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Detailed information for vg0519115261:

Variant ID: vg0519115261 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 19115261
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCGGATCCGTGCTCGCGCTCATCCTCCTCCTCGTCCTCTTCACCGTCGCGGCGCGGGCGCAACAGGAGTACGAGGTCACCTCCTCCTCGTCCTCCTTGCC[G/A]
TCGTGGCGCGGCGCGGGCGAGGGCCATCGGCCGCCGCCTCGGGCGAGGGCCATCGTTCTGCTCCTCCCCACTGCTCTACGCTTCCGCCGTCTTCATCTCC

Reverse complement sequence

GGAGATGAAGACGGCGGAAGCGTAGAGCAGTGGGGAGGAGCAGAACGATGGCCCTCGCCCGAGGCGGCGGCCGATGGCCCTCGCCCGCGCCGCGCCACGA[C/T]
GGCAAGGAGGACGAGGAGGAGGTGACCTCGTACTCCTGTTGCGCCCGCGCCGCGACGGTGAAGAGGACGAGGAGGAGGATGAGCGCGAGCACGGATCCGG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.90% 3.70% 0.95% 0.42% NA
All Indica  2759 97.80% 0.00% 1.52% 0.69% NA
All Japonica  1512 88.20% 11.60% 0.13% 0.07% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.50% 0.00% 0.50% 0.00% NA
Indica II  465 93.50% 0.00% 4.52% 1.94% NA
Indica III  913 98.70% 0.00% 0.55% 0.77% NA
Indica Intermediate  786 98.00% 0.00% 1.65% 0.38% NA
Temperate Japonica  767 92.30% 7.40% 0.13% 0.13% NA
Tropical Japonica  504 89.30% 10.70% 0.00% 0.00% NA
Japonica Intermediate  241 73.00% 26.60% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 0.00% 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
vg0519115261 G -> DEL LOC_Os05g32640.1 N frameshift_variant Average:94.193; most accessible tissue: Zhenshan97 panicle, score: 98.935 N N N N
vg0519115261 G -> A LOC_Os05g32640.1 synonymous_variant ; p.Pro38Pro; LOW synonymous_codon Average:94.193; most accessible tissue: Zhenshan97 panicle, score: 98.935 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)
vg0519115261 G A -0.04 -0.04 -0.04 -0.03 -0.04 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0519115261 8.01E-06 2.55E-07 mr1114 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
vg0519115261 9.44E-06 1.68E-08 mr1117 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
vg0519115261 NA 6.83E-07 mr1118 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
vg0519115261 5.97E-06 4.41E-07 mr1119 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
vg0519115261 NA 7.05E-07 mr1123 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
vg0519115261 NA 6.45E-07 mr1240 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
vg0519115261 NA 5.82E-07 mr1242 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
vg0519115261 3.30E-07 5.38E-09 mr1247 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
vg0519115261 3.07E-06 7.81E-09 mr1496 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
vg0519115261 8.59E-06 1.59E-07 mr1917 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
vg0519115261 NA 4.74E-08 mr1117_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
vg0519115261 NA 3.22E-06 mr1496_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