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Detailed information for vg0434940563:

Variant ID: vg0434940563 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 34940563
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:


TAGCTGTTCCTTTTGGAGATATTGAACTATATGCCACTTTTAGATGTGGCAATTAACTATTTGTTACTGTACCCCCATGTCATAGACACATGTGGACCCA[C/T]
ATGTTATTGAGATAGGAGTGGCAAATAGTTAATTGCCAAATCTAAAAGTGGCAAATAGTTAAAAGCCCCGTTTTTTTTGGTATACATGGCTAGCTTCATA

Reverse complement sequence

TATGAAGCTAGCCATGTATACCAAAAAAAACGGGGCTTTTAACTATTTGCCACTTTTAGATTTGGCAATTAACTATTTGCCACTCCTATCTCAATAACAT[G/A]
TGGGTCCACATGTGTCTATGACATGGGGGTACAGTAACAAATAGTTAATTGCCACATCTAAAAGTGGCATATAGTTCAATATCTCCAAAAGGAACAGCTA

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 82.30% 16.60% 1.04% 0.00% NA
All Indica  2759 73.30% 25.50% 1.27% 0.00% NA
All Japonica  1512 94.80% 4.40% 0.79% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 97.30% 1.20% 1.51% 0.00% NA
Indica II  465 40.20% 58.90% 0.86% 0.00% NA
Indica III  913 70.40% 28.50% 1.10% 0.00% NA
Indica Intermediate  786 77.90% 20.60% 1.53% 0.00% NA
Temperate Japonica  767 98.70% 0.80% 0.52% 0.00% NA
Tropical Japonica  504 91.90% 6.70% 1.39% 0.00% NA
Japonica Intermediate  241 88.40% 11.20% 0.41% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 83.30% 14.40% 2.22% 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
vg0434940563 C -> T LOC_Os04g58750.1 upstream_gene_variant ; 2426.0bp to feature; MODIFIER silent_mutation Average:81.262; most accessible tissue: Minghui63 panicle, score: 90.624 N N N N
vg0434940563 C -> T LOC_Os04g58750.3 upstream_gene_variant ; 2417.0bp to feature; MODIFIER silent_mutation Average:81.262; most accessible tissue: Minghui63 panicle, score: 90.624 N N N N
vg0434940563 C -> T LOC_Os04g58750.2 upstream_gene_variant ; 2426.0bp to feature; MODIFIER silent_mutation Average:81.262; most accessible tissue: Minghui63 panicle, score: 90.624 N N N N
vg0434940563 C -> T LOC_Os04g58750.4 upstream_gene_variant ; 3111.0bp to feature; MODIFIER silent_mutation Average:81.262; most accessible tissue: Minghui63 panicle, score: 90.624 N N N N
vg0434940563 C -> T LOC_Os04g58740.1 downstream_gene_variant ; 910.0bp to feature; MODIFIER silent_mutation Average:81.262; most accessible tissue: Minghui63 panicle, score: 90.624 N N N N
vg0434940563 C -> T LOC_Os04g58740-LOC_Os04g58750 intergenic_region ; MODIFIER silent_mutation Average:81.262; most accessible tissue: Minghui63 panicle, score: 90.624 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)
vg0434940563 C T -0.01 -0.05 -0.04 -0.05 -0.07 -0.08

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0434940563 NA 4.99E-06 mr1103 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
vg0434940563 NA 7.86E-08 mr1410 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
vg0434940563 NA 4.19E-06 mr1949 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
vg0434940563 NA 5.25E-07 mr1233_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
vg0434940563 3.73E-06 NA mr1324_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
vg0434940563 NA 8.15E-08 mr1949_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