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Detailed information for vg0613999068:

Variant ID: vg0613999068 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 13999068
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAGGCTAGCACCGGACCAGCCGCTGCTAAGCGTGACCGACCGCCGCTAGACCAACGCTCCACCACCACTCAACCTCTGCCGCCATGTGGGACCACTGCAC[C/T]
AGCGCCCCCCGCCGGCCAGCCTTCGTGCGCCAAAGACCACCAACATCCACTGGCAGCTCCTCCTCACGCCGAGGTCGCCTCCTCCACCGCCGACCACCCC

Reverse complement sequence

GGGGTGGTCGGCGGTGGAGGAGGCGACCTCGGCGTGAGGAGGAGCTGCCAGTGGATGTTGGTGGTCTTTGGCGCACGAAGGCTGGCCGGCGGGGGGCGCT[G/A]
GTGCAGTGGTCCCACATGGCGGCAGAGGTTGAGTGGTGGTGGAGCGTTGGTCTAGCGGCGGTCGGTCACGCTTAGCAGCGGCTGGTCCGGTGCTAGCCTT

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 91.50% 5.50% 3.05% 0.00% NA
All Indica  2759 86.30% 8.90% 4.78% 0.00% NA
All Japonica  1512 99.80% 0.10% 0.13% 0.00% NA
Aus  269 97.00% 0.00% 2.97% 0.00% NA
Indica I  595 81.00% 7.40% 11.60% 0.00% NA
Indica II  465 93.50% 1.70% 4.73% 0.00% NA
Indica III  913 91.50% 8.10% 0.44% 0.00% NA
Indica Intermediate  786 80.00% 15.30% 4.71% 0.00% NA
Temperate Japonica  767 99.70% 0.10% 0.13% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 89.60% 10.40% 0.00% 0.00% NA
Intermediate  90 94.40% 3.30% 2.22% 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
vg0613999068 C -> T LOC_Os06g23950.1 downstream_gene_variant ; 1749.0bp to feature; MODIFIER silent_mutation Average:70.589; most accessible tissue: Minghui63 panicle, score: 85.556 N N N N
vg0613999068 C -> T LOC_Os06g23960.1 downstream_gene_variant ; 361.0bp to feature; MODIFIER silent_mutation Average:70.589; most accessible tissue: Minghui63 panicle, score: 85.556 N N N N
vg0613999068 C -> T LOC_Os06g23970.1 downstream_gene_variant ; 3672.0bp to feature; MODIFIER silent_mutation Average:70.589; most accessible tissue: Minghui63 panicle, score: 85.556 N N N N
vg0613999068 C -> T LOC_Os06g23950-LOC_Os06g23960 intergenic_region ; MODIFIER silent_mutation Average:70.589; most accessible tissue: Minghui63 panicle, score: 85.556 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)
vg0613999068 C T -0.01 -0.01 -0.01 -0.01 -0.01 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0613999068 NA 4.28E-08 mr1020 Ind_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
vg0613999068 NA 3.98E-06 mr1021 Ind_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
vg0613999068 8.13E-06 4.16E-14 mr1032 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
vg0613999068 NA 1.01E-08 mr1032 Ind_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
vg0613999068 NA 4.54E-08 mr1165 Ind_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
vg0613999068 NA 1.50E-07 mr1477 Ind_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
vg0613999068 1.68E-06 1.34E-14 mr1478 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
vg0613999068 NA 7.78E-09 mr1478 Ind_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
vg0613999068 NA 8.29E-07 mr1503 Ind_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
vg0613999068 NA 2.48E-08 mr1627 Ind_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
vg0613999068 NA 7.12E-08 mr1971 Ind_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
vg0613999068 NA 1.35E-06 mr1165_2 Ind_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
vg0613999068 NA 3.53E-08 mr1183_2 Ind_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
vg0613999068 NA 3.54E-06 mr1268_2 Ind_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
vg0613999068 NA 1.39E-08 mr1478_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
vg0613999068 NA 4.23E-07 mr1478_2 Ind_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
vg0613999068 NA 5.05E-07 mr1971_2 Ind_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