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Detailed information for vg1214642525:

Variant ID: vg1214642525 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 14642525
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.04, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:


ACCCGAACCCGACGACCCTGGCTGGTCTGACCGCTCCTCATGGGCCGGTCTGACCGGAGGTGTGCCGGCGGTCTGACCGGCCTGGCGCCCGGTCTGACCG[G/A]
CCGAGCTGACCTCGTCGTCGTCGTTGTCTCCGCTCTCGTCTTCAAAAATACAACCATCCTCCCCCTGAACCTATGACAGTGTACCTGCAATATCGGGTCT

Reverse complement sequence

AGACCCGATATTGCAGGTACACTGTCATAGGTTCAGGGGGAGGATGGTTGTATTTTTGAAGACGAGAGCGGAGACAACGACGACGACGAGGTCAGCTCGG[C/T]
CGGTCAGACCGGGCGCCAGGCCGGTCAGACCGCCGGCACACCTCCGGTCAGACCGGCCCATGAGGAGCGGTCAGACCAGCCAGGGTCGTCGGGTTCGGGT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 70.20% 15.40% 2.03% 12.27% NA
All Indica  2759 60.10% 16.40% 2.86% 20.59% NA
All Japonica  1512 99.20% 0.40% 0.13% 0.26% NA
Aus  269 26.40% 69.50% 4.09% 0.00% NA
Indica I  595 62.70% 22.20% 0.50% 14.62% NA
Indica II  465 69.50% 3.40% 3.23% 23.87% NA
Indica III  913 53.10% 16.80% 4.49% 25.63% NA
Indica Intermediate  786 60.80% 19.30% 2.54% 17.30% NA
Temperate Japonica  767 99.50% 0.10% 0.00% 0.39% NA
Tropical Japonica  504 99.60% 0.20% 0.20% 0.00% NA
Japonica Intermediate  241 97.50% 1.70% 0.41% 0.41% NA
VI/Aromatic  96 21.90% 68.80% 2.08% 7.29% NA
Intermediate  90 76.70% 20.00% 2.22% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1214642525 G -> DEL LOC_Os12g25380.1 N frameshift_variant Average:20.721; most accessible tissue: Callus, score: 36.725 N N N N
vg1214642525 G -> A LOC_Os12g25380.1 missense_variant ; p.Ala549Val; MODERATE nonsynonymous_codon ; A549V Average:20.721; most accessible tissue: Callus, score: 36.725 unknown unknown TOLERATED 0.63

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1214642525 NA 2.68E-06 mr1346 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
vg1214642525 7.31E-07 NA mr1540 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
vg1214642525 1.10E-07 1.10E-07 mr1540 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
vg1214642525 NA 4.55E-06 mr1577 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
vg1214642525 NA 1.39E-06 mr1630 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
vg1214642525 3.58E-06 8.58E-07 mr1732 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
vg1214642525 9.12E-06 1.23E-07 mr1792 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
vg1214642525 NA 1.73E-08 mr1803 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
vg1214642525 NA 2.65E-06 mr1808 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
vg1214642525 NA 9.41E-06 mr1456_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
vg1214642525 NA 1.66E-06 mr1792_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