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Detailed information for vg0912636580:

Variant ID: vg0912636580 (JBrowse)Variation Type: INDEL
Chromosome: chr09Position: 12636580
Reference Allele: TTTGCAlternative Allele: GTTGC,T
Primary Allele: TTTGCSecondary Allele: GTTGC

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGCCCCCAGGAAATGGACGAACTAGCTGAAGCACTAGCAGCCACAACGCCGACCTGACCTGACCCAGCTGATCGATGGCGAGCTTACATCGGTACCTTTG[TTTGC/GTTGC,T]
GTTTAGTTCACATCAAAATTAAAAATTTAGTTAAAATTAGAACTATATGATAGAAAGGTTAGAAGTTTATATGTATAAAAAAGTTTTCATGTGATAGAAA

Reverse complement sequence

TTTCTATCACATGAAAACTTTTTTATACATATAAACTTCTAACCTTTCTATCATATAGTTCTAATTTTAACTAAATTTTTAATTTTGATGTGAACTAAAC[GCAAA/GCAAC,A]
CAAAGGTACCGATGTAAGCTCGCCATCGATCAGCTGGGTCAGGTCAGGTCGGCGTTGTGGCTGCTAGTGCTTCAGCTAGTTCGTCCATTTCCTGGGGGCC

Allele Frequencies:

Populations Population SizeFrequency of TTTGC(primary allele) Frequency of GTTGC(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.20% 3.80% 0.87% 0.00% T: 0.11%
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 86.10% 11.40% 2.51% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 99.10% 0.40% 0.52% 0.00% NA
Tropical Japonica  504 62.90% 32.10% 4.96% 0.00% NA
Japonica Intermediate  241 93.40% 2.90% 3.73% 0.00% NA
VI/Aromatic  96 94.80% 0.00% 0.00% 0.00% T: 5.21%
Intermediate  90 91.10% 6.70% 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
vg0912636580 TTTGC -> T LOC_Os09g20980.1 upstream_gene_variant ; 1059.0bp to feature; MODIFIER silent_mutation Average:80.045; most accessible tissue: Zhenshan97 panicle, score: 92.533 N N N N
vg0912636580 TTTGC -> T LOC_Os09g20970-LOC_Os09g20980 intergenic_region ; MODIFIER silent_mutation Average:80.045; most accessible tissue: Zhenshan97 panicle, score: 92.533 N N N N
vg0912636580 TTTGC -> GTTGC LOC_Os09g20980.1 upstream_gene_variant ; 1060.0bp to feature; MODIFIER silent_mutation Average:80.045; most accessible tissue: Zhenshan97 panicle, score: 92.533 N N N N
vg0912636580 TTTGC -> GTTGC LOC_Os09g20970-LOC_Os09g20980 intergenic_region ; MODIFIER silent_mutation Average:80.045; most accessible tissue: Zhenshan97 panicle, score: 92.533 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)
vg0912636580 TTTGC GTTGC 0.0 0.0 0.0 0.01 0.0 0.0
vg0912636580 TTTGC T -0.13 0.13 -0.04 0.03 -0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0912636580 NA 1.29E-06 mr1082 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
vg0912636580 NA 8.55E-08 mr1083 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
vg0912636580 NA 1.59E-06 mr1226 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
vg0912636580 1.04E-07 1.04E-07 mr1076_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
vg0912636580 NA 3.11E-06 mr1082_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
vg0912636580 NA 1.52E-07 mr1083_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
vg0912636580 NA 1.44E-06 mr1104_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
vg0912636580 7.79E-06 7.79E-06 mr1145_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
vg0912636580 NA 2.09E-07 mr1226_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
vg0912636580 2.89E-06 NA mr1437_2 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