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Detailed information for vg0617621070:

Variant ID: vg0617621070 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 17621070
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTAGGATAGGGTTTAATCCCAGTCGCATAGGAGGGGGTTTCAGCGCGGGAGATGCAGGGGAGGGAAGCCGAGTTGGTTAGGGACTTGGAGAGGGACATGG[C/T]
GCGGCGGGGCGGCGCATGACTGAGGAGGCGGCGGCTAGGGCAGCCGGCCGGAGGAAGGGGACGGGCCCGACAGGTGGGCCCCACCTGTCGGTGACCCGAC

Reverse complement sequence

GTCGGGTCACCGACAGGTGGGGCCCACCTGTCGGGCCCGTCCCCTTCCTCCGGCCGGCTGCCCTAGCCGCCGCCTCCTCAGTCATGCGCCGCCCCGCCGC[G/A]
CCATGTCCCTCTCCAAGTCCCTAACCAACTCGGCTTCCCTCCCCTGCATCTCCCGCGCTGAAACCCCCTCCTATGCGACTGGGATTAAACCCTATCCTAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.70% 5.20% 0.08% 0.00% NA
All Indica  2759 98.40% 1.60% 0.00% 0.00% NA
All Japonica  1512 91.50% 8.50% 0.00% 0.00% NA
Aus  269 72.50% 26.00% 1.49% 0.00% NA
Indica I  595 97.00% 3.00% 0.00% 0.00% NA
Indica II  465 99.10% 0.90% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 97.60% 2.40% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 77.80% 22.20% 0.00% 0.00% NA
Japonica Intermediate  241 93.80% 6.20% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0617621070 C -> T LOC_Os06g30480.1 upstream_gene_variant ; 2104.0bp to feature; MODIFIER silent_mutation Average:81.737; most accessible tissue: Zhenshan97 panicle, score: 90.661 N N N N
vg0617621070 C -> T LOC_Os06g30480-LOC_Os06g30490 intergenic_region ; MODIFIER silent_mutation Average:81.737; most accessible tissue: Zhenshan97 panicle, score: 90.661 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)
vg0617621070 C T 0.0 -0.01 -0.01 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0617621070 3.29E-06 1.19E-06 mr1860 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
vg0617621070 NA 4.11E-06 mr1098_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
vg0617621070 NA 8.86E-06 mr1508_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
vg0617621070 2.51E-06 NA mr1864_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