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Detailed information for vg0809642891:

Variant ID: vg0809642891 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 9642891
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.67, A: 0.34, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:


AAATTGGGAACTAAACAAGGCCTTAAGCTCTCTTTCGAACATAGCCAAATTTGGTTTGAATCCAGGAATTTCACTGCTTAATTACTGCAGTTGAGCTTGT[A/G]
TAAATCGCACAGTAGCCTGTAGGGCATGGATAAATTGATAATTTGCTGAATCTTGACTGTTTCTTTCTCAGGACACAAATGTCCACCTATTCAGATTATT

Reverse complement sequence

AATAATCTGAATAGGTGGACATTTGTGTCCTGAGAAAGAAACAGTCAAGATTCAGCAAATTATCAATTTATCCATGCCCTACAGGCTACTGTGCGATTTA[T/C]
ACAAGCTCAACTGCAGTAATTAAGCAGTGAAATTCCTGGATTCAAACCAAATTTGGCTATGTTCGAAAGAGAGCTTAAGGCCTTGTTTAGTTCCCAATTT

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 61.70% 38.00% 0.23% 0.00% NA
All Indica  2759 78.50% 21.10% 0.33% 0.00% NA
All Japonica  1512 22.80% 77.10% 0.13% 0.00% NA
Aus  269 97.80% 2.20% 0.00% 0.00% NA
Indica I  595 83.00% 16.80% 0.17% 0.00% NA
Indica II  465 88.80% 11.20% 0.00% 0.00% NA
Indica III  913 72.30% 27.40% 0.33% 0.00% NA
Indica Intermediate  786 76.30% 23.00% 0.64% 0.00% NA
Temperate Japonica  767 12.10% 87.60% 0.26% 0.00% NA
Tropical Japonica  504 39.50% 60.50% 0.00% 0.00% NA
Japonica Intermediate  241 22.00% 78.00% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 54.40% 45.60% 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
vg0809642891 A -> G LOC_Os08g15860.1 downstream_gene_variant ; 3292.0bp to feature; MODIFIER silent_mutation Average:65.647; most accessible tissue: Minghui63 root, score: 94.944 N N N N
vg0809642891 A -> G LOC_Os08g15840-LOC_Os08g15860 intergenic_region ; MODIFIER silent_mutation Average:65.647; most accessible tissue: Minghui63 root, score: 94.944 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)
vg0809642891 A G -0.09 -0.01 0.0 0.02 -0.01 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0809642891 NA 6.74E-08 mr1136 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
vg0809642891 NA 1.44E-10 mr1136_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
vg0809642891 7.59E-06 7.59E-06 mr1541_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