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Detailed information for vg1202638554:

Variant ID: vg1202638554 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 2638554
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGAAACTTTGCAGTATTAACACTGGCGGCTCACAGTGTAACCAGCCAGCGATAATTCATTTTCCCTAGTGGCCTATCTTAGGCTAAACGCCAGCGAAAAT[A/G]
GATCTTTGCTGGCGGCTGGCTTAAGACGACCACCAGCGAAAATGAATTATCGCTGGCGTTCGATAACTGCTAGCGAAGATCTTGATTTTTATTGGCCTTT

Reverse complement sequence

AAAGGCCAATAAAAATCAAGATCTTCGCTAGCAGTTATCGAACGCCAGCGATAATTCATTTTCGCTGGTGGTCGTCTTAAGCCAGCCGCCAGCAAAGATC[T/C]
ATTTTCGCTGGCGTTTAGCCTAAGATAGGCCACTAGGGAAAATGAATTATCGCTGGCTGGTTACACTGTGAGCCGCCAGTGTTAATACTGCAAAGTTTCA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.90% 7.00% 0.04% 0.00% NA
All Indica  2759 92.60% 7.40% 0.04% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 53.50% 46.10% 0.37% 0.00% NA
Indica I  595 97.10% 2.90% 0.00% 0.00% NA
Indica II  465 88.20% 11.80% 0.00% 0.00% NA
Indica III  913 92.10% 7.90% 0.00% 0.00% NA
Indica Intermediate  786 92.40% 7.50% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 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
vg1202638554 A -> G LOC_Os12g05720.1 upstream_gene_variant ; 3218.0bp to feature; MODIFIER silent_mutation Average:87.38; most accessible tissue: Callus, score: 94.283 N N N N
vg1202638554 A -> G LOC_Os12g05709.1 downstream_gene_variant ; 1667.0bp to feature; MODIFIER silent_mutation Average:87.38; most accessible tissue: Callus, score: 94.283 N N N N
vg1202638554 A -> G LOC_Os12g05715.1 downstream_gene_variant ; 96.0bp to feature; MODIFIER silent_mutation Average:87.38; most accessible tissue: Callus, score: 94.283 N N N N
vg1202638554 A -> G LOC_Os12g05715-LOC_Os12g05720 intergenic_region ; MODIFIER silent_mutation Average:87.38; most accessible tissue: Callus, score: 94.283 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)
vg1202638554 A G 0.03 0.03 0.04 0.02 0.04 0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1202638554 2.23E-06 1.80E-06 mr1309 Ind_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
vg1202638554 NA 2.59E-06 mr1574 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
vg1202638554 NA 1.52E-07 mr1774 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
vg1202638554 1.24E-06 4.32E-06 mr1920 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
vg1202638554 NA 8.77E-06 mr1988 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
vg1202638554 NA 6.80E-06 mr1836_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