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Detailed information for vg0432714610:

Variant ID: vg0432714610 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 32714610
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAACGCCTCCCTTCCCCACCTCATGTGGAAAACAACATGCAACACTTAATGGCAGTTCAGACACAAATCTTGCAAGGAATAGCCGCAGCCGTAGCCGGTT[A/T]
TCAGCATAATGCTCATGGAAATGGCCACCCTCACATGGGCAACAATAGATCCAAGCTGACGGATTTTCTGAGGTCACGTCCGCCAGAGTTCTCTCAGACC

Reverse complement sequence

GGTCTGAGAGAACTCTGGCGGACGTGACCTCAGAAAATCCGTCAGCTTGGATCTATTGTTGCCCATGTGAGGGTGGCCATTTCCATGAGCATTATGCTGA[T/A]
AACCGGCTACGGCTGCGGCTATTCCTTGCAAGATTTGTGTCTGAACTGCCATTAAGTGTTGCATGTTGTTTTCCACATGAGGTGGGGAAGGGAGGCGTTC

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 23.50% 0.30% 11.45% 64.75% NA
All Indica  2759 5.00% 0.40% 16.20% 78.40% NA
All Japonica  1512 55.00% 0.00% 1.39% 43.65% NA
Aus  269 33.80% 0.40% 17.84% 47.96% NA
Indica I  595 5.00% 0.00% 4.37% 90.59% NA
Indica II  465 5.20% 1.50% 21.94% 71.40% NA
Indica III  913 3.60% 0.10% 22.34% 73.93% NA
Indica Intermediate  786 6.50% 0.40% 14.63% 78.50% NA
Temperate Japonica  767 78.50% 0.00% 0.26% 21.25% NA
Tropical Japonica  504 33.10% 0.00% 1.79% 65.08% NA
Japonica Intermediate  241 25.70% 0.00% 4.15% 70.12% NA
VI/Aromatic  96 24.00% 0.00% 15.62% 60.42% NA
Intermediate  90 32.20% 1.10% 11.11% 55.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0432714610 A -> DEL LOC_Os04g55020.1 N frameshift_variant Average:8.922; most accessible tissue: Callus, score: 18.216 N N N N
vg0432714610 A -> T LOC_Os04g55020.1 missense_variant ; p.Tyr399Phe; MODERATE nonsynonymous_codon ; Y399F Average:8.922; most accessible tissue: Callus, score: 18.216 benign -0.23 TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0432714610 1.45E-07 9.76E-08 Awn_length Ind_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0432714610 NA 1.80E-06 mr1364 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
vg0432714610 NA 1.57E-06 mr1443 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
vg0432714610 NA 5.97E-07 mr1063_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
vg0432714610 NA 8.86E-06 mr1072_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
vg0432714610 NA 2.25E-06 mr1097_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
vg0432714610 NA 8.52E-07 mr1194_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
vg0432714610 NA 9.54E-06 mr1236_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
vg0432714610 NA 5.55E-06 mr1252_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
vg0432714610 NA 2.24E-07 mr1295_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
vg0432714610 1.95E-08 1.35E-10 mr1498_2 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
vg0432714610 NA 8.25E-06 mr1739_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
vg0432714610 NA 2.37E-06 mr1741_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
vg0432714610 2.58E-06 NA mr1789_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
vg0432714610 2.27E-06 1.99E-09 mr1800_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
vg0432714610 NA 4.48E-06 mr1887_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
vg0432714610 4.75E-06 4.75E-06 mr1925_2 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