Apr 12, 2019 · SNP and indel frequencies around the TSS and the CSS. SNPs and indels in the promoter regions and 5’ UTRs may have direct effects on gene transcription and protein translation. Thus, we investigated SNP densities and distributions around the transcription start site (TSS) and the translation/coding start site (CSS) separately and in more detail.

Oct 8, 2013 · SNP/indel calling with the Coval-Refine and Coval-Call tools resulted in a TPR of 87.6% and an FPR of 0.18% for SNP calling, and a TPR of 79.6% and an FPR of 1.56% for indel calling (Figure 1; Tables S13 and S14).

Jun 27, 2019 · In order to consider a SNP or an indel as significant or suggestive a cut-off was set at FDR≤0.05 or FDR≤0.1, respectively.

Aug 18, 2014 · Insertion and deletion (INDEL) is one of the main events contributing to genetic and phenotypic diversity, which receives less attention than SNP and large structural variation. To gain a better knowledge of INDEL variation in chicken genome, we applied next generation sequencing on 12 diverse chicken breeds at an average effective depth of 8.6.

Oct 16, 2018 · We identified novel loci that contain well-established candidate genes that SNP-based GWAS failed to detect; INDEL-specific QTLs generally have weak local linkage disequilibrium (LD) with nearby SNPs.

Oct 28, 2005 · We demonstrate the superior performance of SNPdetector in SNP and mutation analysis by comparing its results with those derived by human inspection, PolyPhred (a popular SNP detection tool), and independent genotype assays in three large-scale investigations.

May 20, 2021 · Moreover, there is no available tool for massive conversion of MNPs and indels into CAPS markers. Here, we present VCF2CAPS–a new software for identification of restriction endonucleases that recognize SNP/MNP/indel-containing sequences from NGS experiments.

Aug 9, 2017 · We presented two key sources of difficulties in accurate INDEL detection: 1) the presence of repeat, and 2) heterozygous INDELs. Herein we could suggest the accessible algorithms that selectively reduce error rates and thereby facilitate INDEL detection.

Feb 17, 2022 · Based on this separation, small indel calls (< 50bp) and large indel calls (≥ 50bp) from the real sequencing data were evaluated separately. The semi-simulated WGS dataset covering a wide size range of indels with varying coverages and read lengths.

We used SNP density (SNPs per kb) and Tajima’s D statistic [31] to compare the variant distribution of the different genomic elements with each other. Fig 3 illustrates the results for all SNP and indel types from 1000G data. The results for the GoNL data are shown in S1 Fig.