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Detailed information for vg0627993076:

Variant ID: vg0627993076 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 27993076
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGATCCCTTAGCGGTTTTGAGGGTGGTTTTGGCTGACGTGGCGCCTACATGGTTATTTTGACTCGGTCTTCATCTGATGTGGCACTGACGTGGCGCTTAC[G/A]
TGGCAATCCGATACAGAAAAATAATAAAACCTGTGGGCCCCACATGTCAGTCTCACAGAAAAAAATAATAATAATGTGGGACCCACGTGGGCCCCACATG

Reverse complement sequence

CATGTGGGGCCCACGTGGGTCCCACATTATTATTATTTTTTTCTGTGAGACTGACATGTGGGGCCCACAGGTTTTATTATTTTTCTGTATCGGATTGCCA[C/T]
GTAAGCGCCACGTCAGTGCCACATCAGATGAAGACCGAGTCAAAATAACCATGTAGGCGCCACGTCAGCCAAAACCACCCTCAAAACCGCTAAGGGATCT

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 50.80% 2.70% 1.67% 44.82% NA
All Indica  2759 36.50% 0.00% 1.92% 61.58% NA
All Japonica  1512 86.20% 8.40% 0.40% 4.96% NA
Aus  269 8.60% 0.00% 5.20% 86.25% NA
Indica I  595 48.10% 0.00% 1.51% 50.42% NA
Indica II  465 56.30% 0.00% 1.08% 42.58% NA
Indica III  913 16.80% 0.00% 2.85% 80.39% NA
Indica Intermediate  786 38.90% 0.00% 1.65% 59.41% NA
Temperate Japonica  767 82.50% 15.60% 0.52% 1.30% NA
Tropical Japonica  504 87.90% 0.80% 0.40% 10.91% NA
Japonica Intermediate  241 94.60% 1.20% 0.00% 4.15% NA
VI/Aromatic  96 14.60% 0.00% 2.08% 83.33% NA
Intermediate  90 58.90% 1.10% 4.44% 35.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0627993076 G -> A LOC_Os06g46180.1 upstream_gene_variant ; 1759.0bp to feature; MODIFIER silent_mutation Average:49.595; most accessible tissue: Zhenshan97 flower, score: 89.455 N N N N
vg0627993076 G -> A LOC_Os06g46190.1 upstream_gene_variant ; 1772.0bp to feature; MODIFIER silent_mutation Average:49.595; most accessible tissue: Zhenshan97 flower, score: 89.455 N N N N
vg0627993076 G -> A LOC_Os06g46180-LOC_Os06g46190 intergenic_region ; MODIFIER silent_mutation Average:49.595; most accessible tissue: Zhenshan97 flower, score: 89.455 N N N N
vg0627993076 G -> DEL N N silent_mutation Average:49.595; most accessible tissue: Zhenshan97 flower, score: 89.455 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)
vg0627993076 G A 0.02 0.01 0.01 0.0 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0627993076 8.60E-06 8.60E-06 mr1166 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
vg0627993076 3.45E-06 1.59E-09 mr1210 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
vg0627993076 NA 1.68E-07 mr1305 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
vg0627993076 3.42E-07 3.42E-07 mr1389 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
vg0627993076 6.06E-06 6.06E-06 mr1409 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
vg0627993076 NA 4.69E-06 mr1515 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
vg0627993076 NA 4.56E-10 mr1585 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
vg0627993076 6.95E-08 2.03E-11 mr1586 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
vg0627993076 NA 6.17E-09 mr1765 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
vg0627993076 3.39E-07 1.42E-10 mr1305_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
vg0627993076 NA 4.42E-06 mr1559_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
vg0627993076 7.11E-06 4.53E-11 mr1585_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
vg0627993076 7.91E-06 9.16E-09 mr1765_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