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Detailed information for vg0234516971:

Variant ID: vg0234516971 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 34516971
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.90, T: 0.09, others allele: 0.00, population size: 159. )

Flanking Sequence (100 bp) in Reference Genome:


ACCGTTCATGCTTAGGCATCGCATGAGGAGGTCTGCAATCTCTGTTGCCATTTCGTCGTTCATCTCTTTCCTCACTTGGCTGTCCATAAGCTCTCGATGA[C/T]
GACCAGCCTTCACTGCTGTGGTGAAGCGTGACACCAAGCTCATGTCTTCCTCTGGCCCGTCTAGGTACAATGCCTTCTTCCTGGTTAGAAGCTCCAGCAC

Reverse complement sequence

GTGCTGGAGCTTCTAACCAGGAAGAAGGCATTGTACCTAGACGGGCCAGAGGAAGACATGAGCTTGGTGTCACGCTTCACCACAGCAGTGAAGGCTGGTC[G/A]
TCATCGAGAGCTTATGGACAGCCAAGTGAGGAAAGAGATGAACGACGAAATGGCAACAGAGATTGCAGACCTCCTCATGCGATGCCTAAGCATGAACGGT

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 84.80% 6.70% 0.59% 7.89% NA
All Indica  2759 87.00% 3.50% 0.58% 8.92% NA
All Japonica  1512 95.80% 1.20% 0.07% 2.98% NA
Aus  269 21.60% 50.60% 2.23% 25.65% NA
Indica I  595 83.50% 0.00% 1.18% 15.29% NA
Indica II  465 94.00% 0.60% 0.43% 4.95% NA
Indica III  913 83.10% 7.30% 0.33% 9.20% NA
Indica Intermediate  786 90.10% 3.30% 0.51% 6.11% NA
Temperate Japonica  767 99.50% 0.40% 0.00% 0.13% NA
Tropical Japonica  504 90.70% 0.80% 0.20% 8.33% NA
Japonica Intermediate  241 94.60% 4.60% 0.00% 0.83% NA
VI/Aromatic  96 30.20% 60.40% 1.04% 8.33% NA
Intermediate  90 81.10% 8.90% 4.44% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0234516971 C -> T LOC_Os02g56380.1 missense_variant ; p.Arg302His; MODERATE nonsynonymous_codon ; R302H Average:49.037; most accessible tissue: Minghui63 young leaf, score: 94.332 benign 0.391 DELETERIOUS 0.04
vg0234516971 C -> DEL LOC_Os02g56380.1 N frameshift_variant Average:49.037; most accessible tissue: Minghui63 young leaf, score: 94.332 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)
vg0234516971 C T -0.02 -0.02 -0.02 -0.02 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0234516971 2.06E-06 1.16E-06 mr1201 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
vg0234516971 3.99E-07 4.49E-06 mr1219 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
vg0234516971 NA 1.89E-06 mr1219_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