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Detailed information for vg1001142065:

Variant ID: vg1001142065 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 1142065
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTGGTTGGTAGAAACAGATTTTGAGTCTAAATATAATAGGCAATAATTAAGCCCTGATCCTCACCAGTGTGTTTATTTTTTCTTGAAACACTGTACAAAC[A/G]
TAGGCGCCTGCAACACGCTCACCTATACACACGTATCCTACCAGTATAAGCACCGGGGCCGATATATCTTGAGATTGTCTAAGCTACACTCACTTCACCT

Reverse complement sequence

AGGTGAAGTGAGTGTAGCTTAGACAATCTCAAGATATATCGGCCCCGGTGCTTATACTGGTAGGATACGTGTGTATAGGTGAGCGTGTTGCAGGCGCCTA[T/C]
GTTTGTACAGTGTTTCAAGAAAAAATAAACACACTGGTGAGGATCAGGGCTTAATTATTGCCTATTATATTTAGACTCAAAATCTGTTTCTACCAACCAC

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 58.20% 17.40% 0.30% 24.16% NA
All Indica  2759 53.00% 6.70% 0.47% 39.91% NA
All Japonica  1512 64.50% 33.40% 0.00% 2.12% NA
Aus  269 56.50% 43.10% 0.00% 0.37% NA
Indica I  595 31.60% 11.90% 0.84% 55.63% NA
Indica II  465 65.80% 3.90% 0.43% 29.89% NA
Indica III  913 60.90% 4.60% 0.11% 34.39% NA
Indica Intermediate  786 52.30% 6.70% 0.64% 40.33% NA
Temperate Japonica  767 37.40% 62.20% 0.00% 0.39% NA
Tropical Japonica  504 92.70% 1.80% 0.00% 5.56% NA
Japonica Intermediate  241 91.70% 7.90% 0.00% 0.41% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 75.60% 14.40% 1.11% 8.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1001142065 A -> G LOC_Os10g02840.1 upstream_gene_variant ; 632.0bp to feature; MODIFIER silent_mutation Average:42.483; most accessible tissue: Callus, score: 87.286 N N N N
vg1001142065 A -> G LOC_Os10g02850.1 upstream_gene_variant ; 3315.0bp to feature; MODIFIER silent_mutation Average:42.483; most accessible tissue: Callus, score: 87.286 N N N N
vg1001142065 A -> G LOC_Os10g02840-LOC_Os10g02850 intergenic_region ; MODIFIER silent_mutation Average:42.483; most accessible tissue: Callus, score: 87.286 N N N N
vg1001142065 A -> DEL N N silent_mutation Average:42.483; most accessible tissue: Callus, score: 87.286 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)
vg1001142065 A G 0.16 0.02 0.02 0.03 0.05 0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1001142065 NA 4.41E-07 mr1026 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
vg1001142065 NA 1.24E-08 mr1137 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
vg1001142065 7.13E-06 7.13E-06 mr1261 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
vg1001142065 1.33E-08 NA mr1300 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
vg1001142065 NA 1.89E-06 mr1300 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
vg1001142065 4.00E-06 NA mr1310 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
vg1001142065 NA 3.56E-08 mr1310 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
vg1001142065 NA 3.17E-09 mr1617 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
vg1001142065 NA 1.39E-06 mr1627 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
vg1001142065 3.00E-10 NA mr1926 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
vg1001142065 NA 1.92E-10 mr1926 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
vg1001142065 4.27E-06 5.93E-11 mr1959 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
vg1001142065 NA 1.75E-06 mr1057_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
vg1001142065 NA 2.20E-08 mr1137_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
vg1001142065 NA 4.47E-06 mr1161_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
vg1001142065 5.16E-07 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
vg1001142065 NA 2.34E-11 mr1310_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
vg1001142065 NA 6.23E-06 mr1320_2 Ind_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
vg1001142065 NA 2.48E-06 mr1617_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
vg1001142065 NA 1.53E-14 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
vg1001142065 NA 1.13E-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