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Detailed information for vg0806140348:

Variant ID: vg0806140348 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 6140348
Reference Allele: GAlternative Allele: A,T
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


TTGGCTCAAGTTCGATCAATTTCACTGTTTGAAAAGAGTACAAGTGGTCTCCCATTATTGTTGCGGTTTAAATATCTCCGAGTGCTGCATATCATGTTGG[G/A,T]
TCACGGCTGCGAGCGAGCTGACCTCACTGCCGTTAGCAAATTACTTCAACTAAGGTGTTTGATATTTCTTGACTATGGTTGTAAGGTAGAGCTCCCTAGT

Reverse complement sequence

ACTAGGGAGCTCTACCTTACAACCATAGTCAAGAAATATCAAACACCTTAGTTGAAGTAATTTGCTAACGGCAGTGAGGTCAGCTCGCTCGCAGCCGTGA[C/T,A]
CCAACATGATATGCAGCACTCGGAGATATTTAAACCGCAACAATAATGGGAGACCACTTGTACTCTTTTCAAACAGTGAAATTGATCGAACTTGAGCCAA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.30% 8.70% 0.00% 0.00% T: 0.08%
All Indica  2759 89.60% 10.30% 0.00% 0.00% T: 0.14%
All Japonica  1512 96.90% 3.10% 0.00% 0.00% NA
Aus  269 95.20% 4.80% 0.00% 0.00% NA
Indica I  595 99.20% 0.80% 0.00% 0.00% NA
Indica II  465 97.80% 2.20% 0.00% 0.00% NA
Indica III  913 78.20% 21.40% 0.00% 0.00% T: 0.44%
Indica Intermediate  786 90.60% 9.40% 0.00% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 94.80% 5.20% 0.00% 0.00% NA
Japonica Intermediate  241 92.50% 7.50% 0.00% 0.00% NA
VI/Aromatic  96 40.60% 59.40% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 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
vg0806140348 G -> T LOC_Os08g10440.1 missense_variant ; p.Gly596Val; MODERATE nonsynonymous_codon ; G596V Average:88.754; most accessible tissue: Minghui63 flag leaf, score: 99.239 probably damaging 2.427 TOLERATED 0.61
vg0806140348 G -> A LOC_Os08g10440.1 missense_variant ; p.Gly596Asp; MODERATE nonsynonymous_codon ; G596D Average:88.754; most accessible tissue: Minghui63 flag leaf, score: 99.239 probably damaging 2.142 TOLERATED 0.58

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

Var ID Ref Alt Root (RT) Young Leaf (YL) Flag Leaf (FL) Young Panicle (YP) Lemma & Palea (LP) Stamen & Pistil (SP)
vg0806140348 G A -0.17 -0.04 -0.03 -0.04 -0.04 -0.03
vg0806140348 G T -0.16 -0.03 -0.03 -0.03 -0.03 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0806140348 4.95E-07 NA mr1842 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
vg0806140348 NA 9.75E-06 mr1561_2 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
vg0806140348 NA 2.08E-06 mr1561_2 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