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Detailed information for vg1105945195:

Variant ID: vg1105945195 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 5945195
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:


TGTTTACTTTGGTCGCATGTAGAAAATAAATGTATAGGTAGCAGGATATGGTACCCGAAGAAGCTTATGGTTGTATGCGAGATGCGTACGCGGCCGAGAA[G/A]
CCGTGCGAGACGGCGGGTACGTGAGATGCTGCAGGAGAACGTCGTGCGCCATGACATCGCGAAGTGGCCGAGATGGCTGTGTCATTCGTTGGCGTGGAAA

Reverse complement sequence

TTTCCACGCCAACGAATGACACAGCCATCTCGGCCACTTCGCGATGTCATGGCGCACGACGTTCTCCTGCAGCATCTCACGTACCCGCCGTCTCGCACGG[C/T]
TTCTCGGCCGCGTACGCATCTCGCATACAACCATAAGCTTCTTCGGGTACCATATCCTGCTACCTATACATTTATTTTCTACATGCGACCAAAGTAAACA

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 37.30% 9.90% 3.05% 49.72% NA
All Indica  2759 16.80% 16.50% 4.28% 62.45% NA
All Japonica  1512 75.00% 0.00% 0.79% 24.21% NA
Aus  269 12.30% 1.10% 3.72% 82.90% NA
Indica I  595 7.90% 1.50% 3.03% 87.56% NA
Indica II  465 8.60% 36.60% 5.38% 49.46% NA
Indica III  913 23.70% 15.90% 4.16% 56.30% NA
Indica Intermediate  786 20.50% 16.50% 4.71% 58.27% NA
Temperate Japonica  767 68.10% 0.00% 0.78% 31.16% NA
Tropical Japonica  504 83.10% 0.00% 0.60% 16.27% NA
Japonica Intermediate  241 80.10% 0.00% 1.24% 18.67% NA
VI/Aromatic  96 88.50% 2.10% 4.17% 5.21% NA
Intermediate  90 54.40% 8.90% 0.00% 36.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1105945195 G -> A LOC_Os11g10800.1 upstream_gene_variant ; 2168.0bp to feature; MODIFIER silent_mutation Average:49.108; most accessible tissue: Callus, score: 89.143 N N N N
vg1105945195 G -> A LOC_Os11g10790-LOC_Os11g10800 intergenic_region ; MODIFIER silent_mutation Average:49.108; most accessible tissue: Callus, score: 89.143 N N N N
vg1105945195 G -> DEL N N silent_mutation Average:49.108; most accessible tissue: Callus, score: 89.143 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)
vg1105945195 G A -0.06 -0.03 -0.04 -0.02 -0.03 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1105945195 NA 3.55E-07 mr1623_2 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
vg1105945195 3.80E-06 1.37E-09 mr1974_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
vg1105945195 NA 5.14E-06 mr1974_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