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Detailed information for vg1119648094:

Variant ID: vg1119648094 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 19648094
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.83, A: 0.17, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:


ATCGGCCAGCCCGCGCGCTCGTCGTCGTCGGCCACCGCGCACGTCGTCGCCGTCGGCCACGCCGCGCGCCCGTCGCCATCGTCCACCTCACGCGGCGCTT[G/A]
CCGTTCGCCACCGCGCCTCATTCGACTGAGAGAGAGGGGGAGAGATCGGAAGAGAAGGAGACAGTGGGCGGAGGAGAAGAGAAAATGCGAGAAAGAGAAA

Reverse complement sequence

TTTCTCTTTCTCGCATTTTCTCTTCTCCTCCGCCCACTGTCTCCTTCTCTTCCGATCTCTCCCCCTCTCTCTCAGTCGAATGAGGCGCGGTGGCGAACGG[C/T]
AAGCGCCGCGTGAGGTGGACGATGGCGACGGGCGCGCGGCGTGGCCGACGGCGACGACGTGCGCGGTGGCCGACGACGACGAGCGCGCGGGCTGGCCGAT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 86.00% 13.80% 0.30% 0.00% NA
All Indica  2759 79.80% 19.80% 0.40% 0.00% NA
All Japonica  1512 95.50% 4.50% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 80.70% 18.80% 0.50% 0.00% NA
Indica II  465 43.40% 55.50% 1.08% 0.00% NA
Indica III  913 96.90% 3.10% 0.00% 0.00% NA
Indica Intermediate  786 80.90% 18.70% 0.38% 0.00% NA
Temperate Japonica  767 97.30% 2.70% 0.00% 0.00% NA
Tropical Japonica  504 92.50% 7.50% 0.00% 0.00% NA
Japonica Intermediate  241 96.30% 3.70% 0.00% 0.00% NA
VI/Aromatic  96 80.20% 18.80% 1.04% 0.00% NA
Intermediate  90 77.80% 20.00% 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
vg1119648094 G -> A LOC_Os11g33230.1 stop_gained ; p.Gln38*; HIGH stop_gained Average:77.497; most accessible tissue: Zhenshan97 young leaf, score: 90.638 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)
vg1119648094 G A 0.01 0.01 0.01 0.01 0.01 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1119648094 3.42E-06 NA mr1761 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