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Detailed information for vg1122865112:

Variant ID: vg1122865112 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 22865112
Reference Allele: AAlternative Allele: T
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.95, T: 0.08, others allele: 0.00, population size: 36. )

Flanking Sequence (100 bp) in Reference Genome:


AGTTCTGTGCGTCAGGCAAATCAATGTTTTGATGCCCTCATCCGTCGGTGGCTTGTTTATCCTGCTGATATTGGTGCCACAGGAAAGATCAAGAGCTGTG[A/T]
AGTAGGTGATCTAGTTCATGGGTTCATTACCACAATTGCTAGAAAACAACACATTGTGGAGACACGCCTATCACATCACTTGGCTCGCCACTTCTCCATT

Reverse complement sequence

AATGGAGAAGTGGCGAGCCAAGTGATGTGATAGGCGTGTCTCCACAATGTGTTGTTTTCTAGCAATTGTGGTAATGAACCCATGAACTAGATCACCTACT[T/A]
CACAGCTCTTGATCTTTCCTGTGGCACCAATATCAGCAGGATAAACAAGCCACCGACGGATGAGGGCATCAAAACATTGATTTGCCTGACGCACAGAACT

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 35.40% 31.90% 8.89% 23.83% NA
All Indica  2759 28.00% 33.60% 10.15% 28.27% NA
All Japonica  1512 47.60% 36.50% 3.97% 11.90% NA
Aus  269 48.70% 2.60% 3.72% 44.98% NA
Indica I  595 19.50% 71.80% 2.52% 6.22% NA
Indica II  465 12.50% 6.00% 26.24% 55.27% NA
Indica III  913 42.60% 28.10% 4.71% 24.53% NA
Indica Intermediate  786 26.60% 27.40% 12.72% 33.33% NA
Temperate Japonica  767 26.20% 56.30% 6.39% 11.08% NA
Tropical Japonica  504 76.80% 10.90% 0.99% 11.31% NA
Japonica Intermediate  241 54.80% 27.00% 2.49% 15.77% NA
VI/Aromatic  96 26.00% 3.10% 61.46% 9.38% NA
Intermediate  90 25.60% 22.20% 12.22% 40.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1122865112 A -> T LOC_Os11g38580.1 missense_variant ; p.Glu851Val; MODERATE nonsynonymous_codon ; E851V Average:42.544; most accessible tissue: Zhenshan97 root, score: 90.883 probably damaging -2.063 TOLERATED 1.00
vg1122865112 A -> DEL LOC_Os11g38580.1 N frameshift_variant Average:42.544; most accessible tissue: Zhenshan97 root, score: 90.883 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)
vg1122865112 A T 0.0 0.02 0.01 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1122865112 NA 1.99E-06 mr1800 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
vg1122865112 4.41E-06 NA mr1336_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