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Detailed information for vg1204796430:

Variant ID: vg1204796430 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 4796430
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.92, C: 0.08, others allele: 0.00, population size: 66. )

Flanking Sequence (100 bp) in Reference Genome:


GGGAAAGGAGACAATATTTTTATTTTTCAATTATTATATTAATTATAATAATAATCCCCGCAAAAAAAAATCATAAAGACTTGTCTCTTCGTATCGAATA[T/C]
CGATTCCTACCCGGACTCTTTATTTACCTTTCCCCAATTCTCACAAACTGAATGCCACCAAAATCGAATCGCTACAAACCCTATCCACTGCCGCTGGACT

Reverse complement sequence

AGTCCAGCGGCAGTGGATAGGGTTTGTAGCGATTCGATTTTGGTGGCATTCAGTTTGTGAGAATTGGGGAAAGGTAAATAAAGAGTCCGGGTAGGAATCG[A/G]
TATTCGATACGAAGAGACAAGTCTTTATGATTTTTTTTTGCGGGGATTATTATTATAATTAATATAATAATTGAAAAATAAAAATATTGTCTCCTTTCCC

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 58.40% 40.70% 0.83% 0.00% NA
All Indica  2759 87.70% 11.60% 0.65% 0.00% NA
All Japonica  1512 11.50% 87.70% 0.79% 0.00% NA
Aus  269 52.00% 45.00% 2.97% 0.00% NA
Indica I  595 85.90% 13.80% 0.34% 0.00% NA
Indica II  465 86.70% 12.90% 0.43% 0.00% NA
Indica III  913 88.80% 10.30% 0.88% 0.00% NA
Indica Intermediate  786 88.40% 10.80% 0.76% 0.00% NA
Temperate Japonica  767 4.70% 95.30% 0.00% 0.00% NA
Tropical Japonica  504 10.10% 89.70% 0.20% 0.00% NA
Japonica Intermediate  241 36.10% 59.30% 4.56% 0.00% NA
VI/Aromatic  96 2.10% 97.90% 0.00% 0.00% NA
Intermediate  90 28.90% 70.00% 1.11% 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
vg1204796430 T -> C LOC_Os12g09164.1 upstream_gene_variant ; 2205.0bp to feature; MODIFIER silent_mutation Average:96.711; most accessible tissue: Zhenshan97 flower, score: 98.139 N N N N
vg1204796430 T -> C LOC_Os12g09180.1 upstream_gene_variant ; 1579.0bp to feature; MODIFIER silent_mutation Average:96.711; most accessible tissue: Zhenshan97 flower, score: 98.139 N N N N
vg1204796430 T -> C LOC_Os12g09190.1 upstream_gene_variant ; 50.0bp to feature; MODIFIER silent_mutation Average:96.711; most accessible tissue: Zhenshan97 flower, score: 98.139 N N N N
vg1204796430 T -> C LOC_Os12g09180-LOC_Os12g09190 intergenic_region ; MODIFIER silent_mutation Average:96.711; most accessible tissue: Zhenshan97 flower, score: 98.139 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)
vg1204796430 T C 0.0 0.01 0.01 0.03 0.02 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1204796430 NA 8.96E-06 mr1114 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
vg1204796430 NA 3.39E-06 mr1117 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
vg1204796430 NA 1.20E-06 mr1123 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
vg1204796430 NA 1.20E-07 mr1242 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
vg1204796430 3.71E-06 NA mr1679 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
vg1204796430 4.10E-07 5.53E-09 mr1691 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
vg1204796430 4.19E-09 7.36E-14 mr1693 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
vg1204796430 6.62E-06 1.17E-07 mr1720 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
vg1204796430 NA 6.37E-06 mr1114_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
vg1204796430 NA 5.87E-07 mr1117_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
vg1204796430 NA 6.45E-06 mr1118_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
vg1204796430 NA 2.72E-06 mr1119_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
vg1204796430 NA 5.87E-06 mr1123_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
vg1204796430 NA 2.67E-06 mr1242_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
vg1204796430 NA 1.47E-07 mr1496_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
vg1204796430 4.98E-06 3.22E-07 mr1679_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
vg1204796430 1.69E-07 8.11E-11 mr1691_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
vg1204796430 8.75E-07 1.35E-09 mr1720_2 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