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Detailed information for vg0225196797:

Variant ID: vg0225196797 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 25196797
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGCGCGCGTGGCGAGGGTGACGCTGGAGCACTTCTCGTGGGGAGGCGCGCCGCTGCACGTCGTGCGGGGGCCCGGGGAGGCGGGGCGGCACGGCGTGCTG[T/C]
TCTTCAGCGTGCCCGGGAAGATCGCGTGCTACGACGCCGAGAGCCGGGCGGTCTCGGTGGTCTGGCAGGACACGGCGACGACGTCGTCGCCGAAACACTT

Reverse complement sequence

AAGTGTTTCGGCGACGACGTCGTCGCCGTGTCCTGCCAGACCACCGAGACCGCCCGGCTCTCGGCGTCGTAGCACGCGATCTTCCCGGGCACGCTGAAGA[A/G]
CAGCACGCCGTGCCGCCCCGCCTCCCCGGGCCCCCGCACGACGTGCAGCGGCGCGCCTCCCCACGAGAAGTGCTCCAGCGTCACCCTCGCCACGCGCGCG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.50% 5.40% 0.08% 0.00% NA
All Indica  2759 99.40% 0.50% 0.14% 0.00% NA
All Japonica  1512 91.40% 8.60% 0.00% 0.00% NA
Aus  269 70.30% 29.70% 0.00% 0.00% NA
Indica I  595 99.50% 0.30% 0.17% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.00% 1.00% 0.00% 0.00% NA
Indica Intermediate  786 99.40% 0.30% 0.38% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 76.40% 23.60% 0.00% 0.00% NA
Japonica Intermediate  241 95.40% 4.60% 0.00% 0.00% NA
VI/Aromatic  96 69.80% 30.20% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0225196797 T -> C LOC_Os02g41930.1 missense_variant ; p.Phe347Leu; MODERATE nonsynonymous_codon ; F347L Average:89.142; most accessible tissue: Minghui63 panicle, score: 96.016 unknown unknown TOLERATED 1.00

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)
vg0225196797 T C 0.0 0.0 -0.01 0.0 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0225196797 NA 1.47E-07 mr1029 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
vg0225196797 NA 1.25E-07 mr1189 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
vg0225196797 NA 2.09E-08 mr1570 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
vg0225196797 NA 2.20E-06 mr1625 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
vg0225196797 NA 2.43E-06 mr1734 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