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Detailed information for vg0418681664:

Variant ID: vg0418681664 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 18681664
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACTTTGCTTCCCTTCCTTCGATACCTGCAGGTACCTCTCGCACTCCATTCCACTCTGACTGATTTCTCCACCCCCCTCCCCCCACGTTGGCAGTGCTTCA[C/T]
AGCCGCTTTGCATCCCTTCCTCATGTGTATTTTTCTATTTTTTTTGCTTGTGATTTCCTTGCTGATTTTTTCTCCAGCTTATATGGACAGTATCGATTCC

Reverse complement sequence

GGAATCGATACTGTCCATATAAGCTGGAGAAAAAATCAGCAAGGAAATCACAAGCAAAAAAAATAGAAAAATACACATGAGGAAGGGATGCAAAGCGGCT[G/A]
TGAAGCACTGCCAACGTGGGGGGAGGGGGGTGGAGAAATCAGTCAGAGTGGAATGGAGTGCGAGAGGTACCTGCAGGTATCGAAGGAAGGGAAGCAAAGT

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 88.80% 4.70% 2.50% 4.06% NA
All Indica  2759 82.80% 7.80% 3.77% 5.65% NA
All Japonica  1512 99.70% 0.00% 0.33% 0.00% NA
Aus  269 85.10% 0.00% 2.23% 12.64% NA
Indica I  595 79.80% 4.40% 10.76% 5.04% NA
Indica II  465 70.80% 24.90% 2.80% 1.51% NA
Indica III  913 89.40% 0.20% 0.99% 9.42% NA
Indica Intermediate  786 84.50% 9.00% 2.29% 4.20% NA
Temperate Japonica  767 99.50% 0.00% 0.52% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 0.00% 1.04% NA
Intermediate  90 90.00% 5.60% 3.33% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0418681664 C -> DEL N N silent_mutation Average:65.848; most accessible tissue: Zhenshan97 panicle, score: 87.451 N N N N
vg0418681664 C -> T LOC_Os04g31210.1 downstream_gene_variant ; 587.0bp to feature; MODIFIER silent_mutation Average:65.848; most accessible tissue: Zhenshan97 panicle, score: 87.451 N N N N
vg0418681664 C -> T LOC_Os04g31220.1 downstream_gene_variant ; 1529.0bp to feature; MODIFIER silent_mutation Average:65.848; most accessible tissue: Zhenshan97 panicle, score: 87.451 N N N N
vg0418681664 C -> T LOC_Os04g31210.3 downstream_gene_variant ; 587.0bp to feature; MODIFIER silent_mutation Average:65.848; most accessible tissue: Zhenshan97 panicle, score: 87.451 N N N N
vg0418681664 C -> T LOC_Os04g31210.4 downstream_gene_variant ; 587.0bp to feature; MODIFIER silent_mutation Average:65.848; most accessible tissue: Zhenshan97 panicle, score: 87.451 N N N N
vg0418681664 C -> T LOC_Os04g31210.5 downstream_gene_variant ; 587.0bp to feature; MODIFIER silent_mutation Average:65.848; most accessible tissue: Zhenshan97 panicle, score: 87.451 N N N N
vg0418681664 C -> T LOC_Os04g31210-LOC_Os04g31220 intergenic_region ; MODIFIER silent_mutation Average:65.848; most accessible tissue: Zhenshan97 panicle, score: 87.451 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)
vg0418681664 C T -0.05 -0.02 -0.03 -0.06 -0.06 -0.07

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0418681664 NA 1.27E-06 mr1851 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
vg0418681664 2.05E-06 2.10E-08 mr1864 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
vg0418681664 1.10E-06 NA mr1851_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
vg0418681664 1.40E-06 NA mr1864_2 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