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Detailed information for vg0225156203:

Variant ID: vg0225156203 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 25156203
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAGGGAGGTTTTGTTGACGTGGTGGTATTGACTGTGTCTCCTTTACACGTGGCGTTGACGTGGCGTTTAGATGGTATTTAGAATTAAAAAATATATGTGG[G/A]
ACCCATTTGTCATTGACACATAAAAGAAATTGTTAGACCCGTGTCCCTTCTCTCTCCCCCCTCCCTCTAGTTCCTTCTCCCTTCTCGCCGCTCCCTCTAT

Reverse complement sequence

ATAGAGGGAGCGGCGAGAAGGGAGAAGGAACTAGAGGGAGGGGGGAGAGAGAAGGGACACGGGTCTAACAATTTCTTTTATGTGTCAATGACAAATGGGT[C/T]
CCACATATATTTTTTAATTCTAAATACCATCTAAACGCCACGTCAACGCCACGTGTAAAGGAGACACAGTCAATACCACCACGTCAACAAAACCTCCCTT

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 80.00% 19.80% 0.23% 0.00% NA
All Indica  2759 95.00% 4.80% 0.18% 0.00% NA
All Japonica  1512 51.10% 48.50% 0.40% 0.00% NA
Aus  269 95.50% 4.50% 0.00% 0.00% NA
Indica I  595 94.80% 5.00% 0.17% 0.00% NA
Indica II  465 97.80% 2.20% 0.00% 0.00% NA
Indica III  913 94.60% 5.40% 0.00% 0.00% NA
Indica Intermediate  786 94.00% 5.50% 0.51% 0.00% NA
Temperate Japonica  767 65.20% 34.00% 0.78% 0.00% NA
Tropical Japonica  504 30.60% 69.40% 0.00% 0.00% NA
Japonica Intermediate  241 49.40% 50.60% 0.00% 0.00% NA
VI/Aromatic  96 63.50% 36.50% 0.00% 0.00% NA
Intermediate  90 75.60% 24.40% 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
vg0225156203 G -> A LOC_Os02g41840.1 upstream_gene_variant ; 1938.0bp to feature; MODIFIER silent_mutation Average:98.369; most accessible tissue: Minghui63 panicle, score: 99.592 N N N N
vg0225156203 G -> A LOC_Os02g41850.1 upstream_gene_variant ; 346.0bp to feature; MODIFIER silent_mutation Average:98.369; most accessible tissue: Minghui63 panicle, score: 99.592 N N N N
vg0225156203 G -> A LOC_Os02g41840-LOC_Os02g41850 intergenic_region ; MODIFIER silent_mutation Average:98.369; most accessible tissue: Minghui63 panicle, score: 99.592 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)
vg0225156203 G A -0.13 -0.16 -0.1 -0.11 -0.08 -0.09

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0225156203 NA 8.84E-06 mr1045_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
vg0225156203 NA 1.81E-10 mr1084_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
vg0225156203 NA 7.91E-06 mr1194_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
vg0225156203 NA 3.11E-11 mr1205_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
vg0225156203 NA 6.34E-06 mr1206_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
vg0225156203 NA 3.84E-07 mr1302_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
vg0225156203 NA 5.44E-07 mr1418_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
vg0225156203 NA 4.82E-06 mr1419_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
vg0225156203 NA 3.51E-06 mr1420_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
vg0225156203 NA 1.89E-07 mr1488_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
vg0225156203 NA 2.58E-09 mr1506_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
vg0225156203 NA 1.79E-08 mr1604_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
vg0225156203 NA 5.51E-06 mr1779_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
vg0225156203 NA 8.04E-08 mr1805_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
vg0225156203 NA 5.77E-07 mr1824_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