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Detailed information for vg0230093704:

Variant ID: vg0230093704 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 30093704
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGCGAATTTCGCCGTATAAACCAACAGCGCGAGGCAAGGCGAAGACGAGAGAGTGAAACGAATGAGTTGTTCAAATTGTAGTCAAAATAAAACTTACCAA[A/C]
TTTTGACAATATCAAAATTTTAATAAGTTGGCAATATTTATTAAAATTTTGGTATGATTTTCTTATGTATCTATTGAAGTTTAGTGAAAAACTAAACACA

Reverse complement sequence

TGTGTTTAGTTTTTCACTAAACTTCAATAGATACATAAGAAAATCATACCAAAATTTTAATAAATATTGCCAACTTATTAAAATTTTGATATTGTCAAAA[T/G]
TTGGTAAGTTTTATTTTGACTACAATTTGAACAACTCATTCGTTTCACTCTCTCGTCTTCGCCTTGCCTCGCGCTGTTGGTTTATACGGCGAAATTCGCC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.90% 2.70% 0.38% 0.00% NA
All Indica  2759 99.30% 0.70% 0.07% 0.00% NA
All Japonica  1512 92.20% 6.80% 0.99% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 99.70% 0.20% 0.11% 0.00% NA
Indica Intermediate  786 98.50% 1.40% 0.13% 0.00% NA
Temperate Japonica  767 98.30% 0.40% 1.30% 0.00% NA
Tropical Japonica  504 82.50% 16.70% 0.79% 0.00% NA
Japonica Intermediate  241 92.90% 6.60% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 6.70% 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
vg0230093704 A -> C LOC_Os02g49230.2 upstream_gene_variant ; 588.0bp to feature; MODIFIER silent_mutation Average:79.303; most accessible tissue: Zhenshan97 flower, score: 94.311 N N N N
vg0230093704 A -> C LOC_Os02g49230.1 upstream_gene_variant ; 555.0bp to feature; MODIFIER silent_mutation Average:79.303; most accessible tissue: Zhenshan97 flower, score: 94.311 N N N N
vg0230093704 A -> C LOC_Os02g49230.3 upstream_gene_variant ; 558.0bp to feature; MODIFIER silent_mutation Average:79.303; most accessible tissue: Zhenshan97 flower, score: 94.311 N N N N
vg0230093704 A -> C LOC_Os02g49230.4 upstream_gene_variant ; 596.0bp to feature; MODIFIER silent_mutation Average:79.303; most accessible tissue: Zhenshan97 flower, score: 94.311 N N N N
vg0230093704 A -> C LOC_Os02g49230.5 upstream_gene_variant ; 596.0bp to feature; MODIFIER silent_mutation Average:79.303; most accessible tissue: Zhenshan97 flower, score: 94.311 N N N N
vg0230093704 A -> C LOC_Os02g49230.6 upstream_gene_variant ; 596.0bp to feature; MODIFIER silent_mutation Average:79.303; most accessible tissue: Zhenshan97 flower, score: 94.311 N N N N
vg0230093704 A -> C LOC_Os02g49240.1 downstream_gene_variant ; 4745.0bp to feature; MODIFIER silent_mutation Average:79.303; most accessible tissue: Zhenshan97 flower, score: 94.311 N N N N
vg0230093704 A -> C LOC_Os02g49220-LOC_Os02g49230 intergenic_region ; MODIFIER silent_mutation Average:79.303; most accessible tissue: Zhenshan97 flower, score: 94.311 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)
vg0230093704 A C 0.02 0.01 0.02 0.02 0.03 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0230093704 1.93E-06 1.93E-06 mr1085 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
vg0230093704 NA 5.55E-06 mr1104 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
vg0230093704 NA 5.74E-06 mr1155 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
vg0230093704 NA 8.62E-09 mr1213 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
vg0230093704 NA 7.65E-06 mr1437 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
vg0230093704 NA 1.68E-06 mr1620 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
vg0230093704 1.07E-07 4.76E-08 mr1070_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
vg0230093704 2.16E-06 3.03E-06 mr1085_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
vg0230093704 NA 7.92E-06 mr1088_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
vg0230093704 4.72E-06 2.11E-06 mr1103_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
vg0230093704 2.69E-07 1.20E-07 mr1104_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
vg0230093704 3.42E-07 3.42E-07 mr1145_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
vg0230093704 NA 8.27E-08 mr1155_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
vg0230093704 1.85E-06 1.11E-07 mr1224_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
vg0230093704 8.25E-06 NA mr1226_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
vg0230093704 8.69E-06 5.45E-08 mr1246_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
vg0230093704 8.20E-06 8.20E-06 mr1264_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
vg0230093704 NA 2.54E-06 mr1404_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
vg0230093704 5.94E-06 NA mr1408_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
vg0230093704 2.84E-06 5.48E-07 mr1437_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
vg0230093704 3.77E-06 7.00E-07 mr1620_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
vg0230093704 1.33E-07 4.55E-06 mr1949_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