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Detailed information for vg0405735993:

Variant ID: vg0405735993 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 5735993
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.80, A: 0.19, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


AGGAGGGAGCCAGCATGGCTAGCGCCCCCCTCCAATCCTGTTTCTCTCCGTGGAGTTGCGACCTTTTTTTTTATTTTAAACTCGAACGAATAAAATATGT[G/A]
GCCAATAGAATTTTTATGTGAACACATTAGATTAACATAATGCGCTCAATAGATTAACTAGTCAACGTTACTAAATATTTAATCTAATTCAAAATATAAC

Reverse complement sequence

GTTATATTTTGAATTAGATTAAATATTTAGTAACGTTGACTAGTTAATCTATTGAGCGCATTATGTTAATCTAATGTGTTCACATAAAAATTCTATTGGC[C/T]
ACATATTTTATTCGTTCGAGTTTAAAATAAAAAAAAAGGTCGCAACTCCACGGAGAGAAACAGGATTGGAGGGGGGCGCTAGCCATGCTGGCTCCCTCCT

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 81.00% 18.80% 0.19% 0.00% NA
All Indica  2759 92.80% 7.10% 0.14% 0.00% NA
All Japonica  1512 68.40% 31.50% 0.13% 0.00% NA
Aus  269 40.90% 58.40% 0.74% 0.00% NA
Indica I  595 89.40% 10.40% 0.17% 0.00% NA
Indica II  465 97.20% 2.80% 0.00% 0.00% NA
Indica III  913 93.60% 6.20% 0.11% 0.00% NA
Indica Intermediate  786 91.60% 8.10% 0.25% 0.00% NA
Temperate Japonica  767 70.30% 29.70% 0.00% 0.00% NA
Tropical Japonica  504 57.70% 42.10% 0.20% 0.00% NA
Japonica Intermediate  241 84.60% 14.90% 0.41% 0.00% NA
VI/Aromatic  96 53.10% 46.90% 0.00% 0.00% NA
Intermediate  90 81.10% 17.80% 1.11% 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
vg0405735993 G -> A LOC_Os04g10550.1 upstream_gene_variant ; 762.0bp to feature; MODIFIER silent_mutation Average:56.155; most accessible tissue: Minghui63 panicle, score: 83.421 N N N N
vg0405735993 G -> A LOC_Os04g10569.1 upstream_gene_variant ; 3447.0bp to feature; MODIFIER silent_mutation Average:56.155; most accessible tissue: Minghui63 panicle, score: 83.421 N N N N
vg0405735993 G -> A LOC_Os04g10530.1 downstream_gene_variant ; 4041.0bp to feature; MODIFIER silent_mutation Average:56.155; most accessible tissue: Minghui63 panicle, score: 83.421 N N N N
vg0405735993 G -> A LOC_Os04g10530-LOC_Os04g10550 intergenic_region ; MODIFIER silent_mutation Average:56.155; most accessible tissue: Minghui63 panicle, score: 83.421 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)
vg0405735993 G A 0.0 -0.01 -0.01 -0.02 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0405735993 2.53E-06 7.08E-07 mr1035 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
vg0405735993 1.41E-08 1.00E-11 mr1062 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
vg0405735993 NA 1.16E-06 mr1312 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
vg0405735993 NA 9.22E-06 mr1525 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
vg0405735993 2.17E-08 2.17E-08 mr1525 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
vg0405735993 NA 4.14E-06 mr1613 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
vg0405735993 NA 5.91E-07 mr1626 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
vg0405735993 NA 2.88E-06 mr1995 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
vg0405735993 3.50E-08 3.94E-09 mr1035_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
vg0405735993 NA 5.43E-08 mr1062_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
vg0405735993 4.18E-06 2.63E-08 mr1100_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
vg0405735993 NA 4.17E-06 mr1389_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
vg0405735993 1.74E-06 1.74E-06 mr1525_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
vg0405735993 9.87E-08 2.91E-09 mr1631_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
vg0405735993 NA 8.12E-06 mr1913_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
vg0405735993 NA 8.96E-06 mr1962_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