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Detailed information for vg0123979773:

Variant ID: vg0123979773 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 23979773
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, C: 0.00, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:


TAACCGTGGGGTGGAGGTAAGCCCATCTCAAACGGCAGTTTGGTGAAACCTGGTCCCGGGGCTTGATCGCAACGACACGATACGCTACGAGTACTACTAC[T/C]
CGTCACTGCAGGTGCAGGTGCAGCAGAGCTGCAAGTGTATCGGAGTAGTAGCAGCAGCCAATGTGATGGCACGCACCGGTCCAGCGTGAGGCGGAGCATG

Reverse complement sequence

CATGCTCCGCCTCACGCTGGACCGGTGCGTGCCATCACATTGGCTGCTGCTACTACTCCGATACACTTGCAGCTCTGCTGCACCTGCACCTGCAGTGACG[A/G]
GTAGTAGTACTCGTAGCGTATCGTGTCGTTGCGATCAAGCCCCGGGACCAGGTTTCACCAAACTGCCGTTTGAGATGGGCTTACCTCCACCCCACGGTTA

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 83.80% 16.10% 0.02% 0.00% NA
All Indica  2759 93.50% 6.50% 0.00% 0.00% NA
All Japonica  1512 82.10% 17.90% 0.07% 0.00% NA
Aus  269 6.70% 93.30% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 98.30% 1.70% 0.00% 0.00% NA
Indica III  913 88.80% 11.20% 0.00% 0.00% NA
Indica Intermediate  786 91.50% 8.50% 0.00% 0.00% NA
Temperate Japonica  767 99.10% 0.90% 0.00% 0.00% NA
Tropical Japonica  504 62.30% 37.50% 0.20% 0.00% NA
Japonica Intermediate  241 69.30% 30.70% 0.00% 0.00% NA
VI/Aromatic  96 53.10% 46.90% 0.00% 0.00% NA
Intermediate  90 80.00% 20.00% 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
vg0123979773 T -> C LOC_Os01g42294.1 intron_variant ; MODIFIER silent_mutation Average:97.688; most accessible tissue: Zhenshan97 panicle, score: 99.592 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)
vg0123979773 T C 0.0 0.0 -0.02 0.05 0.0 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0123979773 NA 9.91E-11 mr1260 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
vg0123979773 NA 2.02E-07 mr1448 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
vg0123979773 NA 1.82E-07 mr1530 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
vg0123979773 NA 4.42E-13 mr1696 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
vg0123979773 3.97E-06 NA mr1715 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
vg0123979773 NA 3.74E-16 mr1530_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