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Detailed information for vg0331937585:

Variant ID: vg0331937585 (JBrowse)Variation Type: INDEL
Chromosome: chr03Position: 31937585
Reference Allele: TAAlternative Allele: CA,T
Primary Allele: CASecondary Allele: TA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCCTCCATCCTTAAAAAAAATAACTTAAAAAAATAACCTAGACATCCATGGGACATTAAATAGTACAATAAATCTGGACATGAACATGTTTAGATTTATC[TA/CA,T]
TGGGACATTAAATAGTATAACGAATCTGGACACGAACATATTCAGATTCGTTGTGCTATGTAATATCTTATCGGTGTTTAGGTTGTGTTTTATTTGGGAT

Reverse complement sequence

ATCCCAAATAAAACACAACCTAAACACCGATAAGATATTACATAGCACAACGAATCTGAATATGTTCGTGTCCAGATTCGTTATACTATTTAATGTCCCA[TA/TG,A]
GATAAATCTAAACATGTTCATGTCCAGATTTATTGTACTATTTAATGTCCCATGGATGTCTAGGTTATTTTTTTAAGTTATTTTTTTTAAGGATGGAGGG

Allele Frequencies:

Populations Population SizeFrequency of CA(primary allele) Frequency of TA(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 86.50% 7.80% 3.22% 0.00% T: 2.52%
All Indica  2759 95.40% 0.10% 0.40% 0.00% T: 4.06%
All Japonica  1512 67.70% 23.40% 8.93% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 90.50% 0.90% 0.86% 0.00% T: 7.74%
Indica III  913 97.00% 0.00% 0.00% 0.00% T: 2.96%
Indica Intermediate  786 92.90% 0.00% 0.89% 0.00% T: 6.23%
Temperate Japonica  767 46.90% 38.10% 14.99% 0.00% NA
Tropical Japonica  504 95.40% 3.40% 1.19% 0.00% NA
Japonica Intermediate  241 75.50% 18.70% 5.81% 0.00% NA
VI/Aromatic  96 97.90% 0.00% 0.00% 0.00% T: 2.08%
Intermediate  90 75.60% 12.20% 6.67% 0.00% T: 5.56%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0331937585 TA -> T LOC_Os03g56060.1 upstream_gene_variant ; 2962.0bp to feature; MODIFIER silent_mutation Average:87.977; most accessible tissue: Zhenshan97 panicle, score: 98.621 N N N N
vg0331937585 TA -> T LOC_Os03g56070.1 downstream_gene_variant ; 4994.0bp to feature; MODIFIER silent_mutation Average:87.977; most accessible tissue: Zhenshan97 panicle, score: 98.621 N N N N
vg0331937585 TA -> T LOC_Os03g56060-LOC_Os03g56070 intergenic_region ; MODIFIER silent_mutation Average:87.977; most accessible tissue: Zhenshan97 panicle, score: 98.621 N N N N
vg0331937585 TA -> CA LOC_Os03g56060.1 upstream_gene_variant ; 2961.0bp to feature; MODIFIER silent_mutation Average:87.977; most accessible tissue: Zhenshan97 panicle, score: 98.621 N N N N
vg0331937585 TA -> CA LOC_Os03g56070.1 downstream_gene_variant ; 4995.0bp to feature; MODIFIER silent_mutation Average:87.977; most accessible tissue: Zhenshan97 panicle, score: 98.621 N N N N
vg0331937585 TA -> CA LOC_Os03g56060-LOC_Os03g56070 intergenic_region ; MODIFIER silent_mutation Average:87.977; most accessible tissue: Zhenshan97 panicle, score: 98.621 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)
vg0331937585 TA CA -0.02 -0.04 -0.03 -0.02 -0.02 -0.01
vg0331937585 TA T -0.01 0.04 0.06 0.01 -0.01 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0331937585 NA 2.45E-16 Grain_length Ind_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
vg0331937585 NA 5.33E-11 Grain_width Ind_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
vg0331937585 NA 9.79E-14 Heading_date 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
vg0331937585 NA 3.86E-22 Plant_height 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
vg0331937585 NA 1.92E-06 mr1050 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
vg0331937585 NA 8.31E-07 mr1163 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
vg0331937585 NA 4.88E-10 mr1354 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
vg0331937585 NA 6.54E-11 mr1354 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
vg0331937585 NA 5.13E-07 mr1829 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
vg0331937585 NA 4.65E-08 mr1829 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
vg0331937585 NA 6.05E-06 mr1050_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
vg0331937585 NA 8.99E-06 mr1051_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
vg0331937585 NA 2.24E-06 mr1138_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
vg0331937585 NA 5.45E-12 mr1354_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
vg0331937585 NA 1.39E-11 mr1354_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
vg0331937585 NA 4.09E-06 mr1549_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
vg0331937585 NA 3.50E-09 mr1829_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
vg0331937585 NA 1.49E-09 mr1829_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
vg0331937585 NA 1.36E-10 mr1902_2 Jap_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
vg0331937585 NA 1.60E-11 mr1942_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
vg0331937585 NA 9.43E-07 mr1942_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