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Detailed information for vg1128835404:

Variant ID: vg1128835404 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 28835404
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:


TTGGCAAAATGTATTAAAATTTCGTCTGGTGATATATCATTTATTCATACTCTATTCTTTTACTACATAGCAACACATTTCGATGAAGAGCCTGCGTCGT[G/A]
GCAGAAAATCGCAATCGGCAAAGGAGAAATCCAACATATCGTGCGTCGGACAGAAGGAACTCTATCAATGATTGAAAAGAGGCTTCGATGCTGGGGCCGC

Reverse complement sequence

GCGGCCCCAGCATCGAAGCCTCTTTTCAATCATTGATAGAGTTCCTTCTGTCCGACGCACGATATGTTGGATTTCTCCTTTGCCGATTGCGATTTTCTGC[C/T]
ACGACGCAGGCTCTTCATCGAAATGTGTTGCTATGTAGTAAAAGAATAGAGTATGAATAAATGATATATCACCAGACGAAATTTTAATACATTTTGCCAA

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 93.20% 6.30% 0.15% 0.34% NA
All Indica  2759 92.40% 7.50% 0.04% 0.11% NA
All Japonica  1512 95.00% 4.80% 0.13% 0.13% NA
Aus  269 89.20% 6.70% 0.74% 3.35% NA
Indica I  595 93.60% 6.40% 0.00% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 85.30% 14.60% 0.00% 0.11% NA
Indica Intermediate  786 95.70% 3.90% 0.13% 0.25% NA
Temperate Japonica  767 92.40% 7.30% 0.26% 0.00% NA
Tropical Japonica  504 99.20% 0.40% 0.00% 0.40% NA
Japonica Intermediate  241 94.20% 5.80% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 1.00% 2.08% 1.04% NA
Intermediate  90 97.80% 1.10% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1128835404 G -> A LOC_Os11g47820.1 downstream_gene_variant ; 3269.0bp to feature; MODIFIER silent_mutation Average:82.278; most accessible tissue: Zhenshan97 root, score: 91.683 N N N N
vg1128835404 G -> A LOC_Os11g47820.2 downstream_gene_variant ; 3269.0bp to feature; MODIFIER silent_mutation Average:82.278; most accessible tissue: Zhenshan97 root, score: 91.683 N N N N
vg1128835404 G -> A LOC_Os11g47809-LOC_Os11g47820 intergenic_region ; MODIFIER silent_mutation Average:82.278; most accessible tissue: Zhenshan97 root, score: 91.683 N N N N
vg1128835404 G -> DEL N N silent_mutation Average:82.278; most accessible tissue: Zhenshan97 root, score: 91.683 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)
vg1128835404 G A 0.0 -0.03 -0.03 0.0 -0.01 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1128835404 NA 1.54E-06 mr1655_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
vg1128835404 2.41E-06 NA mr1980_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