TABLE 1 

Quality statistics of each sequencing runa

Sequencing platform and runSample typesNo. of mock replicates/runbAvg length of forward reads after QCcAvg length of reverse reads after QCcSequence error rate (%)d% sequences
within
expectations
R2e
MiSeqPE300
    Run 06Amplicons + 10 to 15% PhiXf4286.1261.20.029980.94
    Run 20Amplicons + 10 to 15% PhiXf3285.6244.70.03980.95
    Run 31Amplicons + 10 to 15% PhiXf4278.0221.40.023990.95
    Run 46Amplicons + 10 to 15% PhiXf1252.7216.90.029980.95
    Run 40 (rerun library from the aberrant run)Amplicons + 10 to 15% PhiXg1279.2244.30.028980.94
HiSeqPE250
    Run 365% amplicons + 95% metagenomes1235.9231.70.02920.97
    Run 44Metagenomes + 0.1% mock1235.1233.30.033950.94
    Run 4720% amplicons + 80% metagenomes1237.5228.20.018980.91
    Run 37 (aberrant run)20% amplicons + 80% metagenomes3228.4240.90.021970.73f
  • a The characteristics and results for the aberrant run and the rerun of the library from the aberrant run are shown in boldface type.

  • b Number of mock replicates included in each run.

  • c The trimmed length after quality control (QC) as described in Materials and Methods.

  • d The error rate is defined as the sum of mismatches to the reference divided by sum of bases in query for mock communities using Mothur.

  • e Coefficient of variation of observed staggered mock community versus in silico staggered mock community under log (x + 0.001) at 99% similarity level.

  • f The R2 of the aberrant run is far outside the range of other runs.

  • g The sequencing facility adds 10 to 15% of PhiX174 (phage DNA) for “amplicons-only” runs as recommended by Illumina to increase sample complexity.