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Detailed information for vg0434287265:

Variant ID: vg0434287265 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 34287265
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGTGATGCTTATATAATCAGTCCTTGTATGCTTGTCCTCCTACGTACACATATGTTTGATTACAGCTAACCTTGCCTCCTTAACCCATGTCGTCGTCGTC[A/G]
TCATCATCATCATCATCCACACCCCAAACGGGCAACCTGTCCTAGAGCCTTTGATTCCACGAGTCCGGCCGGTTTTTACCATCCCCAACAACAGCAACGT

Reverse complement sequence

ACGTTGCTGTTGTTGGGGATGGTAAAAACCGGCCGGACTCGTGGAATCAAAGGCTCTAGGACAGGTTGCCCGTTTGGGGTGTGGATGATGATGATGATGA[T/C]
GACGACGACGACATGGGTTAAGGAGGCAAGGTTAGCTGTAATCAAACATATGTGTACGTAGGAGGACAAGCATACAAGGACTGATTATATAAGCATCACA

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 88.80% 11.00% 0.21% 0.00% NA
All Indica  2759 98.70% 1.30% 0.00% 0.00% NA
All Japonica  1512 81.30% 18.30% 0.40% 0.00% NA
Aus  269 29.00% 69.50% 1.49% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.00% 1.00% 0.00% 0.00% NA
Indica Intermediate  786 96.90% 3.10% 0.00% 0.00% NA
Temperate Japonica  767 99.50% 0.40% 0.13% 0.00% NA
Tropical Japonica  504 48.80% 50.20% 0.99% 0.00% NA
Japonica Intermediate  241 91.70% 8.30% 0.00% 0.00% NA
VI/Aromatic  96 83.30% 16.70% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0434287265 A -> G LOC_Os04g57610.1 upstream_gene_variant ; 1396.0bp to feature; MODIFIER silent_mutation Average:97.766; most accessible tissue: Callus, score: 99.529 N N N N
vg0434287265 A -> G LOC_Os04g57610.3 upstream_gene_variant ; 1396.0bp to feature; MODIFIER silent_mutation Average:97.766; most accessible tissue: Callus, score: 99.529 N N N N
vg0434287265 A -> G LOC_Os04g57610-LOC_Os04g57620 intergenic_region ; MODIFIER silent_mutation Average:97.766; most accessible tissue: Callus, score: 99.529 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)
vg0434287265 A G -0.03 0.01 0.03 -0.03 -0.03 -0.06

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0434287265 NA 2.09E-07 mr1057 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
vg0434287265 NA 5.36E-06 mr1417 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
vg0434287265 NA 2.57E-13 mr1047_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
vg0434287265 8.97E-06 3.54E-10 mr1047_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
vg0434287265 NA 5.18E-06 mr1295_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
vg0434287265 NA 4.92E-10 mr1471_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
vg0434287265 NA 1.13E-09 mr1642_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
vg0434287265 NA 5.47E-06 mr1782_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
vg0434287265 NA 2.85E-10 mr1808_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
vg0434287265 NA 3.16E-07 mr1808_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
vg0434287265 NA 6.21E-10 mr1815_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
vg0434287265 NA 4.58E-07 mr1815_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