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Detailed information for vg0325867223:

Variant ID: vg0325867223 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 25867223
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGACGTACTGTCCACACCAACAAATACTCCCCCGTCAAAAAAAACAACCTGTTATTAAGATATGATTTATCCTAATACAATGAATTTGAATATACTCTCT[A/G]
TATCTAAATCCATTGTAATAGAATGTATCACGTCATAATATTTTTTGATTTTTTTGGATGGAGAAAGTAGGTCATGAAGTACGCTGTACTGTTGTTACTG

Reverse complement sequence

CAGTAACAACAGTACAGCGTACTTCATGACCTACTTTCTCCATCCAAAAAAATCAAAAAATATTATGACGTGATACATTCTATTACAATGGATTTAGATA[T/C]
AGAGAGTATATTCAAATTCATTGTATTAGGATAAATCATATCTTAATAACAGGTTGTTTTTTTTGACGGGGGAGTATTTGTTGGTGTGGACAGTACGTCG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.30% 2.30% 1.40% 0.00% NA
All Indica  2759 99.30% 0.00% 0.72% 0.00% NA
All Japonica  1512 90.00% 7.00% 2.98% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.50% 0.00% 1.51% 0.00% NA
Indica II  465 98.90% 0.00% 1.08% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.00% 0.76% 0.00% NA
Temperate Japonica  767 83.20% 11.60% 5.22% 0.00% NA
Tropical Japonica  504 99.60% 0.00% 0.40% 0.00% NA
Japonica Intermediate  241 91.70% 7.10% 1.24% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 1.04% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0325867223 A -> G LOC_Os03g45800.1 upstream_gene_variant ; 659.0bp to feature; MODIFIER silent_mutation Average:94.747; most accessible tissue: Zhenshan97 panicle, score: 98.908 N N N N
vg0325867223 A -> G LOC_Os03g45790.1 downstream_gene_variant ; 4455.0bp to feature; MODIFIER silent_mutation Average:94.747; most accessible tissue: Zhenshan97 panicle, score: 98.908 N N N N
vg0325867223 A -> G LOC_Os03g45810.1 downstream_gene_variant ; 629.0bp to feature; MODIFIER silent_mutation Average:94.747; most accessible tissue: Zhenshan97 panicle, score: 98.908 N N N N
vg0325867223 A -> G LOC_Os03g45800-LOC_Os03g45810 intergenic_region ; MODIFIER silent_mutation Average:94.747; most accessible tissue: Zhenshan97 panicle, score: 98.908 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)
vg0325867223 A G -0.02 -0.01 0.01 -0.01 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0325867223 4.87E-10 4.87E-10 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
vg0325867223 1.56E-16 3.35E-22 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
vg0325867223 4.44E-17 5.32E-22 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
vg0325867223 NA 3.13E-06 mr1358 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
vg0325867223 9.99E-07 3.43E-09 mr1379 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
vg0325867223 2.30E-12 2.30E-12 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
vg0325867223 1.33E-07 5.76E-12 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
vg0325867223 6.32E-08 1.19E-07 mr1559 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
vg0325867223 2.96E-17 2.51E-25 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
vg0325867223 2.29E-15 3.11E-21 mr1586 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
vg0325867223 1.67E-07 1.67E-07 mr1649 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
vg0325867223 5.30E-06 5.30E-06 mr1703 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
vg0325867223 1.42E-10 1.32E-14 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
vg0325867223 NA 4.82E-06 mr1788 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
vg0325867223 NA 3.42E-06 mr1793 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
vg0325867223 3.91E-06 3.91E-06 mr1996 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
vg0325867223 2.77E-08 2.77E-08 mr1166_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
vg0325867223 3.01E-24 1.27E-28 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
vg0325867223 3.54E-07 1.41E-06 mr1379_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
vg0325867223 4.13E-11 1.42E-13 mr1409_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
vg0325867223 4.08E-12 3.07E-13 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
vg0325867223 2.61E-22 3.42E-31 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
vg0325867223 1.84E-07 1.84E-07 mr1649_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
vg0325867223 5.91E-10 1.36E-11 mr1703_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
vg0325867223 1.58E-10 1.04E-13 mr1765_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
vg0325867223 5.14E-06 4.27E-08 mr1793_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