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Detailed information for vg1021136565:

Variant ID: vg1021136565 (JBrowse)Variation Type: INDEL
Chromosome: chr10Position: 21136565
Reference Allele: AAlternative Allele: T,AAT
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CATGGATATCAGAATGTAAAGGAAAAGGGCGGAAACTGTTTTAATCCCTGGAGGGGATATCCCCTCGTTTTTTTGTATGTCACTTAAATGGTAATAAAAA[A/T,AAT]
TTTGAAAAAAATTAGGAAGGTGTATTAACATGTAATATAACACTCCACAAACATACAAGTTCAAATTCAACTTCTACATTTCGTAACGAAAAAAACAAAT

Reverse complement sequence

ATTTGTTTTTTTCGTTACGAAATGTAGAAGTTGAATTTGAACTTGTATGTTTGTGGAGTGTTATATTACATGTTAATACACCTTCCTAATTTTTTTCAAA[T/A,ATT]
TTTTTATTACCATTTAAGTGACATACAAAAAAACGAGGGGATATCCCCTCCAGGGATTAAAACAGTTTCCGCCCTTTTCCTTTACATTCTGATATCCATG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 78.00% 21.50% 0.21% 0.13% AAT: 0.13%
All Indica  2759 99.10% 0.50% 0.11% 0.07% AAT: 0.22%
All Japonica  1512 41.10% 58.50% 0.26% 0.20% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 98.70% 1.30% 0.00% 0.00% NA
Indica III  913 98.80% 0.30% 0.22% 0.00% AAT: 0.66%
Indica Intermediate  786 99.00% 0.80% 0.00% 0.25% NA
Temperate Japonica  767 68.40% 31.30% 0.26% 0.00% NA
Tropical Japonica  504 5.20% 94.00% 0.40% 0.40% NA
Japonica Intermediate  241 29.00% 70.50% 0.00% 0.41% NA
VI/Aromatic  96 9.40% 90.60% 0.00% 0.00% NA
Intermediate  90 62.20% 33.30% 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
vg1021136565 A -> DEL N N silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1021136565 A -> T LOC_Os10g39550.1 intron_variant ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1021136565 A -> AAT LOC_Os10g39550.1 intron_variant ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 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)
vg1021136565 A AAT -0.02 -0.02 -0.03 0.17 0.05 -0.05
vg1021136565 A T -0.02 0.0 0.0 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1021136565 NA 4.63E-13 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
vg1021136565 NA 2.29E-12 Spikelet_length 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
vg1021136565 NA 2.45E-10 mr1128 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
vg1021136565 NA 1.67E-13 mr1137 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
vg1021136565 NA 4.49E-06 mr1182 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
vg1021136565 NA 6.12E-11 mr1617 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
vg1021136565 NA 2.65E-07 mr1057_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
vg1021136565 NA 7.15E-10 mr1137_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
vg1021136565 NA 7.42E-06 mr1164_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
vg1021136565 NA 2.03E-07 mr1182_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
vg1021136565 4.69E-06 NA mr1693_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