Inferring copy number and genotype in tumour exome data

BMC Genomics

Table 1 Summary of the exome sequencing data

Exome platform	Agilent SureSelect Human All Exon Version 4	Roche NimbleGen EZ Exome SeqCap Version 2	Roche NimbleGen EZ Exome SeqCap Version 1
No of paired samples	1 × 2	11 × 2	6 × 2
Target size	51Mbp	36Mbp	26Mbp
Sequencing platform	Illumina HiSeq	Illumina GAIIx	Illumina GAIIx
Read length	101 bp	100 bp	79 bp, 100 bp and 101 bp
Avg. mapped reads (BWA)*	102,082,760	86,607,431	77,433,963
Avg. on target reads*	95,930,467	78,038,985	70,758,116
Avg. bases mapped to target regions*	9.7Gbp	7.8Gbp	6.8Gbp
Average coverage per targeted base	189.28	216.91	204.68

ISSN: 1471-2164