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Table 1 Mapping statistics. For each sample the first four columns list the sample names followed by the capture reaction (number of genomic libraries captured in multiplex), the total number of sequenced bases (Mb) prior to filtering, and the percentage PCR duplicates. The final five columns report the capture efficiency (percentage of reads that mapped to the B. burgdorferi B31 reference genome), the percentage of sequence covered by at least one generated sequence read and the fold coverage (the total number of unique sequence reads which map to each nucleotide in the reference B31 genome) of filtered data for the linear chromosome (911 Kb) and the longest linear plasmid, lp54 (53 Kb), respectively

From: Whole genome capture of vector-borne pathogens from mixed DNA samples: a case study of Borrelia burgdorferi

Sample Capture reaction Sequenced bases (Mb) % duplicate Capture efficiency % Chr covered Coverage depth (Chr) % lp54 covered Coverage depth (lp54)
Bbcap1 20 34.22 42.63 0.44 99 11.71 98 12.77
Bbcap2_L1a 10 108.45 50.1 0.64 100 52.92 100 52.53
Bbcap2_L2b 4 237.68 70.49 0.61 100 109.52 100 113.51
Bbcap3 20 94.32 56.52 0.76 100 52.6 100 59.7
Bbcap4_L1 1 2066.79 92.57 0.10 100 140.83 98 194.75
Bbcap4_L2 4 188.60 61.81 0.56 100 76.92 100 94.68
Bbcap5 20 163.28 61.93 0.81 100 109.28 100 66.03
Bbcap6_L1 10 334.98 69.68 0.81 100 217.77 98 208.67
Bbcap6_L2 20 202.09 64.25 0.81 100 131.54 98 125.66
Bbcap7 20 75.67 55.01 0.65 100 39.08 98 34.93
Bbcap8 20 41.28 47.49 0.49 100 13.87 100 18.71
Bbcap9 10 221.18 67.38 0.76 99 134.32 98 148.14
Bbcap10 20 449.34 81.21 0.91 100 305.33 100 259
Bbcap12 20 185.23 67.57 0.77 100 103.49 98 91.28
Bbcap13 10 617.48 83.63 0.81 100 331.14 98 327.07
Bbcap14 20 140.75 62.89 0.70 100 76.99 98 86.69
Bbcap15 10 69.67 49.41 0.43 99 23.64 99 33.1
Bbcap16 20 119.57 54.98 0.72 99 71.59 99 71.73
Bbcap17 20 344.88 72.98 0.84 100 219.8 100 245.4
Bbcap19 10 53.31 41.46 0.53 100 19.73 100 25.17
Bbcap20 20 128.15 59.07 0.72 100 72.48 100 84.78
Bbcap21 20 135.54 60.87 0.71 99 72.32 98 79.68
Bbcap22 4 976.61 91.94 0.88 100 597.31 100 782.62
Bbcap23 20 159.50 63.51 0.64 99 77.6 98 105.44
Bbcap24 20 84.34 49.5 0.65 100 42.99 100 29.66
Bbcap25 20 61.60 50.95 0.50 99 25.13 98 28.68
Bbcap26 20 75.92 57.04 0.53 99 30.63 98 31.59
Bbcap27 20 73.49 60.97 0.59 100 33.45 100 35.05
Bbcap28 20 123.64 65.07 0.73 100 72.31 99 61.74
Bbcap29 10 255.63 72.17 0.86 100 167.46 100 178.06
Bbcap30_L1 10 343.08 70.18 0.83 100 225.25 99 183.62
Bbcap30_L2 4 825.19 88.1 0.79 100 520.17 100 438.71
Bbcap31_L1 10 292.77 65.76 0.85 100 198.23 100 136.51
Bbcap31_L2 20 232.33 66.08 0.85 100 156.58 100 109.34
Bbcap32 10 164.70 60.74 0.74 99 87.35 98 104.07
Sh834 c Shotgun 9954.53 19.92 6.00E–05 7.7 1.2 0.8 1.23
Sh1589 Shotgun 825.75 18.15 1.40E–04 27.1 1.389 38 1.5
  1. aL1: Samples (indexed genomic libraries after capture) that were sequenced in a half lane
  2. bL2: Samples (indexed genomic libraries after capture) that were sequenced in a different half lane
  3. cSh: samples sequenced using shotgun approach
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