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Detailed information for vg0623214938:

Variant ID: vg0623214938 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 23214938
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.03, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:


TTAGTGACTCACTACGTTGGTTGCTGCGCATACCCAACAAGTATTTCCCATCTGTATAGGCAGCTGCCCACTTCTCCCTTAGTCGGTACATCGATCAGGG[C/T]
GATCCATTGACCATTCCCCGTGCCTCCATTCTCCTTAAAATCAGCCCAACGTCTCTCGAACTCCTCCTCATCCATACTCTTATAAATTAATTTTCTTAGC

Reverse complement sequence

GCTAAGAAAATTAATTTATAAGAGTATGGATGAGGAGGAGTTCGAGAGACGTTGGGCTGATTTTAAGGAGAATGGAGGCACGGGGAATGGTCAATGGATC[G/A]
CCCTGATCGATGTACCGACTAAGGGAGAAGTGGGCAGCTGCCTATACAGATGGGAAATACTTGTTGGGTATGCGCAGCAACCAACGTAGTGAGTCACTAA

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 87.60% 12.30% 0.06% 0.00% NA
All Indica  2759 85.50% 14.40% 0.11% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 37.90% 62.10% 0.00% 0.00% NA
Indica I  595 97.30% 2.70% 0.00% 0.00% NA
Indica II  465 88.40% 11.60% 0.00% 0.00% NA
Indica III  913 78.10% 21.70% 0.22% 0.00% NA
Indica Intermediate  786 83.50% 16.40% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 91.70% 8.30% 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
vg0623214938 C -> T LOC_Os06g39090.1 missense_variant ; p.Ala270Thr; MODERATE nonsynonymous_codon ; A270I Average:54.53; most accessible tissue: Minghui63 young leaf, score: 80.562 possibly damaging 1.935 TOLERATED 0.06
vg0623214938 C -> T LOC_Os06g39090.1 missense_variant ; p.Ala270Thr; MODERATE nonsynonymous_codon ; A270T Average:54.53; most accessible tissue: Minghui63 young leaf, score: 80.562 possibly damaging 1.571 TOLERATED 0.67

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0623214938 NA 8.10E-06 mr1004 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
vg0623214938 2.12E-06 2.96E-06 mr1012 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