATAAAGTCACTTTCAGAAGAACTTTACATGGGATTAGGCTTGAG

Reverse complement sequence

CTCAAGCCTAATCCCATGTAAAGTTCTTCTGAAAGTGACTTTATCCCAACCCCCCTGCAGAACCTTATCCACTGTGATGTGCTTTGTGTTAGTGATACTG[T/G]
ACAGGTCTGAGAATTGCTCATTTAAAGGCCTACCTCCAATCCAATTGTCCTCCCAGAATAAAGTTCATTTGCCATCTCCCAGTTTCTTAGTACAGAATTT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	83.60%	4.60%	0.63%	11.17%	NA
All Indica	2759	79.90%	4.00%	0.94%	15.15%	NA
All Japonica	1512	96.20%	2.50%	0.07%	1.26%	NA
Aus	269	67.70%	21.60%	0.00%	10.78%	NA
Indica I	595	77.80%	4.20%	1.85%	16.13%	NA
Indica II	465	77.20%	0.60%	1.08%	21.08%	NA
Indica III	913	84.10%	4.20%	0.33%	11.39%	NA
Indica Intermediate	786	78.20%	5.60%	0.89%	15.27%	NA
Temperate Japonica	767	97.90%	1.60%	0.00%	0.52%	NA
Tropical Japonica	504	93.70%	4.20%	0.00%	2.18%	NA
Japonica Intermediate	241	95.90%	2.10%	0.41%	1.66%	NA
VI/Aromatic	96	37.50%	5.20%	3.12%	54.17%	NA
Intermediate	90	80.00%	8.90%	0.00%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121751063	A -> DEL	LOC_Os11g36870.1	N	frameshift_variant	Average:42.666; most accessible tissue: Minghui63 panicle, score: 79.811	N	N	N	N
vg1121751063	A -> C	LOC_Os11g36870.1	missense_variant ; p.Tyr938Ser; MODERATE	nonsynonymous_codon ; Y938S	Average:42.666; most accessible tissue: Minghui63 panicle, score: 79.811	unknown	unknown	DELETERIOUS	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121751063	NA	2.43E-06	mr1070	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
vg1121751063	1.18E-06	1.18E-06	mr1151	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
vg1121751063	1.20E-06	1.20E-06	mr1249	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
vg1121751063	NA	6.81E-06	mr1280	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