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Detailed information for vg1222644507:

Variant ID: vg1222644507 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 22644507
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AATCAAGCTAAGAGCATATTAGAGTGTAGTAGCAACTCGTTGTCAACCTTTTGCATGCTTTTCTGATGATTAAATAAACTATCATCAAGTAGCATATTAG[A/T]
TTGGACAAGGTCGCCCAAAAGATTCGATTTCCCCCTTTGTCCATATCTCTGAACATTCCTGTTCATCGTTCCATAGCTTTGTGTTTGTGTACATCCATCT

Reverse complement sequence

AGATGGATGTACACAAACACAAAGCTATGGAACGATGAACAGGAATGTTCAGAGATATGGACAAAGGGGGAAATCGAATCTTTTGGGCGACCTTGTCCAA[T/A]
CTAATATGCTACTTGATGATAGTTTATTTAATCATCAGAAAAGCATGCAAAAGGTTGACAACGAGTTGCTACTACACTCTAATATGCTCTTAGCTTGATT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.90% 2.10% 3.03% 0.00% NA
All Indica  2759 99.00% 0.00% 0.98% 0.00% NA
All Japonica  1512 86.30% 6.30% 7.34% 0.00% NA
Aus  269 99.30% 0.00% 0.74% 0.00% NA
Indica I  595 95.60% 0.20% 4.20% 0.00% NA
Indica II  465 99.80% 0.00% 0.22% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.00% 0.13% 0.00% NA
Temperate Japonica  767 78.20% 10.00% 11.73% 0.00% NA
Tropical Japonica  504 98.20% 0.00% 1.79% 0.00% NA
Japonica Intermediate  241 87.10% 7.90% 4.98% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 0.00% 3.33% 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
vg1222644507 A -> T LOC_Os12g36940.1 upstream_gene_variant ; 3613.0bp to feature; MODIFIER silent_mutation Average:64.762; most accessible tissue: Zhenshan97 root, score: 92.66 N N N N
vg1222644507 A -> T LOC_Os12g36920.1 downstream_gene_variant ; 4310.0bp to feature; MODIFIER silent_mutation Average:64.762; most accessible tissue: Zhenshan97 root, score: 92.66 N N N N
vg1222644507 A -> T LOC_Os12g36930.1 downstream_gene_variant ; 1420.0bp to feature; MODIFIER silent_mutation Average:64.762; most accessible tissue: Zhenshan97 root, score: 92.66 N N N N
vg1222644507 A -> T LOC_Os12g36930-LOC_Os12g36940 intergenic_region ; MODIFIER silent_mutation Average:64.762; most accessible tissue: Zhenshan97 root, score: 92.66 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)
vg1222644507 A T -0.04 -0.05 -0.06 -0.03 -0.01 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1222644507 7.87E-08 5.14E-11 mr1210 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
vg1222644507 5.96E-07 1.39E-09 mr1305 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
vg1222644507 4.00E-07 7.37E-12 mr1585 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
vg1222644507 5.45E-07 5.27E-10 mr1586 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
vg1222644507 1.19E-06 9.59E-09 mr1305_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
vg1222644507 7.29E-06 NA mr1559_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
vg1222644507 6.69E-06 6.13E-10 mr1585_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