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Detailed information for vg0432825867:

Variant ID: vg0432825867 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 32825867
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TATGTATACTTTTATGAAAGTATTTTTCAAGACAAATATATTCATATAATTTTTACATTTTCAAACTCAATAACTTGAGAGTTATTTATGATTTATATTC[T/G]
CAAGGTTTGACTTAAATATTATTCTAAACGACTTTTTTTTTTTTTGAGTATAGAGGGAGTACAAGCCTACTGTATGACCATGTCCAGTTGATTACGCGAA

Reverse complement sequence

TTCGCGTAATCAACTGGACATGGTCATACAGTAGGCTTGTACTCCCTCTATACTCAAAAAAAAAAAAAGTCGTTTAGAATAATATTTAAGTCAAACCTTG[A/C]
GAATATAAATCATAAATAACTCTCAAGTTATTGAGTTTGAAAATGTAAAAATTATATGAATATATTTGTCTTGAAAAATACTTTCATAAAAGTATACATA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 75.20% 4.90% 12.15% 7.68% NA
All Indica  2759 77.00% 0.10% 12.18% 10.66% NA
All Japonica  1512 68.90% 13.50% 14.22% 3.37% NA
Aus  269 90.70% 1.10% 4.46% 3.72% NA
Indica I  595 68.90% 0.20% 23.19% 7.73% NA
Indica II  465 69.00% 0.20% 12.69% 18.06% NA
Indica III  913 86.30% 0.00% 4.71% 8.98% NA
Indica Intermediate  786 77.10% 0.30% 12.21% 10.43% NA
Temperate Japonica  767 72.00% 6.30% 17.08% 4.69% NA
Tropical Japonica  504 75.20% 16.30% 6.35% 2.18% NA
Japonica Intermediate  241 46.10% 30.70% 21.58% 1.66% NA
VI/Aromatic  96 78.10% 16.70% 3.12% 2.08% NA
Intermediate  90 77.80% 6.70% 8.89% 6.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0432825867 T -> DEL N N silent_mutation Average:93.219; most accessible tissue: Minghui63 root, score: 97.93 N N N N
vg0432825867 T -> G LOC_Os04g55220.1 upstream_gene_variant ; 891.0bp to feature; MODIFIER silent_mutation Average:93.219; most accessible tissue: Minghui63 root, score: 97.93 N N N N
vg0432825867 T -> G LOC_Os04g55210.1 downstream_gene_variant ; 435.0bp to feature; MODIFIER silent_mutation Average:93.219; most accessible tissue: Minghui63 root, score: 97.93 N N N N
vg0432825867 T -> G LOC_Os04g55210-LOC_Os04g55220 intergenic_region ; MODIFIER silent_mutation Average:93.219; most accessible tissue: Minghui63 root, score: 97.93 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)
vg0432825867 T G 0.0 0.01 0.01 0.0 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0432825867 NA 2.45E-06 mr1113 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
vg0432825867 1.54E-07 5.98E-08 mr1114 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
vg0432825867 2.67E-07 1.20E-07 mr1116 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
vg0432825867 1.88E-07 1.19E-08 mr1117 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
vg0432825867 2.61E-06 1.36E-06 mr1118 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
vg0432825867 8.99E-06 6.83E-06 mr1120 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
vg0432825867 2.58E-06 6.40E-07 mr1123 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
vg0432825867 1.52E-06 2.92E-07 mr1240 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
vg0432825867 4.83E-06 1.22E-06 mr1247 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
vg0432825867 1.07E-07 2.59E-08 mr1496 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
vg0432825867 3.09E-08 3.27E-09 mr1917 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
vg0432825867 6.65E-07 1.16E-07 mr1936 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
vg0432825867 3.67E-06 1.23E-07 mr1117_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
vg0432825867 NA 9.87E-07 mr1119_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
vg0432825867 NA 7.70E-06 mr1120_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
vg0432825867 NA 1.94E-06 mr1247_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
vg0432825867 NA 1.29E-06 mr1496_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