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Detailed information for vg1123359940:

Variant ID: vg1123359940 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 23359940
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGAGTGCAGAGTGCAGAGCATAACCAAGCTAAATTGAAGGGGGGATACGCTGTTGGATAATGAAAATGTTCTCCCTTTTTTTATCCGACAATTTGCACTT[G/C]
ACCCCAAAACCAGCTCAAGTGACTAGTTCTAGTTCTAGTAGTACTAAGAACAAGTCAACTACTAGTCAATTTAATACTAGTCAATTTAATAGATAATTCA

Reverse complement sequence

TGAATTATCTATTAAATTGACTAGTATTAAATTGACTAGTAGTTGACTTGTTCTTAGTACTACTAGAACTAGAACTAGTCACTTGAGCTGGTTTTGGGGT[C/G]
AAGTGCAAATTGTCGGATAAAAAAAGGGAGAACATTTTCATTATCCAACAGCGTATCCCCCCTTCAATTTAGCTTGGTTATGCTCTGCACTCTGCACTCC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.00% 2.60% 0.36% 2.03% NA
All Indica  2759 98.30% 0.00% 0.14% 1.56% NA
All Japonica  1512 91.10% 8.10% 0.66% 0.20% NA
Aus  269 99.60% 0.00% 0.00% 0.37% NA
Indica I  595 96.00% 0.00% 0.50% 3.53% NA
Indica II  465 99.80% 0.00% 0.00% 0.22% NA
Indica III  913 99.90% 0.00% 0.00% 0.11% NA
Indica Intermediate  786 97.30% 0.00% 0.13% 2.54% NA
Temperate Japonica  767 91.00% 7.70% 1.30% 0.00% NA
Tropical Japonica  504 88.10% 11.70% 0.00% 0.20% NA
Japonica Intermediate  241 97.50% 1.70% 0.00% 0.83% NA
VI/Aromatic  96 52.10% 0.00% 2.08% 45.83% NA
Intermediate  90 91.10% 2.20% 1.11% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1123359940 G -> DEL N N silent_mutation Average:66.005; most accessible tissue: Zhenshan97 root, score: 94.19 N N N N
vg1123359940 G -> C LOC_Os11g39220.1 upstream_gene_variant ; 1622.0bp to feature; MODIFIER silent_mutation Average:66.005; most accessible tissue: Zhenshan97 root, score: 94.19 N N N N
vg1123359940 G -> C LOC_Os11g39220.2 upstream_gene_variant ; 2726.0bp to feature; MODIFIER silent_mutation Average:66.005; most accessible tissue: Zhenshan97 root, score: 94.19 N N N N
vg1123359940 G -> C LOC_Os11g39230.1 downstream_gene_variant ; 1194.0bp to feature; MODIFIER silent_mutation Average:66.005; most accessible tissue: Zhenshan97 root, score: 94.19 N N N N
vg1123359940 G -> C LOC_Os11g39220-LOC_Os11g39230 intergenic_region ; MODIFIER silent_mutation Average:66.005; most accessible tissue: Zhenshan97 root, score: 94.19 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)
vg1123359940 G C -0.4 -0.28 -0.15 -0.04 -0.13 -0.09

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1123359940 6.56E-07 6.55E-07 mr1068 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
vg1123359940 NA 5.29E-06 mr1078 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
vg1123359940 1.12E-06 6.47E-07 mr1211 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