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Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0719259492:

Variant ID: vg0719259492 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 19259492
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, C: 0.03, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:


AGCCGATGGAGCATTCTGCCAATCAGCACCTCACAAGATCCAGGTAGCTCTTTTTCGAGATGCATCAAGGAATCAAGGAATGTATGAACAACTGGTCCGT[T/C]
AAACTTGTCACCAGTAGCCTGCAGCATGTCATCAATACAGTGAAGAGTTTGGCATGTCTCGAGTTGTACAAAGATCAAACTGATAAAATGTGGTGATGAC

Reverse complement sequence

GTCATCACCACATTTTATCAGTTTGATCTTTGTACAACTCGAGACATGCCAAACTCTTCACTGTATTGATGACATGCTGCAGGCTACTGGTGACAAGTTT[A/G]
ACGGACCAGTTGTTCATACATTCCTTGATTCCTTGATGCATCTCGAAAAAGAGCTACCTGGATCTTGTGAGGTGCTGATTGGCAGAATGCTCCATCGGCT

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 93.40% 6.60% 0.00% 0.00% NA
All Indica  2759 99.10% 0.90% 0.00% 0.00% NA
All Japonica  1512 99.60% 0.40% 0.00% 0.00% NA
Aus  269 22.70% 77.30% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.50% 0.50% 0.00% 0.00% NA
Indica Intermediate  786 97.50% 2.50% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 97.90% 2.10% 0.00% 0.00% NA
VI/Aromatic  96 29.20% 70.80% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0719259492 T -> C LOC_Os07g32400.1 missense_variant ; p.Asn429Asp; MODERATE nonsynonymous_codon Average:80.546; most accessible tissue: Callus, score: 89.251 benign -0.188 TOLERATED 0.20
vg0719259492 T -> C LOC_Os07g32400.2 missense_variant ; p.Asn429Asp; MODERATE nonsynonymous_codon Average:80.546; most accessible tissue: Callus, score: 89.251 benign -0.188 TOLERATED 0.22

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)
vg0719259492 T C 0.0 0.0 0.0 0.0 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0719259492 7.32E-06 NA mr1246 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
vg0719259492 2.75E-06 NA mr1542 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
vg0719259492 NA 7.53E-07 mr1662 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
vg0719259492 NA 3.43E-07 mr1126_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
vg0719259492 NA 7.36E-06 mr1522_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
vg0719259492 NA 9.44E-08 mr1567_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
vg0719259492 NA 9.66E-07 mr1762_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