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Detailed information for vg1127656762:

Variant ID: vg1127656762 (JBrowse)Variation Type: INDEL
Chromosome: chr11Position: 27656762
Reference Allele: TAlternative Allele: A,TTGCCGTCGCCGGTGCAGTTGAGTTACTTA
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.91, A: 0.09, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:


AGGTGGGTTTGAACTACTCGCCGTCGCCGGTGCAGTTGAATTACTTGCCGTCACCGGTGCAGTTGAGTTGCTGGGTGTCGCCGGTGCAGTTGAGTTACTT[T/A,TTGCCGTCGCCGGTGCAGTTGAGTTACTTA]
CCGTTGCCGTCGCCGGTGCAGTTGAGTTCCTGGGTATCGCCGATGCGGTTGATTTACTCGCCGTCGAGGTAGATGCCGCTGATTTCCCGCTATTCGATGT

Reverse complement sequence

ACATCGAATAGCGGGAAATCAGCGGCATCTACCTCGACGGCGAGTAAATCAACCGCATCGGCGATACCCAGGAACTCAACTGCACCGGCGACGGCAACGG[A/T,TAAGTAACTCAACTGCACCGGCGACGGCAA]
AAGTAACTCAACTGCACCGGCGACACCCAGCAACTCAACTGCACCGGTGACGGCAAGTAATTCAACTGCACCGGCGACGGCGAGTAGTTCAAACCCACCT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 54.60% 45.20% 0.17% 0.00% TTGCCGTCGCCGGTGCAGTTGAGTTACTTA: 0.06%
All Indica  2759 41.60% 58.30% 0.11% 0.00% NA
All Japonica  1512 77.70% 22.10% 0.20% 0.00% NA
Aus  269 44.20% 53.90% 0.74% 0.00% TTGCCGTCGCCGGTGCAGTTGAGTTACTTA: 1.12%
Indica I  595 11.30% 88.60% 0.17% 0.00% NA
Indica II  465 19.80% 80.20% 0.00% 0.00% NA
Indica III  913 66.50% 33.40% 0.11% 0.00% NA
Indica Intermediate  786 48.60% 51.30% 0.13% 0.00% NA
Temperate Japonica  767 86.80% 13.00% 0.13% 0.00% NA
Tropical Japonica  504 62.30% 37.50% 0.20% 0.00% NA
Japonica Intermediate  241 80.90% 18.70% 0.41% 0.00% NA
VI/Aromatic  96 81.20% 18.80% 0.00% 0.00% NA
Intermediate  90 66.70% 33.30% 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
vg1127656762 T -> TTGCCGTCGCCGGTGCAGTTGAGTTACTTA LOC_Os11g45720.1 frameshift_variant ; p.Glu429fs; HIGH frameshift_variant Average:85.49; most accessible tissue: Callus, score: 93.202 N N N N
vg1127656762 T -> A LOC_Os11g45720.1 missense_variant ; p.Glu429Val; MODERATE nonsynonymous_codon ; E429V Average:85.49; most accessible tissue: Callus, score: 93.202 unknown unknown TOLERATED 0.07

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)
vg1127656762 T A -0.01 0.0 -0.01 -0.01 -0.02 -0.02
vg1127656762 T TTGCC* 0.01 0.25 0.3 0.08 0.14 0.19

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1127656762 1.97E-07 7.04E-16 mr1133 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
vg1127656762 NA 2.12E-06 mr1667 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
vg1127656762 9.48E-07 NA mr1133_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
vg1127656762 2.55E-06 1.82E-13 mr1133_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
vg1127656762 NA 3.43E-08 mr1667_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