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Detailed information for vg0722275425:

Variant ID: vg0722275425 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 22275425
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AATAACCCAATCTGAAATTCGCTCCATGGAAAATAATAAACTTCGTGAGACCCACATAGACGCCACGTTAGCCAAAACCGTCCCCAAAACCACCGAGGGA[T/C]
CTTATCTGCACTGGTTTTGATAGTTGAGTTGAAGGATGAATATCAGATTCGTCTACAAGTTAAGAGACCTCAGATGAACTTATTCCAACAAAAAAAATTG

Reverse complement sequence

CAATTTTTTTTGTTGGAATAAGTTCATCTGAGGTCTCTTAACTTGTAGACGAATCTGATATTCATCCTTCAACTCAACTATCAAAACCAGTGCAGATAAG[A/G]
TCCCTCGGTGGTTTTGGGGACGGTTTTGGCTAACGTGGCGTCTATGTGGGTCTCACGAAGTTTATTATTTTCCATGGAGCGAATTTCAGATTGGGTTATT

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 67.80% 32.00% 0.08% 0.17% NA
All Indica  2759 96.90% 2.80% 0.04% 0.25% NA
All Japonica  1512 7.70% 92.20% 0.07% 0.07% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 94.40% 4.70% 0.00% 0.86% NA
Indica III  913 99.10% 0.80% 0.11% 0.00% NA
Indica Intermediate  786 93.60% 6.00% 0.00% 0.38% NA
Temperate Japonica  767 2.00% 97.80% 0.13% 0.13% NA
Tropical Japonica  504 14.30% 85.70% 0.00% 0.00% NA
Japonica Intermediate  241 12.00% 88.00% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 60.00% 37.80% 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
vg0722275425 T -> DEL N N silent_mutation Average:93.575; most accessible tissue: Callus, score: 96.027 N N N N
vg0722275425 T -> C LOC_Os07g37180.1 upstream_gene_variant ; 1809.0bp to feature; MODIFIER silent_mutation Average:93.575; most accessible tissue: Callus, score: 96.027 N N N N
vg0722275425 T -> C LOC_Os07g37180.2 upstream_gene_variant ; 1809.0bp to feature; MODIFIER silent_mutation Average:93.575; most accessible tissue: Callus, score: 96.027 N N N N
vg0722275425 T -> C LOC_Os07g37180-LOC_Os07g37190 intergenic_region ; MODIFIER silent_mutation Average:93.575; most accessible tissue: Callus, score: 96.027 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)
vg0722275425 T C 0.09 0.13 0.09 0.08 0.08 0.09

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0722275425 NA 7.48E-07 mr1082 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
vg0722275425 NA 1.96E-31 mr1107 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
vg0722275425 NA 9.86E-32 mr1213 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
vg0722275425 NA 1.10E-08 mr1226 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
vg0722275425 NA 8.73E-12 mr1233 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
vg0722275425 NA 3.38E-07 mr1411 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
vg0722275425 NA 8.12E-06 mr1437 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
vg0722275425 NA 2.12E-07 mr1613 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
vg0722275425 NA 2.12E-06 mr1620 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
vg0722275425 NA 9.72E-09 mr1644 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
vg0722275425 NA 3.87E-06 mr1913 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
vg0722275425 NA 1.90E-16 mr1949 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
vg0722275425 NA 1.67E-07 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
vg0722275425 NA 1.43E-37 mr1104_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
vg0722275425 NA 1.46E-36 mr1107_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
vg0722275425 NA 2.05E-29 mr1233_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
vg0722275425 NA 6.54E-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
vg0722275425 NA 2.38E-51 mr1404_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
vg0722275425 NA 7.39E-06 mr1613_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
vg0722275425 NA 4.98E-10 mr1806_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
vg0722275425 NA 9.87E-27 mr1949_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