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Detailed information for vg1225764387:

Variant ID: vg1225764387 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 25764387
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:


CAATTTTGTTTTATAAATAGAGTGCTGACTGCCATGCGTACGCCACGTGGATCAAAACCACTGCGAATTGGGTCGAGGGGGTAATTTGTCCGGTTTGCAT[G/A]
GTTGGGGGTGAAGAATACCCGGTTTTGTGGTTTAGGGGGTAATTCAGACGACCGCGATAGTTCGAGAGGGTAATTCGTACTTTTTCCTTTATTATTTATT

Reverse complement sequence

AATAAATAATAAAGGAAAAAGTACGAATTACCCTCTCGAACTATCGCGGTCGTCTGAATTACCCCCTAAACCACAAAACCGGGTATTCTTCACCCCCAAC[C/T]
ATGCAAACCGGACAAATTACCCCCTCGACCCAATTCGCAGTGGTTTTGATCCACGTGGCGTACGCATGGCAGTCAGCACTCTATTTATAAAACAAAATTG

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 67.40% 23.40% 1.06% 8.19% NA
All Indica  2759 53.80% 31.90% 0.98% 13.34% NA
All Japonica  1512 88.50% 10.20% 1.26% 0.07% NA
Aus  269 94.40% 1.50% 0.74% 3.35% NA
Indica I  595 60.80% 37.10% 1.51% 0.50% NA
Indica II  465 48.40% 25.80% 1.08% 24.73% NA
Indica III  913 44.40% 38.60% 0.55% 16.54% NA
Indica Intermediate  786 62.70% 23.70% 1.02% 12.60% NA
Temperate Japonica  767 99.00% 0.50% 0.52% 0.00% NA
Tropical Japonica  504 73.60% 23.60% 2.78% 0.00% NA
Japonica Intermediate  241 86.30% 12.90% 0.41% 0.41% NA
VI/Aromatic  96 42.70% 49.00% 1.04% 7.29% NA
Intermediate  90 73.30% 23.30% 1.11% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1225764387 G -> DEL N N silent_mutation Average:83.604; most accessible tissue: Zhenshan97 panicle, score: 90.061 N N N N
vg1225764387 G -> A LOC_Os12g41630.1 upstream_gene_variant ; 4777.0bp to feature; MODIFIER silent_mutation Average:83.604; most accessible tissue: Zhenshan97 panicle, score: 90.061 N N N N
vg1225764387 G -> A LOC_Os12g41640.1 upstream_gene_variant ; 513.0bp to feature; MODIFIER silent_mutation Average:83.604; most accessible tissue: Zhenshan97 panicle, score: 90.061 N N N N
vg1225764387 G -> A LOC_Os12g41650.2 upstream_gene_variant ; 4421.0bp to feature; MODIFIER silent_mutation Average:83.604; most accessible tissue: Zhenshan97 panicle, score: 90.061 N N N N
vg1225764387 G -> A LOC_Os12g41650.3 upstream_gene_variant ; 4421.0bp to feature; MODIFIER silent_mutation Average:83.604; most accessible tissue: Zhenshan97 panicle, score: 90.061 N N N N
vg1225764387 G -> A LOC_Os12g41650.4 upstream_gene_variant ; 4421.0bp to feature; MODIFIER silent_mutation Average:83.604; most accessible tissue: Zhenshan97 panicle, score: 90.061 N N N N
vg1225764387 G -> A LOC_Os12g41650.5 upstream_gene_variant ; 4421.0bp to feature; MODIFIER silent_mutation Average:83.604; most accessible tissue: Zhenshan97 panicle, score: 90.061 N N N N
vg1225764387 G -> A LOC_Os12g41634.1 downstream_gene_variant ; 537.0bp to feature; MODIFIER silent_mutation Average:83.604; most accessible tissue: Zhenshan97 panicle, score: 90.061 N N N N
vg1225764387 G -> A LOC_Os12g41634-LOC_Os12g41640 intergenic_region ; MODIFIER silent_mutation Average:83.604; most accessible tissue: Zhenshan97 panicle, score: 90.061 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)
vg1225764387 G A 0.02 0.01 0.01 0.01 0.02 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1225764387 NA 4.40E-07 mr1583 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
vg1225764387 3.65E-06 NA mr1363_2 Jap_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
vg1225764387 1.06E-09 5.77E-14 mr1850_2 Jap_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