The exome of five tumor-normal pairs and two tumor-only samples were sequenced and analyzed for recurrent single nucleotide variations (SNVs) and insertions or deletions.
During the course of this study, genome sequencing of the strains used revealed the presence of a significant number of SNVs (Single Nucleotide Variations) and Indels (Insertions and Deletions) compared to that expected, emphasising the need for researchers to both establish the sequence of the strains in use in their laboratory and to appropriately curate their laboratory strains.
Single nucleotide variation (SNVs) and insertions and deletions (DIPs) between the QM6a reference sequence and the aligned sequences of the two backcrossed lines were identified using CLC Genomic Workbench.
Then protein level variations are identified for both single nucleotide variations and short insertion and deletions.
Single nucleotide variations (SNVs) and insertion and deletion (indels) were called from pileup files using SNooPer, an in-house variant caller that is based on a machine learning approach and developed to minimize false positive variant calling in low-depth sequencing data (manuscript submitted and software available upon request).
In this work, the tra gene of the twelve Anastrepha species showed extraordinarily reduced variation, and no insertions were detected, unlike in some Drosophila species.
Small scale variation including: SNPs and insertions and deletions, were identified by using the SNP detection pipeline of MUMmer [27].
All upstream positions we document are presented in relationship to the translation start site (in negative numbers) and, due to variations in insertions and deletions between the gh genes within their intronic regions, all downstream information is based on nucleotide (nt) numbering as presented in Additional file 1.
Nucleotide variations, including insertions and deletions (indels) and single-nucleotide polymorphisms (SNPs), occurred much more frequently in the two flanking regions and the introns but much less frequently in the exon regions (Fig. 1a).
All high-confidence SNP sites and candidates for DIP variations (deletions, insertions and inversions) were checked by capillary Sanger sequencing of PCR products amplified directly from the genome.
