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Detailed information for vg0203965753:

Variant ID: vg0203965753 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 3965753
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.51, T: 0.50, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:


CAATGCATCGTGGAAGAATGGGACCCCCTATGAAGAGGGATTAGGCTGTGTTCGGGAGGCATGGTTGCCAACCTTGCCTTCCGACGAAAAACAAAGCACG[T/C]
GATTATAGTGAGATTAATTAAGTATTAGCAAAAAAAACTTGAAAAGTGGATTAATATGATTTTTTAAAATAACTTTCATATAATTTTTTTTATAAAAAAT

Reverse complement sequence

ATTTTTTATAAAAAAAATTATATGAAAGTTATTTTAAAAAATCATATTAATCCACTTTTCAAGTTTTTTTTGCTAATACTTAATTAATCTCACTATAATC[A/G]
CGTGCTTTGTTTTTCGTCGGAAGGCAAGGTTGGCAACCATGCCTCCCGAACACAGCCTAATCCCTCTTCATAGGGGGTCCCATTCTTCCACGATGCATTG

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 52.10% 47.10% 0.32% 0.42% NA
All Indica  2759 44.50% 54.50% 0.36% 0.62% NA
All Japonica  1512 62.30% 37.50% 0.13% 0.07% NA
Aus  269 57.20% 42.80% 0.00% 0.00% NA
Indica I  595 40.50% 58.80% 0.34% 0.34% NA
Indica II  465 28.20% 71.00% 0.22% 0.65% NA
Indica III  913 60.40% 39.00% 0.22% 0.44% NA
Indica Intermediate  786 38.90% 59.40% 0.64% 1.02% NA
Temperate Japonica  767 36.10% 63.90% 0.00% 0.00% NA
Tropical Japonica  504 97.40% 2.40% 0.00% 0.20% NA
Japonica Intermediate  241 72.20% 27.00% 0.83% 0.00% NA
VI/Aromatic  96 96.90% 1.00% 2.08% 0.00% NA
Intermediate  90 51.10% 45.60% 1.11% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0203965753 T -> DEL N N silent_mutation Average:80.828; most accessible tissue: Minghui63 panicle, score: 96.161 N N N N
vg0203965753 T -> C LOC_Os02g07640.1 downstream_gene_variant ; 267.0bp to feature; MODIFIER silent_mutation Average:80.828; most accessible tissue: Minghui63 panicle, score: 96.161 N N N N
vg0203965753 T -> C LOC_Os02g07640-LOC_Os02g07650 intergenic_region ; MODIFIER silent_mutation Average:80.828; most accessible tissue: Minghui63 panicle, score: 96.161 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)
vg0203965753 T C -0.03 0.01 0.01 -0.04 -0.02 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0203965753 NA 2.92E-13 Plant_height Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0203965753 NA 7.53E-13 Spikelet_length Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0203965753 NA 8.96E-08 mr1163 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
vg0203965753 NA 4.32E-06 mr1180 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
vg0203965753 NA 1.67E-07 mr1183 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
vg0203965753 NA 6.19E-08 mr1202 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
vg0203965753 NA 1.89E-07 mr1252 Jap_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
vg0203965753 NA 5.14E-06 mr1272 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
vg0203965753 NA 1.39E-06 mr1330 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
vg0203965753 NA 5.42E-07 mr1503 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
vg0203965753 NA 1.82E-06 mr1521 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
vg0203965753 NA 3.23E-06 mr1530 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
vg0203965753 NA 1.41E-06 mr1542 Ind_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
vg0203965753 NA 4.16E-06 mr1548 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
vg0203965753 NA 4.08E-07 mr1723 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
vg0203965753 NA 4.98E-06 mr1729 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
vg0203965753 NA 4.23E-07 mr1739 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
vg0203965753 NA 4.99E-06 mr1129_2 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
vg0203965753 NA 9.89E-06 mr1164_2 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
vg0203965753 NA 9.62E-10 mr1486_2 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
vg0203965753 NA 1.04E-07 mr1542_2 Ind_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
vg0203965753 NA 2.79E-08 mr1794_2 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
vg0203965753 NA 8.59E-06 mr1851_2 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