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Detailed information for vg1016092400:

Variant ID: vg1016092400 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 16092400
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTCTAGCACCAGCTTTGAGAGAAAAGTGGTGAAAAGTGGTGAGCGGAGAGGTTGTGAGCTGCATGTGTGAGAGGAAGCTTAAGTTATTTTATTATGATGT[G/A]
AAGTTGATGGGCCCAGCGTTACAGGTCACTTATTGTATTCACAAGGTGCAAAGAGAGCTACTAGCTGAGTTGAATGGAATTAACGCGGGCTGCCTACGCT

Reverse complement sequence

AGCGTAGGCAGCCCGCGTTAATTCCATTCAACTCAGCTAGTAGCTCTCTTTGCACCTTGTGAATACAATAAGTGACCTGTAACGCTGGGCCCATCAACTT[C/T]
ACATCATAATAAAATAACTTAAGCTTCCTCTCACACATGCAGCTCACAACCTCTCCGCTCACCACTTTTCACCACTTTTCTCTCAAAGCTGGTGCTAGAG

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 88.20% 11.70% 0.08% 0.00% NA
All Indica  2759 99.50% 0.50% 0.00% 0.00% NA
All Japonica  1512 66.80% 32.90% 0.26% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 98.90% 1.10% 0.00% 0.00% NA
Temperate Japonica  767 97.50% 2.50% 0.00% 0.00% NA
Tropical Japonica  504 14.50% 84.90% 0.60% 0.00% NA
Japonica Intermediate  241 78.40% 21.20% 0.41% 0.00% NA
VI/Aromatic  96 75.00% 25.00% 0.00% 0.00% NA
Intermediate  90 82.20% 17.80% 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
vg1016092400 G -> A LOC_Os10g30860.1 upstream_gene_variant ; 373.0bp to feature; MODIFIER silent_mutation Average:94.253; most accessible tissue: Zhenshan97 panicle, score: 98.85 N N N N
vg1016092400 G -> A LOC_Os10g30870.1 downstream_gene_variant ; 3916.0bp to feature; MODIFIER silent_mutation Average:94.253; most accessible tissue: Zhenshan97 panicle, score: 98.85 N N N N
vg1016092400 G -> A LOC_Os10g30850-LOC_Os10g30860 intergenic_region ; MODIFIER silent_mutation Average:94.253; most accessible tissue: Zhenshan97 panicle, score: 98.85 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)
vg1016092400 G A -0.06 -0.04 -0.04 -0.01 -0.04 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1016092400 NA 4.16E-06 mr1543 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
vg1016092400 NA 8.17E-07 mr1642 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
vg1016092400 NA 5.94E-07 mr1870 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
vg1016092400 2.94E-06 1.85E-16 mr1871 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
vg1016092400 2.05E-07 2.13E-23 mr1042_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
vg1016092400 NA 6.14E-07 mr1042_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
vg1016092400 NA 1.22E-07 mr1363_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
vg1016092400 NA 2.98E-08 mr1502_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
vg1016092400 NA 6.86E-11 mr1543_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
vg1016092400 NA 7.93E-06 mr1553_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
vg1016092400 NA 4.66E-09 mr1642_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
vg1016092400 4.39E-07 9.13E-19 mr1742_2 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
vg1016092400 NA 1.44E-09 mr1742_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
vg1016092400 NA 4.85E-08 mr1817_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
vg1016092400 1.68E-07 4.44E-25 mr1871_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
vg1016092400 NA 6.48E-07 mr1966_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