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Detailed information for vg0225196895:

Variant ID: vg0225196895 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 25196895
Reference Allele: CAlternative Allele: A
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.58, A: 0.42, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


TGTTCTTCAGCGTGCCCGGGAAGATCGCGTGCTACGACGCCGAGAGCCGGGCGGTCTCGGTGGTCTGGCAGGACACGGCGACGACGTCGTCGCCGAAACA[C/A]
TTACTGTCTTACACGTGGTTCAACTTTTATGCCTACACTCCGAGCTTTCTTCGTTTATAGGATACCAATTACCAAGCGTCCGTTTTACGAGTCGAAATTA

Reverse complement sequence

TAATTTCGACTCGTAAAACGGACGCTTGGTAATTGGTATCCTATAAACGAAGAAAGCTCGGAGTGTAGGCATAAAAGTTGAACCACGTGTAAGACAGTAA[G/T]
TGTTTCGGCGACGACGTCGTCGCCGTGTCCTGCCAGACCACCGAGACCGCCCGGCTCTCGGCGTCGTAGCACGCGATCTTCCCGGGCACGCTGAAGAACA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 52.60% 47.40% 0.06% 0.00% NA
All Indica  2759 68.80% 31.10% 0.07% 0.00% NA
All Japonica  1512 13.80% 86.10% 0.07% 0.00% NA
Aus  269 94.10% 5.90% 0.00% 0.00% NA
Indica I  595 70.90% 29.10% 0.00% 0.00% NA
Indica II  465 71.80% 28.00% 0.22% 0.00% NA
Indica III  913 68.20% 31.80% 0.00% 0.00% NA
Indica Intermediate  786 66.00% 33.80% 0.13% 0.00% NA
Temperate Japonica  767 0.40% 99.60% 0.00% 0.00% NA
Tropical Japonica  504 35.90% 63.90% 0.20% 0.00% NA
Japonica Intermediate  241 10.40% 89.60% 0.00% 0.00% NA
VI/Aromatic  96 82.30% 17.70% 0.00% 0.00% NA
Intermediate  90 51.10% 48.90% 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
vg0225196895 C -> A LOC_Os02g41930.1 missense_variant ; p.His379Gln; MODERATE nonsynonymous_codon ; H379Q Average:84.607; most accessible tissue: Minghui63 panicle, score: 94.127 unknown unknown TOLERATED 0.46

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)
vg0225196895 C A 0.0 0.0 0.02 0.0 0.02 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0225196895 NA 3.34E-06 mr1646 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