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Detailed information for vg0725372026:

Variant ID: vg0725372026 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 25372026
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGGTGTCCCCACACGTCAGCGATAAGTGAGGGTACAGGATACAGTACGAGATGGGAAAGGGGGTACACGTGGCACCACACGGTGGGTCACATGCCCCCCA[A/T]
CGCCGCATCGGATCCGACCACCTCCTGGGCTCCTCTCTCCACTACCAACCTCTCGCGGAGACCCAAACCCTAGCTCCCAAATCCCGACCAGCCGAAGCAT

Reverse complement sequence

ATGCTTCGGCTGGTCGGGATTTGGGAGCTAGGGTTTGGGTCTCCGCGAGAGGTTGGTAGTGGAGAGAGGAGCCCAGGAGGTGGTCGGATCCGATGCGGCG[T/A]
TGGGGGGCATGTGACCCACCGTGTGGTGCCACGTGTACCCCCTTTCCCATCTCGTACTGTATCCTGTACCCTCACTTATCGCTGACGTGTGGGGACACCG

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 91.90% 8.00% 0.08% 0.00% NA
All Indica  2759 99.60% 0.40% 0.00% 0.00% NA
All Japonica  1512 76.20% 23.70% 0.13% 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 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.40% 0.60% 0.00% 0.00% NA
Temperate Japonica  767 96.20% 3.80% 0.00% 0.00% NA
Tropical Japonica  504 42.30% 57.30% 0.40% 0.00% NA
Japonica Intermediate  241 83.40% 16.60% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 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
vg0725372026 A -> T LOC_Os07g42400.1 5_prime_UTR_variant ; 208.0bp to feature; MODIFIER silent_mutation Average:99.45; most accessible tissue: Callus, score: 99.825 N N N N
vg0725372026 A -> T LOC_Os07g42400.2 5_prime_UTR_variant ; 208.0bp to feature; MODIFIER silent_mutation Average:99.45; most accessible tissue: Callus, score: 99.825 N N N N
vg0725372026 A -> T LOC_Os07g42395.1 upstream_gene_variant ; 219.0bp to feature; MODIFIER silent_mutation Average:99.45; most accessible tissue: Callus, score: 99.825 N N N N
vg0725372026 A -> T LOC_Os07g42395.2 upstream_gene_variant ; 170.0bp to feature; MODIFIER silent_mutation Average:99.45; most accessible tissue: Callus, score: 99.825 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)
vg0725372026 A T -0.07 -0.08 -0.05 -0.06 -0.04 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0725372026 NA 8.12E-11 mr1055 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
vg0725372026 NA 2.05E-10 mr1132 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
vg0725372026 NA 1.40E-06 mr1248 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
vg0725372026 NA 2.87E-18 mr1301 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
vg0725372026 NA 3.85E-09 mr1563 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
vg0725372026 NA 7.09E-08 mr1825 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
vg0725372026 NA 1.37E-06 mr1993 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
vg0725372026 NA 1.38E-13 mr1178_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
vg0725372026 NA 5.96E-06 mr1498_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
vg0725372026 NA 1.14E-11 mr1769_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
vg0725372026 NA 9.95E-14 mr1769_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
vg0725372026 NA 2.95E-11 mr1993_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