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Detailed information for vg1203501263:

Variant ID: vg1203501263 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 3501263
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:


AATAAAATGCATAGTTTGTCATATACGACGTGTTCGCTAAAATGATAAAATCTAAAACATATACAATTAGGTACTTGACGGCCTAAAAGATTGTTTTCGC[A/G]
TATTCACATAAACAAGTATACACTTGCAAATGTAATACTTCACTAATAGTTTGGTGCACTTTTCATCTCCTGATCTAATCACATGCAGATAGATTGACAA

Reverse complement sequence

TTGTCAATCTATCTGCATGTGATTAGATCAGGAGATGAAAAGTGCACCAAACTATTAGTGAAGTATTACATTTGCAAGTGTATACTTGTTTATGTGAATA[T/C]
GCGAAAACAATCTTTTAGGCCGTCAAGTACCTAATTGTATATGTTTTAGATTTTATCATTTTAGCGAACACGTCGTATATGACAAACTATGCATTTTATT

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 67.80% 32.20% 0.00% 0.00% NA
All Indica  2759 96.90% 3.10% 0.00% 0.00% NA
All Japonica  1512 14.00% 86.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.20% 1.80% 0.00% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 95.20% 4.80% 0.00% 0.00% NA
Indica Intermediate  786 96.80% 3.20% 0.00% 0.00% NA
Temperate Japonica  767 3.30% 96.70% 0.00% 0.00% NA
Tropical Japonica  504 27.60% 72.40% 0.00% 0.00% NA
Japonica Intermediate  241 19.50% 80.50% 0.00% 0.00% NA
VI/Aromatic  96 10.40% 89.60% 0.00% 0.00% NA
Intermediate  90 43.30% 56.70% 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
vg1203501263 A -> G LOC_Os12g07120.1 downstream_gene_variant ; 3826.0bp to feature; MODIFIER silent_mutation Average:77.149; most accessible tissue: Minghui63 flag leaf, score: 84.42 N N N N
vg1203501263 A -> G LOC_Os12g07150.1 downstream_gene_variant ; 1851.0bp to feature; MODIFIER silent_mutation Average:77.149; most accessible tissue: Minghui63 flag leaf, score: 84.42 N N N N
vg1203501263 A -> G LOC_Os12g07150.2 downstream_gene_variant ; 1851.0bp to feature; MODIFIER silent_mutation Average:77.149; most accessible tissue: Minghui63 flag leaf, score: 84.42 N N N N
vg1203501263 A -> G LOC_Os12g07140.1 intron_variant ; MODIFIER silent_mutation Average:77.149; most accessible tissue: Minghui63 flag leaf, score: 84.42 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)
vg1203501263 A G 0.01 0.01 0.0 0.01 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1203501263 NA 1.58E-13 mr1239 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
vg1203501263 NA 4.48E-12 mr1846 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
vg1203501263 1.75E-07 NA mr1871 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
vg1203501263 NA 2.30E-06 mr1871 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
vg1203501263 1.24E-07 NA mr1871_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