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Detailed information for vg0601414570:

Variant ID: vg0601414570 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 1414570
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGGGAGAAGAAGAGGAGGAGAGGAGGATGCTGGGAGCGAGCCCTAAGGCCAAGAAAGGCGCGACGGTGAAGTTCGGGTCGATGAAGAATCCTCCTCCTCC[C/T]
CCGGTGGTTGGCGCCGCCGCCGGAGCAGCGGCGGCGGCGGCGGGTGGGAAGGTGCCGGCGGAGGAGGTGTGGGAGGTGCGGCCAGGCGGGATGCTGGTGC

Reverse complement sequence

GCACCAGCATCCCGCCTGGCCGCACCTCCCACACCTCCTCCGCCGGCACCTTCCCACCCGCCGCCGCCGCCGCTGCTCCGGCGGCGGCGCCAACCACCGG[G/A]
GGAGGAGGAGGATTCTTCATCGACCCGAACTTCACCGTCGCGCCTTTCTTGGCCTTAGGGCTCGCTCCCAGCATCCTCCTCTCCTCCTCTTCTTCTCCCC

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 81.10% 18.90% 0.04% 0.00% NA
All Indica  2759 78.10% 21.80% 0.04% 0.00% NA
All Japonica  1512 90.70% 9.30% 0.00% 0.00% NA
Aus  269 67.70% 32.30% 0.00% 0.00% NA
Indica I  595 94.80% 5.20% 0.00% 0.00% NA
Indica II  465 71.80% 28.00% 0.22% 0.00% NA
Indica III  913 70.90% 29.10% 0.00% 0.00% NA
Indica Intermediate  786 77.70% 22.30% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 73.00% 27.00% 0.00% 0.00% NA
Japonica Intermediate  241 97.90% 2.10% 0.00% 0.00% NA
VI/Aromatic  96 60.40% 39.60% 0.00% 0.00% NA
Intermediate  90 71.10% 27.80% 1.11% 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
vg0601414570 C -> T LOC_Os06g03640.1 synonymous_variant ; p.Pro25Pro; LOW synonymous_codon Average:83.559; most accessible tissue: Minghui63 young leaf, score: 93.647 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)
vg0601414570 C T -0.02 -0.01 -0.02 -0.02 -0.02 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0601414570 7.15E-07 2.53E-09 mr1310 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
vg0601414570 NA 3.37E-10 mr1498 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
vg0601414570 NA 3.08E-06 mr1310_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
vg0601414570 NA 1.15E-09 mr1769_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
vg0601414570 NA 2.08E-06 mr1951_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