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Detailed information for vg0310240761:

Variant ID: vg0310240761 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 10240761
Reference Allele: AAlternative Allele: C
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATCGATAAATAGCCGGACTTTTTGCAAAATGACCAGGGCCGACGCGGACGCACGAGAAATCCCACCGTTTTCCAGCACGCGTCCACGCGTCGCGACCTCG[A/C]
GATGGCCACGCCAGCTCAAAATGCCGTGGGAGCTTCATTTCCCAGTAGGTTTGAAGACTTTAGACTAGAGTTAGCGCGCCGCACCAATGGCATCAGAAAA

Reverse complement sequence

TTTTCTGATGCCATTGGTGCGGCGCGCTAACTCTAGTCTAAAGTCTTCAAACCTACTGGGAAATGAAGCTCCCACGGCATTTTGAGCTGGCGTGGCCATC[T/G]
CGAGGTCGCGACGCGTGGACGCGTGCTGGAAAACGGTGGGATTTCTCGTGCGTCCGCGTCGGCCCTGGTCATTTTGCAAAAAGTCCGGCTATTTATCGAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 73.10% 26.30% 0.55% 0.00% NA
All Indica  2759 99.60% 0.40% 0.00% 0.00% NA
All Japonica  1512 19.10% 79.30% 1.59% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.30% 0.70% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.80% 0.00% 0.00% NA
Temperate Japonica  767 22.00% 75.10% 2.87% 0.00% NA
Tropical Japonica  504 14.10% 85.70% 0.20% 0.00% NA
Japonica Intermediate  241 20.30% 79.30% 0.41% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 63.30% 34.40% 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
vg0310240761 A -> C LOC_Os03g18264.1 upstream_gene_variant ; 319.0bp to feature; MODIFIER silent_mutation Average:98.936; most accessible tissue: Callus, score: 99.418 N N N N
vg0310240761 A -> C LOC_Os03g18270.1 downstream_gene_variant ; 488.0bp to feature; MODIFIER silent_mutation Average:98.936; most accessible tissue: Callus, score: 99.418 N N N N
vg0310240761 A -> C LOC_Os03g18264-LOC_Os03g18270 intergenic_region ; MODIFIER silent_mutation Average:98.936; most accessible tissue: Callus, score: 99.418 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)
vg0310240761 A C 0.02 0.06 0.07 0.04 0.03 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0310240761 NA 3.38E-08 mr1162 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
vg0310240761 NA 6.66E-07 mr1382 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
vg0310240761 NA 5.33E-06 mr1414 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
vg0310240761 2.39E-06 2.39E-06 mr1464 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
vg0310240761 NA 6.42E-07 mr1510 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
vg0310240761 NA 3.50E-26 mr1617 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
vg0310240761 NA 1.19E-11 mr1626 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
vg0310240761 NA 1.36E-10 mr1637 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
vg0310240761 NA 2.15E-20 mr1676 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
vg0310240761 NA 1.60E-06 mr1748 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
vg0310240761 NA 1.67E-07 mr1804 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
vg0310240761 NA 4.79E-06 mr1830 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
vg0310240761 NA 4.03E-06 mr1875 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
vg0310240761 NA 3.16E-10 mr1905 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
vg0310240761 NA 5.06E-20 mr1383_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
vg0310240761 NA 5.88E-11 mr1761_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