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Detailed information for vg0211320189:

Variant ID: vg0211320189 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 11320189
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACAAGGCGGCGCGGGAAGGGATCAGGCGGGAGGTGGATGGGACTGCGGAGGGAGTTGGAGGGGAACACGTCGGGAGGCGACGGATTTGGGGTTACGGCGG[A/C]
GATGGCGCCGGCAAGATGAGAAAAGCGGATCTGAGGCCAATGAGTCGATACCTATGCGATTTGAGGTGAGCCGAGCGAGGCTGGATTTTTCGCATTTTGA

Reverse complement sequence

TCAAAATGCGAAAAATCCAGCCTCGCTCGGCTCACCTCAAATCGCATAGGTATCGACTCATTGGCCTCAGATCCGCTTTTCTCATCTTGCCGGCGCCATC[T/G]
CCGCCGTAACCCCAAATCCGTCGCCTCCCGACGTGTTCCCCTCCAACTCCCTCCGCAGTCCCATCCACCTCCCGCCTGATCCCTTCCCGCGCCGCCTTGT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.40% 5.50% 0.72% 0.38% NA
All Indica  2759 99.60% 0.40% 0.04% 0.00% NA
All Japonica  1512 81.00% 15.70% 2.12% 1.12% 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% 0.90% 0.22% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.40% 0.60% 0.00% 0.00% NA
Temperate Japonica  767 96.10% 3.00% 0.91% 0.00% NA
Tropical Japonica  504 56.50% 36.50% 4.17% 2.78% NA
Japonica Intermediate  241 84.20% 12.90% 1.66% 1.24% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 86.70% 11.10% 1.11% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0211320189 A -> DEL N N silent_mutation Average:85.938; most accessible tissue: Zhenshan97 panicle, score: 90.268 N N N N
vg0211320189 A -> C LOC_Os02g19380.1 upstream_gene_variant ; 1575.0bp to feature; MODIFIER silent_mutation Average:85.938; most accessible tissue: Zhenshan97 panicle, score: 90.268 N N N N
vg0211320189 A -> C LOC_Os02g19380-LOC_Os02g19390 intergenic_region ; MODIFIER silent_mutation Average:85.938; most accessible tissue: Zhenshan97 panicle, score: 90.268 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)
vg0211320189 A C 0.07 0.11 0.15 0.09 0.09 0.11

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0211320189 NA 6.68E-06 mr1124 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
vg0211320189 NA 6.02E-10 mr1251 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
vg0211320189 NA 7.97E-11 mr1435 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
vg0211320189 NA 1.21E-10 mr1539 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
vg0211320189 NA 3.70E-29 mr1699 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
vg0211320189 NA 8.61E-13 mr1732 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
vg0211320189 NA 1.63E-06 mr1039_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
vg0211320189 NA 3.64E-09 mr1379_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
vg0211320189 NA 3.72E-08 mr1510_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
vg0211320189 NA 1.14E-06 mr1510_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
vg0211320189 NA 7.03E-07 mr1632_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
vg0211320189 NA 9.26E-09 mr1696_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
vg0211320189 NA 3.05E-07 mr1696_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
vg0211320189 NA 1.59E-11 mr1705_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
vg0211320189 NA 1.63E-06 mr1705_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
vg0211320189 NA 5.37E-09 mr1807_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
vg0211320189 NA 4.33E-09 mr1819_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
vg0211320189 NA 5.18E-09 mr1905_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