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Detailed information for vg0722872422:

Variant ID: vg0722872422 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 22872422
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCCAATTTCCTGGCCCATGTACGCAGATAGGCTAGATCTATTATATTATTAAGACAGCTCGAAAAGAAGACATCACGTTTACCGTGGAGGCTAGAAATTC[T/C]
CACGTTAATCGAAGAAAATATAAATTATTTACACCGTTGGATTGTAAGAGGCATAGATTTCAATGTCTGAGATTTAACACAAACTTAGCATGTTAACTGA

Reverse complement sequence

TCAGTTAACATGCTAAGTTTGTGTTAAATCTCAGACATTGAAATCTATGCCTCTTACAATCCAACGGTGTAAATAATTTATATTTTCTTCGATTAACGTG[A/G]
GAATTTCTAGCCTCCACGGTAAACGTGATGTCTTCTTTTCGAGCTGTCTTAATAATATAATAGATCTAGCCTATCTGCGTACATGGGCCAGGAAATTGGG

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 29.90% 28.40% 1.40% 40.29% NA
All Indica  2759 28.50% 4.90% 1.20% 65.39% NA
All Japonica  1512 17.90% 78.00% 1.65% 2.38% NA
Aus  269 81.40% 0.70% 1.12% 16.73% NA
Indica I  595 3.20% 3.40% 3.53% 89.92% NA
Indica II  465 41.10% 8.60% 1.29% 49.03% NA
Indica III  913 39.40% 1.30% 0.33% 58.93% NA
Indica Intermediate  786 27.60% 8.00% 0.38% 63.99% NA
Temperate Japonica  767 16.40% 80.30% 1.30% 1.96% NA
Tropical Japonica  504 16.70% 81.50% 0.40% 1.39% NA
Japonica Intermediate  241 25.30% 63.50% 5.39% 5.81% NA
VI/Aromatic  96 99.00% 0.00% 1.04% 0.00% NA
Intermediate  90 45.60% 28.90% 4.44% 21.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0722872422 T -> DEL N N silent_mutation Average:86.942; most accessible tissue: Minghui63 panicle, score: 96.296 N N N N
vg0722872422 T -> C LOC_Os07g38130.1 downstream_gene_variant ; 1830.0bp to feature; MODIFIER silent_mutation Average:86.942; most accessible tissue: Minghui63 panicle, score: 96.296 N N N N
vg0722872422 T -> C LOC_Os07g38120-LOC_Os07g38130 intergenic_region ; MODIFIER silent_mutation Average:86.942; most accessible tissue: Minghui63 panicle, score: 96.296 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)
vg0722872422 T C -0.01 -0.01 -0.02 0.0 -0.01 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0722872422 NA 2.39E-14 Awn_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
vg0722872422 NA 5.89E-07 mr1057 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
vg0722872422 NA 1.85E-06 mr1201 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
vg0722872422 NA 3.30E-06 mr1274 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
vg0722872422 NA 5.96E-07 mr1530 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
vg0722872422 NA 5.69E-09 mr1624 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
vg0722872422 NA 2.64E-08 mr1860 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
vg0722872422 NA 1.38E-08 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
vg0722872422 NA 1.68E-08 mr1057_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
vg0722872422 NA 7.50E-10 mr1126_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
vg0722872422 NA 2.38E-10 mr1166_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
vg0722872422 NA 3.53E-07 mr1585_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
vg0722872422 NA 6.83E-08 mr1612_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
vg0722872422 NA 5.97E-10 mr1624_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
vg0722872422 NA 5.99E-06 mr1633_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
vg0722872422 NA 5.51E-07 mr1733_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
vg0722872422 NA 6.48E-08 mr1765_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
vg0722872422 NA 7.32E-06 mr1842_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