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Detailed information for vg0225196029:

Variant ID: vg0225196029 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 25196029
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTTCCTCAACGACGAGATCCACGAGACGTTCAGCTACAACCCCCTCCTCCGAGGCTATTCCAGCCCCGACCTCTCGTTCATCCCGACCACCGCCGACACG[G/T]
CTAACTCCGAGACCTACGTCACCAGCTCCTGCCACGGGCTTCTCCTCTGCCGCCGCCGTCGACGCATCGACGGCGAGCTTGGCGTGTACAGAGCACGGCA

Reverse complement sequence

TGCCGTGCTCTGTACACGCCAAGCTCGCCGTCGATGCGTCGACGGCGGCGGCAGAGGAGAAGCCCGTGGCAGGAGCTGGTGACGTAGGTCTCGGAGTTAG[C/A]
CGTGTCGGCGGTGGTCGGGATGAACGAGAGGTCGGGGCTGGAATAGCCTCGGAGGAGGGGGTTGTAGCTGAACGTCTCGTGGATCTCGTCGTTGAGGAAG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.00% 6.90% 0.02% 0.00% NA
All Indica  2759 91.30% 8.70% 0.04% 0.00% NA
All Japonica  1512 98.00% 2.00% 0.00% 0.00% NA
Aus  269 82.20% 17.80% 0.00% 0.00% NA
Indica I  595 87.10% 12.80% 0.17% 0.00% NA
Indica II  465 97.80% 2.20% 0.00% 0.00% NA
Indica III  913 94.60% 5.40% 0.00% 0.00% NA
Indica Intermediate  786 86.60% 13.40% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 94.80% 5.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 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
vg0225196029 G -> T LOC_Os02g41930.1 missense_variant ; p.Ala91Ser; MODERATE nonsynonymous_codon ; A91S Average:81.077; most accessible tissue: Minghui63 panicle, score: 92.928 unknown unknown TOLERATED 0.71

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)
vg0225196029 G T 0.02 -0.01 -0.01 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0225196029 NA 3.16E-07 mr1533_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