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Detailed information for vg1204993459:

Variant ID: vg1204993459 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 4993459
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCCATACCGGAGGCACCAGTAATGGAAGACGCCGGCGCCTCCGAATCGCAAGGATTCGGAGGCATTTAAGAATGCCTCAACTACTTAAAAAAATACCTCC[A/C]
ATCCTTAAAGAAGGCACTTAAAAAAGTGTTGGATATACTATTGTAGGGAAAGGGATTTTAAGGCACTTTTTCAAAATGCCTTCATAAGTATAGATGAAGG

Reverse complement sequence

CCTTCATCTATACTTATGAAGGCATTTTGAAAAAGTGCCTTAAAATCCCTTTCCCTACAATAGTATATCCAACACTTTTTTAAGTGCCTTCTTTAAGGAT[T/G]
GGAGGTATTTTTTTAAGTAGTTGAGGCATTCTTAAATGCCTCCGAATCCTTGCGATTCGGAGGCGCCGGCGTCTTCCATTACTGGTGCCTCCGGTATGGC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 56.00% 11.40% 18.47% 14.16% NA
All Indica  2759 50.70% 1.50% 28.02% 19.75% NA
All Japonica  1512 67.50% 28.40% 3.37% 0.73% NA
Aus  269 30.90% 17.10% 12.27% 39.78% NA
Indica I  595 52.90% 0.70% 33.95% 12.44% NA
Indica II  465 49.90% 1.50% 31.61% 16.99% NA
Indica III  913 53.30% 0.80% 21.25% 24.64% NA
Indica Intermediate  786 46.60% 2.90% 29.26% 21.25% NA
Temperate Japonica  767 94.10% 2.70% 2.48% 0.65% NA
Tropical Japonica  504 21.40% 72.60% 4.76% 1.19% NA
Japonica Intermediate  241 79.30% 17.40% 3.32% 0.00% NA
VI/Aromatic  96 93.80% 2.10% 3.12% 1.04% NA
Intermediate  90 57.80% 22.20% 14.44% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1204993459 A -> C LOC_Os12g09510.1 upstream_gene_variant ; 4712.0bp to feature; MODIFIER silent_mutation Average:75.814; most accessible tissue: Zhenshan97 flower, score: 91.09 N N N N
vg1204993459 A -> C LOC_Os12g09500-LOC_Os12g09510 intergenic_region ; MODIFIER silent_mutation Average:75.814; most accessible tissue: Zhenshan97 flower, score: 91.09 N N N N
vg1204993459 A -> DEL N N silent_mutation Average:75.814; most accessible tissue: Zhenshan97 flower, score: 91.09 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)
vg1204993459 A C 0.0 0.0 -0.01 0.0 0.0 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1204993459 NA 5.93E-06 mr1345 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
vg1204993459 2.18E-06 NA mr1362 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
vg1204993459 NA 3.13E-06 mr1401 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
vg1204993459 NA 1.61E-07 mr1551 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
vg1204993459 NA 3.40E-08 mr1593 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
vg1204993459 NA 4.00E-06 mr1852 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
vg1204993459 NA 4.06E-06 mr1942 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
vg1204993459 NA 4.45E-06 mr1039_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
vg1204993459 NA 1.05E-08 mr1261_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
vg1204993459 NA 1.53E-10 mr1398_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
vg1204993459 NA 9.11E-06 mr1398_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
vg1204993459 NA 6.75E-07 mr1632_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
vg1204993459 NA 3.25E-07 mr1696_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
vg1204993459 NA 6.00E-08 mr1819_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
vg1204993459 NA 7.34E-10 mr1942_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