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Detailed information for vg0221025908:

Variant ID: vg0221025908 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 21025908
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGTTTAATATTTCAAATATGTGTCAGTATATACGATGTAACACGCCAAAATTTTACACCTATGAATCTAAACACCCCCTTAGTGTGCGTGAAGATTCTGA[C/T]
GCCAAAGTTGTTCGGCGACCCCATCAATTGTGGTACTTAATATTGTGGTTAATATTGTGGTTTATACGAAGTTCTCGGTTTCAAAGCAGTAAGAAAATTT

Reverse complement sequence

AAATTTTCTTACTGCTTTGAAACCGAGAACTTCGTATAAACCACAATATTAACCACAATATTAAGTACCACAATTGATGGGGTCGCCGAACAACTTTGGC[G/A]
TCAGAATCTTCACGCACACTAAGGGGGTGTTTAGATTCATAGGTGTAAAATTTTGGCGTGTTACATCGTATATACTGACACATATTTGAAATATTAAACG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 57.50% 0.50% 1.35% 40.58% NA
All Indica  2759 39.30% 0.70% 1.34% 58.68% NA
All Japonica  1512 94.10% 0.10% 0.13% 5.69% NA
Aus  269 21.90% 1.50% 8.55% 68.03% NA
Indica I  595 21.80% 0.80% 0.34% 76.97% NA
Indica II  465 36.10% 0.60% 1.08% 62.15% NA
Indica III  913 57.80% 0.40% 1.86% 39.87% NA
Indica Intermediate  786 32.70% 1.00% 1.65% 64.63% NA
Temperate Japonica  767 93.40% 0.10% 0.13% 6.39% NA
Tropical Japonica  504 95.00% 0.00% 0.20% 4.76% NA
Japonica Intermediate  241 94.60% 0.00% 0.00% 5.39% NA
VI/Aromatic  96 96.90% 0.00% 1.04% 2.08% NA
Intermediate  90 67.80% 0.00% 1.11% 31.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0221025908 C -> T LOC_Os02g35039.1 upstream_gene_variant ; 1821.0bp to feature; MODIFIER silent_mutation Average:36.163; most accessible tissue: Zhenshan97 flower, score: 69.437 N N N N
vg0221025908 C -> T LOC_Os02g35039.2 upstream_gene_variant ; 1821.0bp to feature; MODIFIER silent_mutation Average:36.163; most accessible tissue: Zhenshan97 flower, score: 69.437 N N N N
vg0221025908 C -> T LOC_Os02g35020-LOC_Os02g35039 intergenic_region ; MODIFIER silent_mutation Average:36.163; most accessible tissue: Zhenshan97 flower, score: 69.437 N N N N
vg0221025908 C -> DEL N N silent_mutation Average:36.163; most accessible tissue: Zhenshan97 flower, score: 69.437 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0221025908 3.00E-06 NA mr1095 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
vg0221025908 3.50E-07 3.50E-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
vg0221025908 1.05E-07 1.05E-07 mr1099 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
vg0221025908 7.24E-12 5.76E-09 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
vg0221025908 5.01E-06 8.00E-06 mr1113 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
vg0221025908 4.53E-07 3.19E-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
vg0221025908 7.63E-09 1.40E-07 mr1150 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
vg0221025908 NA 9.36E-08 mr1162 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
vg0221025908 2.09E-07 7.12E-06 mr1242 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
vg0221025908 6.45E-07 1.38E-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
vg0221025908 NA 1.13E-12 mr1441 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
vg0221025908 NA 3.54E-07 mr1510 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
vg0221025908 2.24E-06 2.24E-06 mr1589 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
vg0221025908 1.23E-06 4.74E-06 mr1754 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
vg0221025908 4.84E-07 5.01E-06 mr1858 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
vg0221025908 4.85E-07 5.01E-06 mr1859 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
vg0221025908 9.46E-06 9.46E-06 mr1880 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
vg0221025908 2.03E-06 7.10E-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
vg0221025908 NA 6.88E-06 mr1921 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
vg0221025908 1.89E-08 3.76E-09 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
vg0221025908 2.23E-07 2.03E-06 mr1099_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
vg0221025908 6.11E-06 2.50E-06 mr1114_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
vg0221025908 NA 5.59E-06 mr1120_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
vg0221025908 8.20E-08 4.02E-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
vg0221025908 9.28E-06 3.14E-06 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
vg0221025908 4.98E-06 3.29E-06 mr1247_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
vg0221025908 NA 7.86E-06 mr1961_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