WES of mus musculus: melanoma tumor
DNA was extracted from tumors grown from B2905 mouse melanoma sublines using the DNAeasy kit (#69504, Qiagen, USA) according to the manufacturers instructions. 25 exome samples were pooled and sequenced on HiSeq run using Agilent SureSelect XT (All Exon V5 +UTR) and paired end sequencing. The samples have 172 to 251 million pass filter reads with a base call quality of above 92% of bases with Q30 and above. Reads of the samples were trimmed for adapters and low-quality bases using Trimmomatic software before alignment with the reference genome Mouse - mm10 using BWA mapping software. Total alignment with reference genome (Mouse - mm10) is 99% for all the samples. Unique alignment is above 73%. There are 1 to 1% of unmapped reads. Library complexity is measured in terms of unique fragments in the mapped reads using Picards MarkDuplicate utility. The samples have 73-80% non-duplicate reads. The capture efficiency is measured by the percentage of the reads mapped on target region or overlap with the target regions. There are between 62-67% reads are on target. The mean coverage on target region is between 231x and 342x and above 98% of the target regions have 30x or more coverage. Single nucleotide variant (SNV) calling from exomes was performed using VarScan (v.2.4.4) (Koboldt et al., 2009) with parameters --p-value 0.05 --min-coverage 10 --min-var-freq 0.15. SNV annotation was performed using ANNOVAR (http://www.openbioinformatics.org/annovar).