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Detailed information for vg0402179876:

Variant ID: vg0402179876 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 2179876
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCTGCTAACTTGTTCTGCGGCGGTGGAGCATTGTTGTTCCCTTGGTTGAGCTGGTTCTGCTGGTTCTGGAGTTGCTGCATCATCATGTTCATAAGCTGTG[T/C]
CTGTTGAGCCAGAACCTGGGCAAGTGTGGGATTCTCTCCATTGTTGTTGTTATTGTTATTGTTGGGGCCATTCCCGTTGCTGCGAGTGAGCACCATCTGG

Reverse complement sequence

CCAGATGGTGCTCACTCGCAGCAACGGGAATGGCCCCAACAATAACAATAACAACAACAATGGAGAGAATCCCACACTTGCCCAGGTTCTGGCTCAACAG[A/G]
CACAGCTTATGAACATGATGATGCAGCAACTCCAGAACCAGCAGAACCAGCTCAACCAAGGGAACAACAATGCTCCACCGCCGCAGAACAAGTTAGCAGA

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 48.20% 4.00% 21.58% 26.22% NA
All Indica  2759 45.00% 2.10% 21.93% 30.95% NA
All Japonica  1512 60.80% 3.50% 16.47% 19.25% NA
Aus  269 14.50% 26.80% 44.24% 14.50% NA
Indica I  595 54.10% 1.00% 10.76% 34.12% NA
Indica II  465 43.90% 1.10% 21.94% 33.12% NA
Indica III  913 41.70% 3.70% 26.94% 27.60% NA
Indica Intermediate  786 42.50% 1.80% 24.55% 31.17% NA
Temperate Japonica  767 79.00% 3.10% 4.04% 13.82% NA
Tropical Japonica  504 38.30% 1.20% 35.52% 25.00% NA
Japonica Intermediate  241 49.80% 9.50% 16.18% 24.48% NA
VI/Aromatic  96 26.00% 3.10% 31.25% 39.58% NA
Intermediate  90 58.90% 3.30% 18.89% 18.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0402179876 T -> C LOC_Os04g04550.1 missense_variant ; p.Thr33Ala; MODERATE nonsynonymous_codon ; T33A Average:7.31; most accessible tissue: Zhenshan97 young leaf, score: 14.714 unknown unknown TOLERATED 0.39
vg0402179876 T -> DEL LOC_Os04g04550.1 N frameshift_variant Average:7.31; most accessible tissue: Zhenshan97 young leaf, score: 14.714 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0402179876 6.20E-07 6.20E-07 mr1098 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
vg0402179876 7.24E-06 1.15E-08 mr1101 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
vg0402179876 NA 2.79E-06 mr1118 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
vg0402179876 NA 8.81E-06 mr1123 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
vg0402179876 NA 2.26E-07 mr1150 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
vg0402179876 NA 2.85E-06 mr1247 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
vg0402179876 NA 2.15E-07 mr1495 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
vg0402179876 NA 4.92E-06 mr1858 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
vg0402179876 NA 4.91E-06 mr1859 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
vg0402179876 9.72E-06 3.22E-08 mr1098_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
vg0402179876 NA 2.99E-06 mr1099_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
vg0402179876 NA 2.09E-06 mr1118_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
vg0402179876 NA 1.34E-06 mr1123_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
vg0402179876 NA 1.92E-08 mr1150_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
vg0402179876 NA 6.33E-07 mr1240_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
vg0402179876 NA 6.99E-06 mr1861_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