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Detailed information for vg0412476197:

Variant ID: vg0412476197 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 12476197
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATGAAGTTGGCAAAGTCATAGATCAGGGGTGGTCTGACCGGCATTGCACGGCCGGTCTGACTGGTGGTACCCGCGGTCTAACCGGCTCTGCATGGCCGGT[C/T]
TGACCGGGCAGACAGGGTGGTCTGACCGGCATTGCGTGTCCGGTCTGACCGATCCCAGACAGGAGGCTGGGGGGCACGTTACAATTGATTAAAAGGCCGA

Reverse complement sequence

TCGGCCTTTTAATCAATTGTAACGTGCCCCCCAGCCTCCTGTCTGGGATCGGTCAGACCGGACACGCAATGCCGGTCAGACCACCCTGTCTGCCCGGTCA[G/A]
ACCGGCCATGCAGAGCCGGTTAGACCGCGGGTACCACCAGTCAGACCGGCCGTGCAATGCCGGTCAGACCACCCCTGATCTATGACTTTGCCAACTTCAT

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 99.50% 0.00% 0.23% 0.23% NA
All Indica  2759 99.70% 0.00% 0.14% 0.11% NA
All Japonica  1512 99.90% 0.00% 0.07% 0.00% NA
Aus  269 95.50% 0.00% 1.86% 2.60% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.80% 0.00% 0.11% 0.11% NA
Indica Intermediate  786 99.50% 0.00% 0.25% 0.25% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 0.00% 1.11% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0412476197 C -> T LOC_Os04g22020.1 downstream_gene_variant ; 1923.0bp to feature; MODIFIER N Average:14.022; most accessible tissue: Callus, score: 29.748 N N N N
vg0412476197 C -> T LOC_Os04g22030.1 intron_variant ; MODIFIER N Average:14.022; most accessible tissue: Callus, score: 29.748 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0412476197 NA 2.93E-07 mr1149_2 Ind_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