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Detailed information for vg0432718715:

Variant ID: vg0432718715 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 32718715
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCAAGTTAGCACCCCGCTACATCGGCCCCTACCTCATAACCGCCAGACGTGGCGAAGTGGCTTATCAGCTTGAGTTACCTGAAGGTCTCGCAGATGTGCA[T/C]
AACGTGTTTCACGTATCCCAGTTAAAGAAATGTCTTCGAGTTCCAGAAGAGCAAGTTCCCCTGGGTAATATCGTGCTGGAAAAGAATCTGACCTACAAGG

Reverse complement sequence

CCTTGTAGGTCAGATTCTTTTCCAGCACGATATTACCCAGGGGAACTTGCTCTTCTGGAACTCGAAGACATTTCTTTAACTGGGATACGTGAAACACGTT[A/G]
TGCACATCTGCGAGACCTTCAGGTAACTCAAGCTGATAAGCCACTTCGCCACGTCTGGCGGTTATGAGGTAGGGGCCGATGTAGCGGGGTGCTAACTTGC

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 21.50% 2.40% 5.56% 70.59% NA
All Indica  2759 3.90% 3.20% 5.55% 87.35% NA
All Japonica  1512 53.10% 0.80% 5.16% 40.94% NA
Aus  269 25.30% 1.90% 6.69% 66.17% NA
Indica I  595 4.00% 3.00% 4.20% 88.74% NA
Indica II  465 6.90% 2.20% 5.16% 85.81% NA
Indica III  913 1.60% 4.30% 6.79% 87.29% NA
Indica Intermediate  786 4.60% 2.80% 5.34% 87.28% NA
Temperate Japonica  767 76.70% 0.30% 6.26% 16.82% NA
Tropical Japonica  504 31.20% 1.60% 4.96% 62.30% NA
Japonica Intermediate  241 24.10% 0.80% 2.07% 73.03% NA
VI/Aromatic  96 10.40% 4.20% 9.38% 76.04% NA
Intermediate  90 30.00% 2.20% 5.56% 62.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0432718715 T -> C LOC_Os04g55020.1 synonymous_variant ; p.His1680His; LOW synonymous_codon Average:8.073; most accessible tissue: Zhenshan97 panicle, score: 16.188 N N N N
vg0432718715 T -> DEL LOC_Os04g55020.1 N frameshift_variant Average:8.073; most accessible tissue: Zhenshan97 panicle, score: 16.188 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0432718715 3.87E-06 1.94E-07 mr1022 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
vg0432718715 NA 7.43E-07 mr1040 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
vg0432718715 8.74E-07 NA mr1079 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
vg0432718715 NA 5.39E-06 mr1114 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
vg0432718715 3.90E-06 1.94E-07 mr1116 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
vg0432718715 NA 3.91E-06 mr1117 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
vg0432718715 NA 7.17E-06 mr1240 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
vg0432718715 4.79E-06 NA mr1489 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
vg0432718715 6.29E-06 NA mr1491 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
vg0432718715 4.79E-06 NA mr1491 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
vg0432718715 NA 3.83E-06 mr1745 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
vg0432718715 NA 5.15E-06 mr1917 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
vg0432718715 NA 7.63E-08 mr1794_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