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Detailed information for vg1205331763:

Variant ID: vg1205331763 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 5331763
Reference Allele: TAlternative Allele: C,A
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:


ATTTTAGCTTTGATTTTTGATCTTCGATGGCTTTGGGCAGATCGGCAAGCTTCTGTTCTTCAAGGGCAATCTGTGCACTGCATTGCTCCAATTCAGCTAG[T/C,A]
AGTTTTATCTGCCGAGTGTTCAGCCGATCGATGTTGGCTTGAGTAGAACTTGGACCAGCTTCCAACTCATCAAGTTTTGCTTTTTCCTCATTGATAGAGG

Reverse complement sequence

CCTCTATCAATGAGGAAAAAGCAAAACTTGATGAGTTGGAAGCTGGTCCAAGTTCTACTCAAGCCAACATCGATCGGCTGAACACTCGGCAGATAAAACT[A/G,T]
CTAGCTGAATTGGAGCAATGCAGTGCACAGATTGCCCTTGAAGAACAGAAGCTTGCCGATCTGCCCAAAGCCATCGAAGATCAAAAATCAAAGCTAAAAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 23.70% 11.20% 6.96% 55.78% A: 2.45%
All Indica  2759 4.10% 0.70% 6.89% 84.23% A: 4.13%
All Japonica  1512 54.30% 32.50% 7.94% 5.29% NA
Aus  269 19.70% 0.40% 2.60% 76.58% A: 0.74%
Indica I  595 3.70% 0.30% 11.60% 81.68% A: 2.69%
Indica II  465 3.40% 1.50% 9.89% 81.94% A: 3.23%
Indica III  913 2.30% 0.30% 2.85% 87.84% A: 6.68%
Indica Intermediate  786 6.70% 0.90% 6.23% 83.33% A: 2.80%
Temperate Japonica  767 32.10% 54.00% 10.30% 3.65% NA
Tropical Japonica  504 87.70% 4.20% 3.17% 4.96% NA
Japonica Intermediate  241 55.20% 23.20% 10.37% 11.20% NA
VI/Aromatic  96 93.80% 0.00% 3.12% 3.12% NA
Intermediate  90 46.70% 17.80% 10.00% 25.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1205331763 T -> C LOC_Os12g10070.1 synonymous_variant ; p.Leu595Leu; LOW synonymous_codon Average:17.391; most accessible tissue: Callus, score: 72.532 N N N N
vg1205331763 T -> DEL LOC_Os12g10070.1 N frameshift_variant Average:17.391; most accessible tissue: Callus, score: 72.532 N N N N
vg1205331763 T -> A LOC_Os12g10070.1 synonymous_variant ; p.Leu595Leu; LOW synonymous_codon Average:17.391; most accessible tissue: Callus, score: 72.532 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1205331763 NA 3.50E-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
vg1205331763 2.58E-09 NA mr1354 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
vg1205331763 3.72E-06 NA mr1354 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
vg1205331763 NA 1.05E-12 mr1441 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
vg1205331763 NA 4.91E-06 mr1441 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
vg1205331763 NA 2.91E-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
vg1205331763 NA 1.37E-10 mr1712 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
vg1205331763 NA 2.01E-06 mr1977 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
vg1205331763 NA 9.71E-06 mr1159_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
vg1205331763 NA 7.29E-06 mr1648_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
vg1205331763 NA 9.05E-06 mr1655_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
vg1205331763 NA 1.22E-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