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

From: Whole-exome sequencing of a pedigree segregating asthma

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