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Detailed information for vg0219377038:

Variant ID: vg0219377038 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 19377038
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTGTTGCTTCTGAGGTTCTACATTCGTAGCCTGCTTATAGCTTCTTGGTTTATTTCTTTGGTTTGTTTTGCAGCTCACATTTCTTCGAAGGGATTTCACG[C/T]
TGTCGGCTAGGCTGCGCTACAAGGTAAAGACATTGTTTCTTTCTGTGCCTTACCAGTGCATTGCTTCCTTGCATTTGTGTTTGTCTCCGATGGTTTCTTG

Reverse complement sequence

CAAGAAACCATCGGAGACAAACACAAATGCAAGGAAGCAATGCACTGGTAAGGCACAGAAAGAAACAATGTCTTTACCTTGTAGCGCAGCCTAGCCGACA[G/A]
CGTGAAATCCCTTCGAAGAAATGTGAGCTGCAAAACAAACCAAAGAAATAAACCAAGAAGCTATAAGCAGGCTACGAATGTAGAACCTCAGAAGCAACAA

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 97.40% 1.80% 0.89% 0.00% NA
All Indica  2759 99.60% 0.00% 0.40% 0.00% NA
All Japonica  1512 92.80% 5.40% 1.85% 0.00% NA
Aus  269 99.30% 0.00% 0.74% 0.00% NA
Indica I  595 99.30% 0.00% 0.67% 0.00% NA
Indica II  465 99.60% 0.00% 0.43% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.10% 0.64% 0.00% NA
Temperate Japonica  767 89.20% 7.40% 3.39% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 89.60% 10.00% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 1.10% 1.11% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0219377038 C -> T LOC_Os02g32660-LOC_Os02g32680 intergenic_region ; MODIFIER silent_mutation Average:40.076; most accessible tissue: Callus, score: 94.999 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0219377038 NA 7.14E-06 mr1071 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
vg0219377038 NA 3.79E-06 mr1140 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
vg0219377038 1.54E-06 1.54E-06 mr1160 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
vg0219377038 NA 4.27E-06 mr1203 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
vg0219377038 NA 4.53E-06 mr1395 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
vg0219377038 7.47E-07 7.47E-07 mr1609 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
vg0219377038 NA 9.41E-08 mr1613 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
vg0219377038 NA 9.29E-06 mr1618 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
vg0219377038 NA 6.63E-06 mr1619 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
vg0219377038 1.51E-06 1.51E-06 mr1191_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