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Detailed information for vg1022934549:

Variant ID: vg1022934549 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 22934549
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACTAACACCCCCCGTGCTGTTCTACAGCTGTAACAAACACATACTTCCTCCGTTTCACAATATAAGACTTTCTAGCATTACCCACATTCATGTCTAGATT[T/C]
ATTAACATCTAAATAAATATGGGTAATGCTAGAATAAATGAATGTAGACAATGCTAAAAAGTCAGTACATTATAAAACGGAGGGAGTAATAAAACCAGGA

Reverse complement sequence

TCCTGGTTTTATTACTCCCTCCGTTTTATAATGTACTGACTTTTTAGCATTGTCTACATTCATTTATTCTAGCATTACCCATATTTATTTAGATGTTAAT[A/G]
AATCTAGACATGAATGTGGGTAATGCTAGAAAGTCTTATATTGTGAAACGGAGGAAGTATGTGTTTGTTACAGCTGTAGAACAGCACGGGGGGTGTTAGT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.50% 9.40% 0.08% 0.00% NA
All Indica  2759 91.80% 8.10% 0.07% 0.00% NA
All Japonica  1512 85.80% 14.20% 0.07% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 72.40% 27.60% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 97.20% 2.80% 0.00% 0.00% NA
Indica Intermediate  786 95.50% 4.20% 0.25% 0.00% NA
Temperate Japonica  767 92.30% 7.70% 0.00% 0.00% NA
Tropical Japonica  504 74.40% 25.60% 0.00% 0.00% NA
Japonica Intermediate  241 88.80% 10.80% 0.41% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 94.40% 4.40% 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
vg1022934549 T -> C LOC_Os10g42510.1 upstream_gene_variant ; 1869.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1022934549 T -> C LOC_Os10g42520.1 upstream_gene_variant ; 360.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1022934549 T -> C LOC_Os10g42540.1 upstream_gene_variant ; 4406.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1022934549 T -> C LOC_Os10g42510-LOC_Os10g42520 intergenic_region ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 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)
vg1022934549 T C -0.01 -0.01 0.0 -0.02 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1022934549 1.21E-06 1.21E-06 mr1258 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
vg1022934549 NA 2.57E-07 mr1706 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
vg1022934549 NA 1.95E-08 mr1739 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