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Detailed information for vg0108525900:

Variant ID: vg0108525900 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 8525900
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGTTCTTCTCTCCTTCCAAAAAATTTGTCGATTGGGAGGAAAGATACCTGCTCGTGCTCATTGATGTCCTCTTCTTTGCCGTGCCGATTATCTCCATTCC[A/G]
TTGTGCTTTTGTTATTTTGGTGCTCATCGTTGGCGATGCCGTCGTGCGTGGCAACGCCTATAGCACGAGGCGGATGACGCTCAGCCTGATGGCGCCGTCG

Reverse complement sequence

CGACGGCGCCATCAGGCTGAGCGTCATCCGCCTCGTGCTATAGGCGTTGCCACGCACGACGGCATCGCCAACGATGAGCACCAAAATAACAAAAGCACAA[T/C]
GGAATGGAGATAATCGGCACGGCAAAGAAGAGGACATCAATGAGCACGAGCAGGTATCTTTCCTCCCAATCGACAAATTTTTTGGAAGGAGAGAAGAACA

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 92.70% 7.00% 0.28% 0.00% NA
All Indica  2759 99.70% 0.30% 0.00% 0.00% NA
All Japonica  1512 78.00% 21.20% 0.79% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.50% 0.00% 0.00% NA
Temperate Japonica  767 98.00% 2.00% 0.00% 0.00% NA
Tropical Japonica  504 43.70% 54.00% 2.38% 0.00% NA
Japonica Intermediate  241 86.30% 13.70% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 5.60% 1.11% 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
vg0108525900 A -> G LOC_Os01g15200.1 upstream_gene_variant ; 4346.0bp to feature; MODIFIER silent_mutation Average:89.831; most accessible tissue: Zhenshan97 flag leaf, score: 94.038 N N N N
vg0108525900 A -> G LOC_Os01g15210.1 upstream_gene_variant ; 1710.0bp to feature; MODIFIER silent_mutation Average:89.831; most accessible tissue: Zhenshan97 flag leaf, score: 94.038 N N N N
vg0108525900 A -> G LOC_Os01g15229.1 upstream_gene_variant ; 1654.0bp to feature; MODIFIER silent_mutation Average:89.831; most accessible tissue: Zhenshan97 flag leaf, score: 94.038 N N N N
vg0108525900 A -> G LOC_Os01g15220.1 intron_variant ; MODIFIER silent_mutation Average:89.831; most accessible tissue: Zhenshan97 flag leaf, score: 94.038 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)
vg0108525900 A G 0.02 0.01 0.02 0.01 0.02 0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0108525900 NA 3.76E-08 mr1248 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
vg0108525900 NA 3.10E-07 mr1338 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
vg0108525900 NA 1.08E-06 mr1364 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
vg0108525900 NA 9.51E-08 mr1443 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
vg0108525900 NA 7.13E-13 mr1449 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
vg0108525900 NA 3.10E-06 mr1471 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
vg0108525900 NA 6.04E-09 mr1539 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
vg0108525900 NA 2.33E-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
vg0108525900 NA 5.67E-34 mr1699 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
vg0108525900 NA 7.42E-13 mr1864 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
vg0108525900 NA 1.80E-06 mr1880 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
vg0108525900 NA 4.78E-10 mr1364_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
vg0108525900 NA 1.74E-11 mr1364_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
vg0108525900 NA 1.10E-06 mr1653_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
vg0108525900 NA 1.03E-09 mr1696_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
vg0108525900 NA 6.62E-08 mr1696_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
vg0108525900 NA 1.91E-28 mr1699_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