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Detailed information for vg0700157168:

Variant ID: vg0700157168 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 157168
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:


TATAGCTTAACAAAGTACTACTCAACATATAAATACCTTGTTACTGACTAGAGTGTCTGACTTGGAAGCTCTTGCCGTGCTAGGCTCTTGAGGGTGGCAC[A/G]
TCTTTATGTTCTTCACACTGCACATGCATGCCGGCCCACCCCATCGATCGATTTTTCACATATATATGCACGCCAAGTAGTAATATAATTTATTTCAACA

Reverse complement sequence

TGTTGAAATAAATTATATTACTACTTGGCGTGCATATATATGTGAAAAATCGATCGATGGGGTGGGCCGGCATGCATGTGCAGTGTGAAGAACATAAAGA[T/C]
GTGCCACCCTCAAGAGCCTAGCACGGCAAGAGCTTCCAAGTCAGACACTCTAGTCAGTAACAAGGTATTTATATGTTGAGTAGTACTTTGTTAAGCTATA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.40% 2.60% 0.02% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 92.20% 7.70% 0.07% 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 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 77.40% 22.40% 0.20% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0700157168 A -> G LOC_Os07g01260.1 missense_variant ; p.Met238Thr; MODERATE nonsynonymous_codon ; M238T Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 benign 0.942 DELETERIOUS 0.00
vg0700157168 A -> G LOC_Os07g01260.2 missense_variant ; p.Met238Thr; MODERATE nonsynonymous_codon ; M238T Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 benign 0.874 DELETERIOUS 0.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0700157168 8.91E-07 8.90E-07 mr1266 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
vg0700157168 NA 3.79E-06 mr1352 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