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Detailed information for vg1214008434:

Variant ID: vg1214008434 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 14008434
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAATATTGGTGTTTGTTTTTCTCTAAAACCGACACATATAATTGTTCAAAGGTGCCGATTATATATTCGATCGCATGAGTGGGTTTATCTATTTCGGCAC[C/T]
AATATACCAACCTTTATGTGCTTTTTTATAGTAGTGCTTCCTAATTCTCAAATAAAAAGAAATAGACACCAAGCAAGAAATTGGTGTCAATGGTTTCTGC

Reverse complement sequence

GCAGAAACCATTGACACCAATTTCTTGCTTGGTGTCTATTTCTTTTTATTTGAGAATTAGGAAGCACTACTATAAAAAAGCACATAAAGGTTGGTATATT[G/A]
GTGCCGAAATAGATAAACCCACTCATGCGATCGAATATATAATCGGCACCTTTGAACAATTATATGTGTCGGTTTTAGAGAAAAACAAACACCAATATTA

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 85.90% 11.10% 0.97% 2.01% NA
All Indica  2759 97.00% 2.60% 0.11% 0.29% NA
All Japonica  1512 66.80% 26.40% 1.98% 4.83% NA
Aus  269 83.60% 11.90% 0.74% 3.72% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 89.20% 10.10% 0.22% 0.43% NA
Indica III  913 98.60% 0.90% 0.22% 0.33% NA
Indica Intermediate  786 97.60% 2.00% 0.00% 0.38% NA
Temperate Japonica  767 89.20% 9.40% 0.52% 0.91% NA
Tropical Japonica  504 33.70% 50.80% 3.97% 11.51% NA
Japonica Intermediate  241 64.70% 29.50% 2.49% 3.32% NA
VI/Aromatic  96 82.30% 10.40% 6.25% 1.04% NA
Intermediate  90 77.80% 13.30% 5.56% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1214008434 C -> DEL N N silent_mutation Average:75.227; most accessible tissue: Zhenshan97 young leaf, score: 85.184 N N N N
vg1214008434 C -> T LOC_Os12g24530.1 downstream_gene_variant ; 1582.0bp to feature; MODIFIER silent_mutation Average:75.227; most accessible tissue: Zhenshan97 young leaf, score: 85.184 N N N N
vg1214008434 C -> T LOC_Os12g24540.1 downstream_gene_variant ; 4357.0bp to feature; MODIFIER silent_mutation Average:75.227; most accessible tissue: Zhenshan97 young leaf, score: 85.184 N N N N
vg1214008434 C -> T LOC_Os12g24519-LOC_Os12g24530 intergenic_region ; MODIFIER silent_mutation Average:75.227; most accessible tissue: Zhenshan97 young leaf, score: 85.184 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)
vg1214008434 C T 0.07 0.01 0.01 0.01 0.02 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1214008434 NA 6.81E-07 mr1058 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
vg1214008434 3.29E-06 3.29E-06 mr1058 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
vg1214008434 3.75E-06 NA mr1284 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
vg1214008434 1.30E-06 NA mr1293 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
vg1214008434 2.74E-06 1.38E-06 mr1293 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
vg1214008434 NA 1.68E-06 mr1345 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
vg1214008434 8.36E-06 3.31E-06 mr1345 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
vg1214008434 6.31E-06 6.30E-06 mr1494 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
vg1214008434 1.10E-06 NA mr1604 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
vg1214008434 7.70E-07 1.34E-06 mr1604 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
vg1214008434 9.63E-08 9.62E-08 mr1605 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
vg1214008434 NA 8.39E-07 mr1653 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
vg1214008434 2.53E-06 8.73E-08 mr1700 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
vg1214008434 4.67E-06 NA mr1809 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
vg1214008434 5.68E-06 NA mr1810 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
vg1214008434 3.95E-06 3.96E-06 mr1813 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
vg1214008434 4.05E-06 4.05E-06 mr1813 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
vg1214008434 4.08E-08 4.06E-08 mr1856 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