Whole-exome sequencing of a pedigree segregating asthma

BMC Medical Genetics

Table 2 Number of reads, variants and variant coverage by sample

Sample	Paired reads²	Unpaired reads³	Unmapped reads⁴	Read pair duplicates⁵	Unpaired read duplicates⁶	# Variants⁷	Avg. variant coverage⁸	#Variants: passed QC filters⁹	Avg. variant coverage: passed QC filters¹⁰
Mother	89,967,478	2,061,484	10,764,768	8,577,327	1,636,019	36,275	156.0	28,232	148.7
Father	107,937,586	2,297,044	12,181,833	10,863,150	1,863,721	36,650	187.3	28,007	183.0
Child 1	105,231,048	2,088,137	10,883,542	12,455,453	1,705,727	37,267	174.7	28,370	169.6
Child 2	129,947,192	2,401,685	11,122,401	15,054,214	2,012,381	37,457	213.4	28,413	210.4
Child 3	52,005,299	932,213	3,544,678	2,870,062	634,587	34,826	100.4	27,376	92.9
Child 4	118,061,614	2,832,204	15,671,206	13,849,071	2,369,338	36,946	195.4	28,374	190.7
Total Unique¹						55,370		38,103

¹Total number of unique variants across all six samples.
²Number of pairs of reads (reads from the opposite ends of the same DNA molecule) for which the corresponding read pair was identified.
³Number of reads for which the corresponding read pair was not identified.
⁴Number of reads that could not be mapped to the reference human genome.
⁵Number of read pairs that were the result of PCR duplicates.
⁶Number of unpaired reads that were the result of PCR duplicates.
⁷Total number of variants called by the Genome Analysis Toolkit (SNPs and indels).
⁸Average depth of coverage across all variants called for an individual sample.
⁹Number of variants that passed the quality control filters (see Alignment, Variant Identification and Filtering section above).
¹⁰Average depth of coverage across all variants that passed the quality control filters for an individual sample.

ISSN: 1471-2350