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Detailed information for vg0625198261:

Variant ID: vg0625198261 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 25198261
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: Unkown

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTCCGGCTACCACTCTAGCTTAAGCAGTCTAGCGAGCTCATCGCGTCGCGCTCTTCTCGACGAGCTCCAATTTCAGGCAAGATGTCGATGCTGCCGCGCT[T/C]
CCTCCTCCTCGTCGTGCTGCTCGCGGTGCCGATGACGGCGGCGCAGCAGCAGTACGAGGCCAACGCGCAGGGCGACTGCTACACCGACAACGGCAGCTCC

Reverse complement sequence

GGAGCTGCCGTTGTCGGTGTAGCAGTCGCCCTGCGCGTTGGCCTCGTACTGCTGCTGCGCCGCCGTCATCGGCACCGCGAGCAGCACGACGAGGAGGAGG[A/G]
AGCGCGGCAGCATCGACATCTTGCCTGAAATTGGAGCTCGTCGAGAAGAGCGCGACGCGATGAGCTCGCTAGACTGCTTAAGCTAGAGTGGTAGCCGGAG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of Unkown(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.10% 0.00% 0.80% 9.10% NA
All Indica  2759 83.40% 0.00% 1.38% 15.26% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 94.30% 0.00% 0.34% 5.38% NA
Indica II  465 85.40% 0.00% 2.58% 12.04% NA
Indica III  913 76.70% 0.00% 1.97% 21.36% NA
Indica Intermediate  786 81.70% 0.00% 0.76% 17.56% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 0.00% 1.04% NA
Intermediate  90 91.10% 0.00% 0.00% 8.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0625198261 T -> C LOC_Os06g41980.1 missense_variant ; p.Phe7Ser; MODERATE N Average:95.202; most accessible tissue: Zhenshan97 young leaf, score: 96.922 N N N N
vg0625198261 T -> C LOC_Os06g41990.1 downstream_gene_variant ; 2015.0bp to feature; MODIFIER N Average:95.202; most accessible tissue: Zhenshan97 young leaf, score: 96.922 N N N N
vg0625198261 T -> C LOC_Os06g41990.2 downstream_gene_variant ; 2015.0bp to feature; MODIFIER N Average:95.202; most accessible tissue: Zhenshan97 young leaf, score: 96.922 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)
vg0625198261 T C -0.05 -0.07 -0.03 0.0 -0.02 -0.01