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Detailed information for vg0330585710:

Variant ID: vg0330585710 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 30585710
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATAAATATAGTAAGATCAAATTTACATGATTAATATTTTTAACTTTTTTACTATTAATAGGCAAAATTTAAAAAATTTGACTTGGCACTATTCTAAAAAT[A/G]
CTTATATTTTGATAGGGGGGAGTAGCTCTTAAACAGGGATTGAGCAATGAAGGACCAATAAGATTTCTACCTTGTTGGTCGAAATCAAGAATCGCATATA

Reverse complement sequence

TATATGCGATTCTTGATTTCGACCAACAAGGTAGAAATCTTATTGGTCCTTCATTGCTCAATCCCTGTTTAAGAGCTACTCCCCCCTATCAAAATATAAG[T/C]
ATTTTTAGAATAGTGCCAAGTCAAATTTTTTAAATTTTGCCTATTAATAGTAAAAAAGTTAAAAATATTAATCATGTAAATTTGATCTTACTATATTTAT

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 86.00% 12.10% 1.86% 0.00% NA
All Indica  2759 98.60% 1.00% 0.40% 0.00% NA
All Japonica  1512 60.20% 34.90% 4.96% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 97.60% 2.00% 0.34% 0.00% NA
Indica II  465 97.20% 2.60% 0.22% 0.00% NA
Indica III  913 99.90% 0.00% 0.11% 0.00% NA
Indica Intermediate  786 98.70% 0.40% 0.89% 0.00% NA
Temperate Japonica  767 37.90% 55.50% 6.52% 0.00% NA
Tropical Japonica  504 90.70% 7.70% 1.59% 0.00% NA
Japonica Intermediate  241 67.20% 25.70% 7.05% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 76.70% 21.10% 2.22% 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
vg0330585710 A -> G LOC_Os03g53280.1 upstream_gene_variant ; 3666.0bp to feature; MODIFIER silent_mutation Average:61.97; most accessible tissue: Zhenshan97 root, score: 91.119 N N N N
vg0330585710 A -> G LOC_Os03g53280-LOC_Os03g53300 intergenic_region ; MODIFIER silent_mutation Average:61.97; most accessible tissue: Zhenshan97 root, score: 91.119 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)
vg0330585710 A G 0.0 -0.01 0.0 -0.01 -0.01 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0330585710 NA 8.64E-06 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
vg0330585710 4.56E-06 4.56E-06 mr1597 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
vg0330585710 NA 5.79E-06 mr1153_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
vg0330585710 6.49E-06 NA mr1238_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
vg0330585710 2.98E-06 NA mr1310_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
vg0330585710 6.61E-07 NA mr1484_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
vg0330585710 3.03E-07 NA mr1945_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
vg0330585710 3.38E-07 6.35E-15 mr1959_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
vg0330585710 NA 1.50E-07 mr1959_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