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Detailed information for vg0224736708:

Variant ID: vg0224736708 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 24736708
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.66, G: 0.34, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


TCGGAAATCAAGTCAGCATGATTGTGTGGTACAAGGCCCTCCGGCAACTTTCATTTTCGGTGCTTCATGTATGTCCGTTAAGTGGATGTCTTCGTGTCCG[G/A]
TAGCTCTGATGTGAATGGCTTCAGCCTTGATTTCCACTTTTCTTCGGTGCAACATCAGCAAAGATATGACCTAGGATGCTAGCATTAGTTTGTGCTTGGC

Reverse complement sequence

GCCAAGCACAAACTAATGCTAGCATCCTAGGTCATATCTTTGCTGATGTTGCACCGAAGAAAAGTGGAAATCAAGGCTGAAGCCATTCACATCAGAGCTA[C/T]
CGGACACGAAGACATCCACTTAACGGACATACATGAAGCACCGAAAATGAAAGTTGCCGGAGGGCCTTGTACCACACAATCATGCTGACTTGATTTCCGA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 60.00% 39.50% 0.47% 0.00% NA
All Indica  2759 85.60% 14.00% 0.40% 0.00% NA
All Japonica  1512 14.40% 85.10% 0.60% 0.00% NA
Aus  269 74.30% 25.30% 0.37% 0.00% NA
Indica I  595 94.50% 5.20% 0.34% 0.00% NA
Indica II  465 91.80% 8.20% 0.00% 0.00% NA
Indica III  913 81.50% 18.30% 0.22% 0.00% NA
Indica Intermediate  786 79.90% 19.20% 0.89% 0.00% NA
Temperate Japonica  767 7.40% 91.50% 1.04% 0.00% NA
Tropical Japonica  504 30.40% 69.40% 0.20% 0.00% NA
Japonica Intermediate  241 2.90% 97.10% 0.00% 0.00% NA
VI/Aromatic  96 12.50% 86.50% 1.04% 0.00% NA
Intermediate  90 52.20% 47.80% 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
vg0224736708 G -> A LOC_Os02g40810.1 upstream_gene_variant ; 3537.0bp to feature; MODIFIER silent_mutation Average:88.361; most accessible tissue: Minghui63 flower, score: 96.217 N N N N
vg0224736708 G -> A LOC_Os02g40820.1 downstream_gene_variant ; 1333.0bp to feature; MODIFIER silent_mutation Average:88.361; most accessible tissue: Minghui63 flower, score: 96.217 N N N N
vg0224736708 G -> A LOC_Os02g40820.2 downstream_gene_variant ; 270.0bp to feature; MODIFIER silent_mutation Average:88.361; most accessible tissue: Minghui63 flower, score: 96.217 N N N N
vg0224736708 G -> A LOC_Os02g40810-LOC_Os02g40820 intergenic_region ; MODIFIER silent_mutation Average:88.361; most accessible tissue: Minghui63 flower, score: 96.217 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)
vg0224736708 G A -0.01 -0.02 -0.03 -0.01 -0.03 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0224736708 8.21E-06 7.19E-06 mr1099 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
vg0224736708 4.90E-06 NA mr1101 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
vg0224736708 5.20E-06 NA mr1868 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
vg0224736708 2.25E-06 NA mr1918 Ind_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
vg0224736708 1.32E-06 NA mr1098_2 Ind_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
vg0224736708 1.80E-07 NA mr1099_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
vg0224736708 9.42E-06 NA mr1123_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
vg0224736708 NA 5.12E-07 mr1850_2 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
vg0224736708 4.80E-06 NA mr1911_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