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Detailed information for vg0225363637:

Variant ID: vg0225363637 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 25363637
Reference Allele: AAlternative Allele: C
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 38. )

Flanking Sequence (100 bp) in Reference Genome:


ATTATGAATTAATTAGGCTTAAAAATTTATCTCACGAATTAGCTCTCATTTATGAAATTAATTTTATAATTAGTCTATGTTTAATACTCTAAATTAGCGT[A/C]
CACGTATCCGATGTGATATGAGTATCCGATGTGATAGGAATAAAGTTTAGTCATGGATCCGAACACCACCGCGTAGCTGAGTCAGTCCACATAAATCGAA

Reverse complement sequence

TTCGATTTATGTGGACTGACTCAGCTACGCGGTGGTGTTCGGATCCATGACTAAACTTTATTCCTATCACATCGGATACTCATATCACATCGGATACGTG[T/G]
ACGCTAATTTAGAGTATTAAACATAGACTAATTATAAAATTAATTTCATAAATGAGAGCTAATTCGTGAGATAAATTTTTAAGCCTAATTAATTCATAAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 47.10% 8.40% 1.08% 43.40% NA
All Indica  2759 39.10% 0.50% 0.72% 59.62% NA
All Japonica  1512 66.20% 24.70% 1.72% 7.41% NA
Aus  269 5.60% 0.00% 0.00% 94.42% NA
Indica I  595 62.50% 0.80% 0.84% 35.80% NA
Indica II  465 28.80% 0.60% 1.08% 69.46% NA
Indica III  913 34.60% 0.00% 0.00% 65.39% NA
Indica Intermediate  786 32.80% 0.80% 1.27% 65.14% NA
Temperate Japonica  767 49.50% 45.60% 3.39% 1.43% NA
Tropical Japonica  504 85.70% 1.20% 0.00% 13.10% NA
Japonica Intermediate  241 78.40% 7.10% 0.00% 14.52% NA
VI/Aromatic  96 88.50% 0.00% 0.00% 11.46% NA
Intermediate  90 51.10% 11.10% 5.56% 32.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0225363637 A -> DEL N N silent_mutation Average:82.637; most accessible tissue: Minghui63 young leaf, score: 96.129 N N N N
vg0225363637 A -> C LOC_Os02g42160.1 upstream_gene_variant ; 3626.0bp to feature; MODIFIER silent_mutation Average:82.637; most accessible tissue: Minghui63 young leaf, score: 96.129 N N N N
vg0225363637 A -> C LOC_Os02g42170.1 upstream_gene_variant ; 997.0bp to feature; MODIFIER silent_mutation Average:82.637; most accessible tissue: Minghui63 young leaf, score: 96.129 N N N N
vg0225363637 A -> C LOC_Os02g42180.1 upstream_gene_variant ; 3303.0bp to feature; MODIFIER silent_mutation Average:82.637; most accessible tissue: Minghui63 young leaf, score: 96.129 N N N N
vg0225363637 A -> C LOC_Os02g42160-LOC_Os02g42170 intergenic_region ; MODIFIER silent_mutation Average:82.637; most accessible tissue: Minghui63 young leaf, score: 96.129 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)
vg0225363637 A C -0.04 0.01 0.01 0.0 -0.02 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0225363637 NA 6.33E-06 mr1910 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
vg0225363637 NA 4.26E-07 mr1977 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
vg0225363637 NA 8.20E-08 mr1010_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
vg0225363637 NA 4.23E-07 mr1568_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
vg0225363637 9.59E-06 NA mr1770_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
vg0225363637 NA 1.45E-07 mr1880_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
vg0225363637 NA 8.08E-07 mr1910_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
vg0225363637 1.42E-06 9.56E-10 mr1946_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
vg0225363637 1.42E-06 9.56E-10 mr1948_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
vg0225363637 NA 2.00E-07 mr1977_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