Table 2 Sequencing statistics
Control ReadsExperimental Reads (Remaining 88 Samples)
GenomeaStatisticRR722RR666RR3131MeanSDMinMax
NoneQC-passed2,133,6842,331,0042,012,6501,859,324705,545795,4763,667,922
% QC-failedb45.6847.8144.0148.6213.9624.172.48
Rd reference% Alignedc99.9599.9487.6699.740.2498.3199.95
Median depthd55 ± 2561 ± 2749 ± 2549 ± 2318 ± 1221 ± 994 ± 56
Unmappede6741,200112,0111,7901,1723755,888
% Coveragef99.8199.7991.3599.680.1599.1999.89
86-028NP reference% Alignedc92.1691.7699.8991.760.2290.3792.06
Median depthd56 ± 2761 ± 2750 ± 2449 ± 2318 ± 1221 ± 994 ± 56
Unmappede241,928242,2451,821243,0561,625236,352246,081
% Coveragef87.0187.0099.6586.690.1486.4487.21
  • QC, quality control; MAD, median absolute deviation

  • a The sequence reference used for short-read alignment.

  • b %QC-failed reads accounts for both those that had failed the Illumina chastity filter and those that were removed by the utility sortPairedReads, which identifies and culls read pairs containing the sequencing adaptors. The vast majority of these were adaptor dimers.

  • c %QC-passed reads mapped indicates how many reads were aligned to the reference genome indicated.

  • d Median ± MAD read depth across all reference positions supported by at least one read.

  • e Number of reference positions with no supporting aligned read (read depth = 0).

  • f Fraction of reference genome positions covered by at least three reads.