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Detailed information for vg0131483290:

Variant ID: vg0131483290 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 31483290
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTTATTCAAAAATTTTATGCGAATGTATAAGATATAAATCACACTTAAAGTACTATGAGTGATAAAACAACTCATAGCAAAATAAATTATAATTACGTAA[A/T]
TTTTTTGGATAAGACATGGTCAAACATGTGAAAAAAAGTCAATGGCGTCATCTATTAAAAAATGGAGGGAGTACTAACTAAAGAAGCATGTATAGCAACG

Reverse complement sequence

CGTTGCTATACATGCTTCTTTAGTTAGTACTCCCTCCATTTTTTAATAGATGACGCCATTGACTTTTTTTCACATGTTTGACCATGTCTTATCCAAAAAA[T/A]
TTACGTAATTATAATTTATTTTGCTATGAGTTGTTTTATCACTCATAGTACTTTAAGTGTGATTTATATCTTATACATTCGCATAAAATTTTTGAATAAG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.70% 4.20% 0.04% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 87.10% 12.80% 0.13% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 99.60% 0.30% 0.13% 0.00% NA
Tropical Japonica  504 63.70% 36.10% 0.20% 0.00% NA
Japonica Intermediate  241 96.30% 3.70% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 0.00% 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
vg0131483290 A -> T LOC_Os01g54730.1 downstream_gene_variant ; 3824.0bp to feature; MODIFIER silent_mutation Average:42.328; most accessible tissue: Zhenshan97 root, score: 78.34 N N N N
vg0131483290 A -> T LOC_Os01g54730.2 downstream_gene_variant ; 3824.0bp to feature; MODIFIER silent_mutation Average:42.328; most accessible tissue: Zhenshan97 root, score: 78.34 N N N N
vg0131483290 A -> T LOC_Os01g54714.1 intron_variant ; MODIFIER silent_mutation Average:42.328; most accessible tissue: Zhenshan97 root, score: 78.34 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0131483290 NA 7.70E-06 mr1239_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
vg0131483290 NA 9.31E-07 mr1250_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
vg0131483290 NA 7.20E-06 mr1405_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
vg0131483290 4.14E-06 2.25E-07 mr1736_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
vg0131483290 NA 2.25E-06 mr1870_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