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Detailed information for vg0113687946:

Variant ID: vg0113687946 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 13687946
Reference Allele: TAlternative Allele: A
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.88, T: 0.12, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:


TTCGGCTGTGGTTATTTTCCAGGAGCTAAACAATGATTCTTTATATTTTTGGTCGAAGTGGAAGCTCCTATGTTGCTCTCAATTTTCCCACTCTTCTCCA[T/A]
TGCCCCCCGGTCAGACCGGCCACTGAGCCCGGTCAGACCGGCCACAAGCCGTCGGTCAGACCGGCCAGTAAGGTCGGTCAGACCGGCCGTAGATTGGCGG

Reverse complement sequence

CCGCCAATCTACGGCCGGTCTGACCGACCTTACTGGCCGGTCTGACCGACGGCTTGTGGCCGGTCTGACCGGGCTCAGTGGCCGGTCTGACCGGGGGGCA[A/T]
TGGAGAAGAGTGGGAAAATTGAGAGCAACATAGGAGCTTCCACTTCGACCAAAAATATAAAGAATCATTGTTTAGCTCCTGGAAAATAACCACAGCCGAA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 39.30% 38.80% 13.31% 8.61% NA
All Indica  2759 56.80% 17.30% 19.64% 6.23% NA
All Japonica  1512 3.80% 84.70% 2.58% 8.99% NA
Aus  269 49.10% 5.20% 15.24% 30.48% NA
Indica I  595 30.80% 24.40% 26.55% 18.32% NA
Indica II  465 88.00% 8.80% 2.58% 0.65% NA
Indica III  913 58.70% 15.30% 23.00% 2.96% NA
Indica Intermediate  786 55.90% 19.30% 20.61% 4.20% NA
Temperate Japonica  767 0.30% 96.90% 1.69% 1.17% NA
Tropical Japonica  504 9.90% 64.90% 3.57% 21.63% NA
Japonica Intermediate  241 2.10% 87.10% 3.32% 7.47% NA
VI/Aromatic  96 66.70% 22.90% 3.12% 7.29% NA
Intermediate  90 38.90% 45.60% 4.44% 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
vg0113687946 T -> A LOC_Os01g24294.1 intron_variant ; MODIFIER silent_mutation Average:24.389; most accessible tissue: Minghui63 young leaf, score: 43.347 N N N N
vg0113687946 T -> DEL N N silent_mutation Average:24.389; most accessible tissue: Minghui63 young leaf, score: 43.347 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0113687946 NA 1.67E-06 mr1064 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
vg0113687946 NA 5.46E-06 mr1136 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
vg0113687946 NA 4.40E-06 mr1215 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
vg0113687946 NA 2.53E-06 mr1304 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
vg0113687946 NA 6.19E-18 mr1557 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
vg0113687946 4.01E-06 4.01E-06 mr1601 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
vg0113687946 NA 7.06E-12 mr1741 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
vg0113687946 NA 5.52E-08 mr1741 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
vg0113687946 NA 2.56E-08 mr1819 Jap_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
vg0113687946 NA 4.59E-06 mr1884 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
vg0113687946 NA 2.78E-06 mr1887 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
vg0113687946 NA 1.06E-06 mr1124_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