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Detailed information for vg0102595003:

Variant ID: vg0102595003 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 2595003
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.01, others allele: 0.00, population size: 68. )

Flanking Sequence (100 bp) in Reference Genome:


ATGTGGGTATACATGGTAAATGGTTACTTACCACATTTAAGAGTGGCAAAATAATTAAATGTCTCTAGTCTAGAAATAAATGCATGCTTCATTGTATTAG[G/A]
GAATAAATATAAATGGGTAGAGAATTTGGGTGGTTCAATCTTCAACATCATATAGTCTTAAATTAATCAATCATTAGTGTCACATCAGGAAGCACATGCA

Reverse complement sequence

TGCATGTGCTTCCTGATGTGACACTAATGATTGATTAATTTAAGACTATATGATGTTGAAGATTGAACCACCCAAATTCTCTACCCATTTATATTTATTC[C/T]
CTAATACAATGAAGCATGCATTTATTTCTAGACTAGAGACATTTAATTATTTTGCCACTCTTAAATGTGGTAAGTAACCATTTACCATGTATACCCACAT

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 73.00% 25.70% 1.31% 0.00% NA
All Indica  2759 76.00% 22.70% 1.34% 0.00% NA
All Japonica  1512 72.60% 26.50% 0.93% 0.00% NA
Aus  269 36.10% 60.60% 3.35% 0.00% NA
Indica I  595 89.40% 10.10% 0.50% 0.00% NA
Indica II  465 67.10% 30.10% 2.80% 0.00% NA
Indica III  913 72.80% 26.10% 1.10% 0.00% NA
Indica Intermediate  786 74.80% 23.80% 1.40% 0.00% NA
Temperate Japonica  767 54.20% 44.30% 1.43% 0.00% NA
Tropical Japonica  504 96.80% 3.20% 0.00% 0.00% NA
Japonica Intermediate  241 80.50% 18.30% 1.24% 0.00% NA
VI/Aromatic  96 84.40% 14.60% 1.04% 0.00% NA
Intermediate  90 85.60% 13.30% 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
vg0102595003 G -> A LOC_Os01g05490.1 upstream_gene_variant ; 1362.0bp to feature; MODIFIER silent_mutation Average:89.758; most accessible tissue: Callus, score: 98.281 N N N N
vg0102595003 G -> A LOC_Os01g05500.1 upstream_gene_variant ; 4847.0bp to feature; MODIFIER silent_mutation Average:89.758; most accessible tissue: Callus, score: 98.281 N N N N
vg0102595003 G -> A LOC_Os01g05490.2 upstream_gene_variant ; 1362.0bp to feature; MODIFIER silent_mutation Average:89.758; most accessible tissue: Callus, score: 98.281 N N N N
vg0102595003 G -> A LOC_Os01g05500.2 upstream_gene_variant ; 4847.0bp to feature; MODIFIER silent_mutation Average:89.758; most accessible tissue: Callus, score: 98.281 N N N N
vg0102595003 G -> A LOC_Os01g05490-LOC_Os01g05500 intergenic_region ; MODIFIER silent_mutation Average:89.758; most accessible tissue: Callus, score: 98.281 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)
vg0102595003 G A -0.02 0.01 0.0 -0.02 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0102595003 1.17E-06 NA mr1588_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