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Detailed information for vg0219342441:

Variant ID: vg0219342441 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 19342441
Reference Allele: TAlternative Allele: G
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, T: 0.08, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


CGACCCCACCGGCGTCTTCGCCCTCGGCTTCCTCCGCGTCAACTCCACCATGCTCGACCTCGCCGTGGTCCACCTCCCGTCCTCGTTCCCGCTCTGGAGC[T/G]
CCATCCCCGACCGCCCCGCGCAGTGGTCCGCGCCCGCTTCGCTCTCCTTCGACGGCGACCTCGTCCTCACCGACCCCGCCGCCAACAAGGTCCTCTGGTC

Reverse complement sequence

GACCAGAGGACCTTGTTGGCGGCGGGGTCGGTGAGGACGAGGTCGCCGTCGAAGGAGAGCGAAGCGGGCGCGGACCACTGCGCGGGGCGGTCGGGGATGG[A/C]
GCTCCAGAGCGGGAACGAGGACGGGAGGTGGACCACGGCGAGGTCGAGCATGGTGGAGTTGACGCGGAGGAAGCCGAGGGCGAAGACGCCGGTGGGGTCG

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 56.60% 42.60% 0.49% 0.32% NA
All Indica  2759 78.00% 21.30% 0.40% 0.33% NA
All Japonica  1512 28.60% 70.60% 0.60% 0.26% NA
Aus  269 6.30% 93.70% 0.00% 0.00% NA
Indica I  595 58.00% 41.30% 0.34% 0.34% NA
Indica II  465 79.10% 20.00% 0.43% 0.43% NA
Indica III  913 93.90% 5.80% 0.22% 0.11% NA
Indica Intermediate  786 73.90% 24.90% 0.64% 0.51% NA
Temperate Japonica  767 18.50% 80.20% 1.04% 0.26% NA
Tropical Japonica  504 29.80% 69.80% 0.00% 0.40% NA
Japonica Intermediate  241 58.10% 41.50% 0.41% 0.00% NA
VI/Aromatic  96 32.30% 67.70% 0.00% 0.00% NA
Intermediate  90 48.90% 45.60% 3.33% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0219342441 T -> G LOC_Os02g32620.1 missense_variant ; p.Ser92Ala; MODERATE nonsynonymous_codon ; S92A Average:90.449; most accessible tissue: Zhenshan97 flag leaf, score: 95.494 benign -0.983 TOLERATED 1.00
vg0219342441 T -> DEL LOC_Os02g32620.1 N frameshift_variant Average:90.449; most accessible tissue: Zhenshan97 flag leaf, score: 95.494 N N N N

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)
vg0219342441 T G 0.01 0.01 0.02 0.01 0.02 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0219342441 NA 9.30E-07 mr1180_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
vg0219342441 NA 2.03E-07 mr1885_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