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Detailed information for vg1124948132:

Variant ID: vg1124948132 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 24948132
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTAATCAATTTGTCAACGCCCAAATACGAGCTTGTAGGGATTTTAGCTAAGCTCTCGGGCCTTCAGAAGAAGCGCTGCCGTTGGATCTATCATAGACGG[C/T]
CCAGATGGGGAGACACGTGGTTGGACTCACATTTTTGCGCATAAGCCCTCCGAGATTATATATAAAAAAGTATAATTTATTATTATATAGCACAAGTCAA

Reverse complement sequence

TTGACTTGTGCTATATAATAATAAATTATACTTTTTTATATATAATCTCGGAGGGCTTATGCGCAAAAATGTGAGTCCAACCACGTGTCTCCCCATCTGG[G/A]
CCGTCTATGATAGATCCAACGGCAGCGCTTCTTCTGAAGGCCCGAGAGCTTAGCTAAAATCCCTACAAGCTCGTATTTGGGCGTTGACAAATTGATTAAT

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 86.20% 13.80% 0.00% 0.00% NA
All Indica  2759 99.60% 0.40% 0.00% 0.00% NA
All Japonica  1512 58.40% 41.60% 0.00% 0.00% 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 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.80% 0.00% 0.00% NA
Temperate Japonica  767 42.20% 57.80% 0.00% 0.00% NA
Tropical Japonica  504 74.80% 25.20% 0.00% 0.00% NA
Japonica Intermediate  241 75.50% 24.50% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 88.90% 11.10% 0.00% 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
vg1124948132 C -> T LOC_Os11g41590.1 upstream_gene_variant ; 154.0bp to feature; MODIFIER silent_mutation Average:86.625; most accessible tissue: Minghui63 young leaf, score: 96.765 N N N N
vg1124948132 C -> T LOC_Os11g41600.1 downstream_gene_variant ; 2649.0bp to feature; MODIFIER silent_mutation Average:86.625; most accessible tissue: Minghui63 young leaf, score: 96.765 N N N N
vg1124948132 C -> T LOC_Os11g41600.2 downstream_gene_variant ; 2649.0bp to feature; MODIFIER silent_mutation Average:86.625; most accessible tissue: Minghui63 young leaf, score: 96.765 N N N N
vg1124948132 C -> T LOC_Os11g41580-LOC_Os11g41590 intergenic_region ; MODIFIER silent_mutation Average:86.625; most accessible tissue: Minghui63 young leaf, score: 96.765 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)
vg1124948132 C T -0.13 -0.23 -0.22 -0.22 -0.21 -0.27

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1124948132 2.24E-12 2.80E-27 mr1238 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
vg1124948132 7.18E-07 NA mr1238 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
vg1124948132 1.35E-08 NA mr1309 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
vg1124948132 NA 7.73E-06 mr1382 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
vg1124948132 3.78E-11 9.84E-21 mr1484 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
vg1124948132 6.96E-07 NA mr1484 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
vg1124948132 NA 3.21E-07 mr1696 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
vg1124948132 8.46E-07 NA mr1841 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
vg1124948132 8.24E-07 NA mr1900 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
vg1124948132 2.70E-14 8.19E-32 mr1238_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
vg1124948132 2.38E-08 7.88E-06 mr1238_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
vg1124948132 7.33E-14 6.22E-30 mr1484_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
vg1124948132 9.06E-11 NA mr1841_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
vg1124948132 8.29E-07 NA mr1841_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
vg1124948132 8.85E-10 3.79E-21 mr1900_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
vg1124948132 8.98E-07 NA mr1900_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
vg1124948132 3.99E-11 1.40E-22 mr1945_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