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Table 3 Error model statistics for Illumina v4, Illumina v5, and Roche/454

From: GemSIM: general, error-model based simulator of next-generation sequencing data

  Ill. v4 1st read Ill. v4 2nd read Ill. v5 1st read Ill. v5 2nd read Roche/454
Overall (%) 0.99 2.40 0.28 0.34 0.12
A (%) 1.23 2.86 0.25 0.33 0.14
T (%) 0.91 2.19 0.34 0.39 0.10
G (%) 0.78 2.00 0.23 0.23 0.12
C (%) 1.12 2.78 0.29 0.41 0.12
1st most freq. (%) GGGT A - > GGGG A (4.47) ACAA G - > ACAC G (3.94) GGGT C - > GGGG C (5.85) AGGT G- > AGGG G (3.69) AAAC A - > AAAA A (1.07)
2nd most freq. (%) AGGT G - > AGGG G (3.71) AGGT G - > AGGG G (3.29) CTCG G - > CTCC G (5.83) CGGT G - > CGGG G (2.7) CCCA C - > CCCC C (1.02)
3rd most freq. (%) CCCA A - > CCCC A (3.15) CCCA A - > CCCC A (3.24) GGGC G - > GGGG G (4.06) GGGT G - > GGGG G (2.45) CCCC G - > CCCA G (0.75)
4th most freq. (%) CGGT G - > CGGG G (3.06) GGGT A - > GGGG A (3.14) CGGT G - > CGGG G (3.65) GGGT C - > GGGG G (2.03) AAAG G - > AAAA G (0.70)
5th most freq. (%) GGGT G - > GGGG G (2.71) ACAA A - > ACAC A (2.97) GGGT A - > GGGG A (3.20) CGGT C - > CGGG C (1.98) AGGA A - > AGGG A (0.52)
Insertions (%) 0.000723 0.000935 0.000622 0.001300 0.290000
Deletions (%) 0.000434 0.000482 0.000353 0.000484 0.270000
  1. Values give the error rates for each technology. Several measures of error rate are given, including: overall error rates; average error rate for each nucleotide; error rates for the five sequence-context words most likely to result in mismatches (1st most freq. to 5th most freq); and average insertion and deletion rates. For the top five mismatches, the sequence-context word is given with the actual mismatch base in bold (true sequence - > error sequence).