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Detailed information for vg0225193157:

Variant ID: vg0225193157 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 25193157
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGCTTGCTGCTCTTCGGAATTCCGGGCAAGATCATGGCTTACGGCATGGAGGACCAGGCGATTTCGGTGGTCTGGGAAGATGCCGCGCCGCCACAACCTC[G/A]
GTTCTTCCGCTACGCTTGGTTCGACTTTTATCCGTACACCGCAGGCTTGTTTGCCGTGTAACAAGTTCAGTTTTGTTTGAGAAGAAAAGGGCCGTTTTTG

Reverse complement sequence

CAAAAACGGCCCTTTTCTTCTCAAACAAAACTGAACTTGTTACACGGCAAACAAGCCTGCGGTGTACGGATAAAAGTCGAACCAAGCGTAGCGGAAGAAC[C/T]
GAGGTTGTGGCGGCGCGGCATCTTCCCAGACCACCGAAATCGCCTGGTCCTCCATGCCGTAAGCCATGATCTTGCCCGGAATTCCGAAGAGCAGCAAGCT

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 93.30% 5.90% 0.85% 0.00% NA
All Indica  2759 98.60% 1.40% 0.00% 0.00% NA
All Japonica  1512 82.20% 15.20% 2.58% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 99.00% 1.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 96.20% 3.80% 0.00% 0.00% NA
Temperate Japonica  767 81.00% 14.00% 5.08% 0.00% NA
Tropical Japonica  504 92.50% 7.50% 0.00% 0.00% NA
Japonica Intermediate  241 64.70% 35.30% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 92.20% 6.70% 1.11% 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
vg0225193157 G -> A LOC_Os02g41910.1 missense_variant ; p.Arg384Gln; MODERATE nonsynonymous_codon ; R384Q Average:89.769; most accessible tissue: Minghui63 panicle, score: 97.248 unknown unknown TOLERATED 0.38

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)
vg0225193157 G A -0.06 -0.05 -0.05 0.01 0.0 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0225193157 4.87E-06 4.99E-12 mr1691 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
vg0225193157 NA 1.02E-06 mr1691 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
vg0225193157 NA 4.58E-12 mr1693 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
vg0225193157 NA 1.30E-07 mr1693 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
vg0225193157 NA 8.00E-09 mr1691_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