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Detailed information for vg0702311463:

Variant ID: vg0702311463 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 2311463
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.79, A: 0.21, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:


CTTTGCAATCCGCGAGTTCTTTCGTCCGTGTTCAAACTTCAAAGTAGAGAGATCAATGGCGGCAGAGAAGAAGGAGGTTGCCGACGCCGCCGCCGGCAGC[G/A]
GCAGCGACACAATCCTCCTAATCAGCTCCGACGGCGAGCACTTCAACGTGCCGTCGGCGGCGGCGAGCCTGTCACAGCTCGTCTCCAACATGATCGAGGA

Reverse complement sequence

TCCTCGATCATGTTGGAGACGAGCTGTGACAGGCTCGCCGCCGCCGACGGCACGTTGAAGTGCTCGCCGTCGGAGCTGATTAGGAGGATTGTGTCGCTGC[C/T]
GCTGCCGGCGGCGGCGTCGGCAACCTCCTTCTTCTCTGCCGCCATTGATCTCTCTACTTTGAAGTTTGAACACGGACGAAAGAACTCGCGGATTGCAAAG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 58.00% 41.90% 0.13% 0.00% NA
All Indica  2759 87.00% 12.80% 0.18% 0.00% NA
All Japonica  1512 0.90% 99.10% 0.00% 0.00% NA
Aus  269 97.40% 2.60% 0.00% 0.00% NA
Indica I  595 95.80% 4.20% 0.00% 0.00% NA
Indica II  465 51.00% 48.40% 0.65% 0.00% NA
Indica III  913 98.90% 1.10% 0.00% 0.00% NA
Indica Intermediate  786 87.90% 11.80% 0.25% 0.00% NA
Temperate Japonica  767 0.00% 100.00% 0.00% 0.00% NA
Tropical Japonica  504 2.80% 97.20% 0.00% 0.00% NA
Japonica Intermediate  241 0.00% 100.00% 0.00% 0.00% NA
VI/Aromatic  96 27.10% 72.90% 0.00% 0.00% NA
Intermediate  90 42.20% 56.70% 1.11% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0702311463 G -> A LOC_Os07g05180.1 missense_variant ; p.Gly16Ser; MODERATE nonsynonymous_codon ; G16S Average:62.697; most accessible tissue: Zhenshan97 panicle, score: 83.41 unknown unknown TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0702311463 NA 1.94E-07 mr1004 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
vg0702311463 NA 6.86E-13 mr1005 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
vg0702311463 NA 5.04E-06 mr1005 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
vg0702311463 NA 7.82E-15 mr1146 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
vg0702311463 NA 3.30E-22 mr1150 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
vg0702311463 NA 1.14E-13 mr1874 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
vg0702311463 NA 2.97E-15 mr1950 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
vg0702311463 NA 1.02E-09 mr1158_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
vg0702311463 NA 8.49E-19 mr1195_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
vg0702311463 NA 2.31E-11 mr1383_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
vg0702311463 NA 1.55E-07 mr1654_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
vg0702311463 NA 2.51E-19 mr1874_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