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Detailed information for vg0301153934:

Variant ID: vg0301153934 (JBrowse)Variation Type: INDEL
Chromosome: chr03Position: 1153934
Reference Allele: GAlternative Allele: C,GCCGCCGCCGC
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACGCACCGCTTCGCCCACCACCTCCCTTCCTCCATCCCCTTCGCTCCCTGGGCGCACCACCACGGACACGGAGCCGCCGCCGCCGCCGCCGCCGCCGCCG[G/C,GCCGCCGCCGC]
CGCCAGGTTTCTCCTGCCTCCCTCCTCGACTCCCATCTACGACCACCACCGCCGACACGCCCACGCCGTCGGGTACGACGCGTACGCCGCGGCCACCAGC

Reverse complement sequence

GCTGGTGGCCGCGGCGTACGCGTCGTACCCGACGGCGTGGGCGTGTCGGCGGTGGTGGTCGTAGATGGGAGTCGAGGAGGGAGGCAGGAGAAACCTGGCG[C/G,GCGGCGGCGGC]
CGGCGGCGGCGGCGGCGGCGGCGGCGGCTCCGTGTCCGTGGTGGTGCGCCCAGGGAGCGAAGGGGATGGAGGAAGGGAGGTGGTGGGCGAAGCGGTGCGT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 79.10% 19.90% 0.97% 0.00% GCCGCCGCCGC: 0.06%
All Indica  2759 98.20% 1.80% 0.04% 0.00% GCCGCCGCCGC: 0.04%
All Japonica  1512 55.80% 41.60% 2.51% 0.00% GCCGCCGCCGC: 0.13%
Aus  269 25.70% 73.20% 1.12% 0.00% NA
Indica I  595 98.50% 1.50% 0.00% 0.00% NA
Indica II  465 98.70% 1.30% 0.00% 0.00% NA
Indica III  913 99.20% 0.70% 0.00% 0.00% GCCGCCGCCGC: 0.11%
Indica Intermediate  786 96.30% 3.60% 0.13% 0.00% NA
Temperate Japonica  767 74.30% 23.50% 2.22% 0.00% NA
Tropical Japonica  504 20.40% 76.20% 2.98% 0.00% GCCGCCGCCGC: 0.40%
Japonica Intermediate  241 70.50% 27.00% 2.49% 0.00% NA
VI/Aromatic  96 53.10% 46.90% 0.00% 0.00% NA
Intermediate  90 73.30% 22.20% 4.44% 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
vg0301153934 G -> C LOC_Os03g02900.1 N nonsynonymous_codon ; G185A Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 unknown unknown TOLERATED 0.10
vg0301153934 G -> GCCGCCGCCGC LOC_Os03g02900.1 frameshift_variant ; p.Ala186fs; HIGH frameshift_variant Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 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)
vg0301153934 G C -0.01 0.0 0.0 0.0 0.0 0.0
vg0301153934 G GCCGC* 0.34 0.25 0.19 0.18 0.24 0.21

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0301153934 NA 7.79E-08 mr1249 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
vg0301153934 NA 1.67E-07 mr1559 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
vg0301153934 NA 8.39E-09 mr1002_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
vg0301153934 NA 3.31E-06 mr1092_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
vg0301153934 NA 6.91E-06 mr1152_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
vg0301153934 NA 1.44E-06 mr1154_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
vg0301153934 NA 6.55E-21 mr1164_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
vg0301153934 NA 2.40E-07 mr1164_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
vg0301153934 NA 4.30E-06 mr1263_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
vg0301153934 NA 2.55E-06 mr1359_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
vg0301153934 NA 1.38E-07 mr1548_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