Table B1 Selected statistics for haploid paired-end sequence data by platform and fragment size
PlatformMedian fragment size (bp)Sequenced GbpError-corrected GbpRead 1 expected error-corrected length (bp)Read 2 expected error-corrected length (bp)Expected gap size (bp)Gaps filled (%)Maximal super-reads (%)
GAIIx 160+1562092.32.2157.0151.3−99.3966
2202.92.8157.1151.3−88.4967
2343.33.1157.6149.7−73.3958
2462.32.2157.8151.7−63.5949
2602.42.3157.8150.9−48.7949
273263252157.5150.0−34.59212
2852.42.3157.8151.4−24.29212
3252.22.1157.5149.318.39115
4411.91.8157.1141.7142.28418
5651.51.4156.9140.5267.67622
63724.01.1156.6134.8345.67123
HiSeq 2x125273326.0315.4123.8122.027.1839
HiSeq 2x12822096.692.9126.5124.1−30.6906
23459.557.7127.2125.4−18.6876
24661.659.6126.6125.3−5.9877
260100.297.1127.1125.1−2.3849
28595.691.7126.4123.235.48610
32592.388.9126.2124.374.58012
44135.834.4126.2124.0190.87315
56543.441.4125.7122.2317.16819
MiSeq 2x2553252.52.38248.2238.8−162.09514
4412.01.85247.5232.2−38.68918
5651.61.44246.9246.996.08323
6371.21.03246.6246.6177.97924
  • The percentage of reads that are gap filled is from the total number of reads entering gap fill, and the percentage of reads becoming maximal super-reads is from those passing error correction. As fragment size increases, so does the expected gap size. Both the error-corrected read length and the rate at which the gaps are successfully filled are decreasing functions of the fragment size. Nevertheless, the overall trend is that participation in the formation of super-reads increases with insert size. Only the paired-end reads that are successfully transformed into maximal super-reads are passed to subsequent assembly steps.