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Detailed information for vg0335045132:

Variant ID: vg0335045132 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 35045132
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATCATCGTACAAACTAATTTGTTTCATAAATGTTATCGTTGTTAGGGTTTTGTCCAGCCTGTCCTGTTAAATACGTTGTTCATCCTATAACATTTAAACC[T/C]
TAACAATGATAGTATTTATGGGATAAAGTCAATTGTACGATAACATTTTATGGAACTTACACTTGTTTTTTATATTTCTTAGAATTGTGCGCCTTGCCAA

Reverse complement sequence

TTGGCAAGGCGCACAATTCTAAGAAATATAAAAAACAAGTGTAAGTTCCATAAAATGTTATCGTACAATTGACTTTATCCCATAAATACTATCATTGTTA[A/G]
GGTTTAAATGTTATAGGATGAACAACGTATTTAACAGGACAGGCTGGACAAAACCCTAACAACGATAACATTTATGAAACAAATTAGTTTGTACGATGAT

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 81.60% 13.80% 4.42% 0.11% NA
All Indica  2759 94.20% 1.80% 3.99% 0.04% NA
All Japonica  1512 54.00% 39.40% 6.35% 0.26% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 83.70% 4.70% 11.60% 0.00% NA
Indica II  465 95.10% 2.40% 2.58% 0.00% NA
Indica III  913 99.80% 0.10% 0.00% 0.11% NA
Indica Intermediate  786 95.00% 1.30% 3.69% 0.00% NA
Temperate Japonica  767 28.40% 61.40% 9.91% 0.26% NA
Tropical Japonica  504 86.90% 10.30% 2.58% 0.20% NA
Japonica Intermediate  241 66.80% 29.90% 2.90% 0.41% NA
VI/Aromatic  96 99.00% 0.00% 1.04% 0.00% NA
Intermediate  90 87.80% 10.00% 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
vg0335045132 T -> C LOC_Os03g61810.1 upstream_gene_variant ; 478.0bp to feature; MODIFIER silent_mutation Average:82.918; most accessible tissue: Minghui63 panicle, score: 91.034 N N N N
vg0335045132 T -> C LOC_Os03g61800.1 downstream_gene_variant ; 3505.0bp to feature; MODIFIER silent_mutation Average:82.918; most accessible tissue: Minghui63 panicle, score: 91.034 N N N N
vg0335045132 T -> C LOC_Os03g61800.2 downstream_gene_variant ; 3505.0bp to feature; MODIFIER silent_mutation Average:82.918; most accessible tissue: Minghui63 panicle, score: 91.034 N N N N
vg0335045132 T -> C LOC_Os03g61800.3 downstream_gene_variant ; 3505.0bp to feature; MODIFIER silent_mutation Average:82.918; most accessible tissue: Minghui63 panicle, score: 91.034 N N N N
vg0335045132 T -> C LOC_Os03g61810-LOC_Os03g61829 intergenic_region ; MODIFIER silent_mutation Average:82.918; most accessible tissue: Minghui63 panicle, score: 91.034 N N N N
vg0335045132 T -> DEL N N silent_mutation Average:82.918; most accessible tissue: Minghui63 panicle, score: 91.034 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)
vg0335045132 T C -0.01 -0.01 -0.01 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0335045132 NA 6.17E-16 Plant_height Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0335045132 NA 1.47E-09 mr1002 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
vg0335045132 NA 8.80E-08 mr1002 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
vg0335045132 1.15E-08 2.84E-16 mr1002_2 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
vg0335045132 6.71E-06 9.06E-13 mr1002_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
vg0335045132 NA 1.91E-07 mr1648_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
vg0335045132 NA 3.67E-09 mr1794_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
vg0335045132 NA 2.14E-08 mr1940_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