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Detailed information for vg0207234669:

Variant ID: vg0207234669 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 7234669
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAACTAGGAAATTAAAGTTGCTTAAGAGCAAGTTTAATAGTATAGCCCACTACTATCTCCAAATCATCTATAGCCAATATCATAGCCAATTCATGCAATA[A/G]
TTGCTTACTATACTATTAATACCTGGTCCTACCTGTCATCCACACATTACGTCTTGGTGTCCGTGTTACAGCTGGCTATAAATCTGTAGCCCGCTAGTCT

Reverse complement sequence

AGACTAGCGGGCTACAGATTTATAGCCAGCTGTAACACGGACACCAAGACGTAATGTGTGGATGACAGGTAGGACCAGGTATTAATAGTATAGTAAGCAA[T/C]
TATTGCATGAATTGGCTATGATATTGGCTATAGATGATTTGGAGATAGTAGTGGGCTATACTATTAAACTTGCTCTTAAGCAACTTTAATTTCCTAGTTT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 70.90% 8.30% 0.83% 19.97% NA
All Indica  2759 94.60% 0.20% 0.07% 5.18% NA
All Japonica  1512 33.40% 25.00% 2.25% 39.35% NA
Aus  269 35.30% 0.00% 0.74% 63.94% NA
Indica I  595 99.50% 0.20% 0.17% 0.17% NA
Indica II  465 85.40% 0.60% 0.00% 13.98% NA
Indica III  913 96.90% 0.00% 0.00% 3.07% NA
Indica Intermediate  786 93.50% 0.10% 0.13% 6.23% NA
Temperate Japonica  767 35.90% 46.30% 3.39% 14.47% NA
Tropical Japonica  504 21.00% 1.60% 0.79% 76.59% NA
Japonica Intermediate  241 51.50% 6.20% 1.66% 40.66% NA
VI/Aromatic  96 81.20% 0.00% 1.04% 17.71% NA
Intermediate  90 73.30% 7.80% 0.00% 18.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0207234669 A -> G LOC_Os02g13510-LOC_Os02g13520 intergenic_region ; MODIFIER silent_mutation Average:76.247; most accessible tissue: Minghui63 flag leaf, score: 88.103 N N N N
vg0207234669 A -> DEL N N silent_mutation Average:76.247; most accessible tissue: Minghui63 flag leaf, score: 88.103 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)
vg0207234669 A G -0.02 -0.04 -0.05 -0.03 -0.04 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0207234669 NA 2.36E-11 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
vg0207234669 NA 1.63E-14 Spikelet_length 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
vg0207234669 NA 6.12E-09 mr1137 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
vg0207234669 NA 1.22E-06 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
vg0207234669 NA 1.68E-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
vg0207234669 NA 7.00E-10 mr1627 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
vg0207234669 NA 1.92E-07 mr1763 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
vg0207234669 NA 3.50E-06 mr1977 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
vg0207234669 NA 3.95E-10 mr1010_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
vg0207234669 NA 2.16E-06 mr1051_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
vg0207234669 NA 4.24E-08 mr1137_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
vg0207234669 NA 2.69E-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
vg0207234669 NA 6.56E-06 mr1206_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
vg0207234669 NA 2.82E-07 mr1229_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
vg0207234669 NA 6.01E-07 mr1229_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
vg0207234669 NA 9.79E-06 mr1263_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
vg0207234669 NA 8.36E-06 mr1441_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
vg0207234669 NA 4.90E-11 mr1530_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
vg0207234669 NA 3.42E-07 mr1617_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
vg0207234669 9.35E-07 NA mr1627_2 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
vg0207234669 NA 2.39E-09 mr1627_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
vg0207234669 NA 3.81E-06 mr1763_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
vg0207234669 NA 5.20E-09 mr1880_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
vg0207234669 NA 7.65E-08 mr1880_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