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Detailed information for vg1200140958:

Variant ID: vg1200140958 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 140958
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:


GAAGATGATGATCCATATTGGATCCGGCGGGGGCGGGGGGCAAGGGAAGTTGGAGGTGGGCGAGGGCGGCGCGGGCGGCGGCCACCATGGGGTGCTCCGA[C/T]
CCGGACATAGCTCACCACGACGACGAGCAGGAGGATTTGCGGCGGCCGGCGGGGGGTAGTTCCCCGTCCCCGGCCGCGGAGGAGGAAGAAGAGGCCACCA

Reverse complement sequence

TGGTGGCCTCTTCTTCCTCCTCCGCGGCCGGGGACGGGGAACTACCCCCCGCCGGCCGCCGCAAATCCTCCTGCTCGTCGTCGTGGTGAGCTATGTCCGG[G/A]
TCGGAGCACCCCATGGTGGCCGCCGCCCGCGCCGCCCTCGCCCACCTCCAACTTCCCTTGCCCCCCGCCCCCGCCGGATCCAATATGGATCATCATCTTC

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 92.60% 6.60% 0.17% 0.61% NA
All Indica  2759 89.60% 9.20% 0.22% 0.98% NA
All Japonica  1512 98.40% 1.50% 0.07% 0.00% NA
Aus  269 99.30% 0.00% 0.00% 0.74% NA
Indica I  595 91.40% 7.60% 0.50% 0.50% NA
Indica II  465 94.40% 5.40% 0.00% 0.22% NA
Indica III  913 85.20% 12.90% 0.11% 1.75% NA
Indica Intermediate  786 90.30% 8.50% 0.25% 0.89% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 95.80% 4.00% 0.20% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 71.90% 27.10% 1.04% 0.00% NA
Intermediate  90 88.90% 11.10% 0.00% 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
vg1200140958 C -> DEL LOC_Os12g01240.1 N frameshift_variant Average:96.429; most accessible tissue: Minghui63 panicle, score: 98.021 N N N N
vg1200140958 C -> T LOC_Os12g01240.1 synonymous_variant ; p.Gly3Gly; LOW synonymous_codon Average:96.429; most accessible tissue: Minghui63 panicle, score: 98.021 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)
vg1200140958 C T 0.0 -0.01 0.0 -0.02 0.0 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1200140958 NA 1.96E-06 mr1216 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
vg1200140958 NA 6.26E-06 mr1448 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
vg1200140958 1.02E-06 NA mr1350_2 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
vg1200140958 8.70E-06 2.95E-07 mr1350_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