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Detailed information for vg0629600574:

Variant ID: vg0629600574 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 29600574
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACTCCCTGGGTGGTTTTGGAGAGTGGTTTCACTGACGTGGCGATTATGTGGTGGTGTTGACTTCGTCTTCTTCCAACGTGGTGTTGACTAGCACTTATAT[G/A]
GCATTAGAATTAAAAAAATATATGCGGGACCCATTTTTCATTCACCAAAATAAATATTATGGGCCCCACTAACATGTGGACCCCACATGTTAGTCTCTCT

Reverse complement sequence

AGAGAGACTAACATGTGGGGTCCACATGTTAGTGGGGCCCATAATATTTATTTTGGTGAATGAAAAATGGGTCCCGCATATATTTTTTTAATTCTAATGC[C/T]
ATATAAGTGCTAGTCAACACCACGTTGGAAGAAGACGAAGTCAACACCACCACATAATCGCCACGTCAGTGAAACCACTCTCCAAAACCACCCAGGGAGT

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 91.40% 8.60% 0.02% 0.00% NA
All Indica  2759 94.10% 5.90% 0.00% 0.00% NA
All Japonica  1512 91.30% 8.70% 0.00% 0.00% NA
Aus  269 91.80% 7.80% 0.37% 0.00% NA
Indica I  595 90.60% 9.40% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 95.80% 4.20% 0.00% 0.00% NA
Indica Intermediate  786 91.10% 8.90% 0.00% 0.00% NA
Temperate Japonica  767 98.80% 1.20% 0.00% 0.00% NA
Tropical Japonica  504 89.10% 10.90% 0.00% 0.00% NA
Japonica Intermediate  241 71.80% 28.20% 0.00% 0.00% NA
VI/Aromatic  96 15.60% 84.40% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 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
vg0629600574 G -> A LOC_Os06g48880.1 upstream_gene_variant ; 2279.0bp to feature; MODIFIER silent_mutation Average:74.922; most accessible tissue: Minghui63 young leaf, score: 87.373 N N N N
vg0629600574 G -> A LOC_Os06g48900.1 upstream_gene_variant ; 4323.0bp to feature; MODIFIER silent_mutation Average:74.922; most accessible tissue: Minghui63 young leaf, score: 87.373 N N N N
vg0629600574 G -> A LOC_Os06g48870.1 downstream_gene_variant ; 4804.0bp to feature; MODIFIER silent_mutation Average:74.922; most accessible tissue: Minghui63 young leaf, score: 87.373 N N N N
vg0629600574 G -> A LOC_Os06g48880-LOC_Os06g48900 intergenic_region ; MODIFIER silent_mutation Average:74.922; most accessible tissue: Minghui63 young leaf, score: 87.373 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)
vg0629600574 G A 0.0 0.0 0.0 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0629600574 NA 9.53E-06 mr1187_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
vg0629600574 7.20E-08 7.20E-08 mr1312_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
vg0629600574 2.70E-07 2.70E-07 mr1663_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
vg0629600574 NA 2.04E-06 mr1665_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
vg0629600574 8.48E-06 8.47E-06 mr1688_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
vg0629600574 NA 5.77E-06 mr1812_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
vg0629600574 7.56E-06 7.56E-06 mr1832_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
vg0629600574 NA 3.61E-06 mr1833_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
vg0629600574 1.55E-06 1.55E-06 mr1843_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
vg0629600574 3.73E-06 3.73E-06 mr1847_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
vg0629600574 NA 1.04E-08 mr1952_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