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Detailed information for vg1215729643:

Variant ID: vg1215729643 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 15729643
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.76, T: 0.24, others allele: 0.00, population size: 58. )

Flanking Sequence (100 bp) in Reference Genome:


TTTGCAGTGTGAGATGGCATAGAGTAGCCTGAGACAATAATGCTTTTTTTGGTAAATACTAAGGAGCTTGATTTGCTAGTTGGTGTCTCATCTGTTGCAG[T/C]
AGCAGGAGTGTATTTTGTTGGTGTTGAAGTGCCCTGTGTTGGTATGATGGCTAATTGCGATTCGGTGCTTGTTTCACTTGGTGTTGGTGCTGTCTGGAGA

Reverse complement sequence

TCTCCAGACAGCACCAACACCAAGTGAAACAAGCACCGAATCGCAATTAGCCATCATACCAACACAGGGCACTTCAACACCAACAAAATACACTCCTGCT[A/G]
CTGCAACAGATGAGACACCAACTAGCAAATCAAGCTCCTTAGTATTTACCAAAAAAAGCATTATTGTCTCAGGCTACTCTATGCCATCTCACACTGCAAA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 28.80% 8.60% 1.04% 61.60% NA
All Indica  2759 12.50% 10.70% 0.25% 76.55% NA
All Japonica  1512 61.50% 0.90% 2.38% 35.25% NA
Aus  269 14.10% 2.20% 1.12% 82.53% NA
Indica I  595 16.00% 7.90% 0.34% 75.80% NA
Indica II  465 22.60% 9.00% 0.00% 68.39% NA
Indica III  913 1.90% 13.00% 0.00% 85.10% NA
Indica Intermediate  786 16.20% 11.20% 0.64% 72.01% NA
Temperate Japonica  767 92.80% 0.30% 0.00% 6.91% NA
Tropical Japonica  504 12.90% 0.80% 6.15% 80.16% NA
Japonica Intermediate  241 63.50% 2.90% 2.07% 31.54% NA
VI/Aromatic  96 15.60% 81.20% 2.08% 1.04% NA
Intermediate  90 35.60% 15.60% 1.11% 47.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1215729643 T -> C LOC_Os12g26850.1 missense_variant ; p.Thr1076Ala; MODERATE nonsynonymous_codon ; T1076A Average:7.252; most accessible tissue: Callus, score: 32.134 unknown unknown TOLERATED 0.68
vg1215729643 T -> DEL LOC_Os12g26850.1 N frameshift_variant Average:7.252; most accessible tissue: Callus, score: 32.134 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1215729643 NA 8.62E-06 mr1083 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
vg1215729643 NA 4.69E-06 mr1082_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
vg1215729643 NA 2.02E-07 mr1181_2 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
vg1215729643 NA 7.04E-06 mr1272_2 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
vg1215729643 NA 2.20E-08 mr1408_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
vg1215729643 1.08E-06 2.53E-07 mr1574_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