Skip to main content

Advertisement

Table 4 Comparison of nanopore contigs and trimmed reads with GenBank and determination of single nucleotide differences (SNPs) in MEGA

From: Lost in plasmids: next generation sequencing and the complex genome of the tick-borne pathogen Borrelia burgdorferi

B31-GB genome (length) Nanopore contig name Nanopore contig length Identity with B31-GB Id % Gaps Gaps % Start query (subject) Stop query (subject) SNPs NP MEGA % SNPs PB MEGA %
main (910,724) 241244 878,078 659,561/683,765 96 24,016/683,765 3 205,813 (213,067) 865,577 (897,715 nd nd   
cp26 (26,498) 241245 46,144 25,597/26,496 97 8,951/26,496 3 13,432 (1) 39,032 (26,496) 15/26,498 0.05 4/26,498 0.01
lp54 (53,657) 241246 51,693 51,381/53,655 96 2,222/53,655 4 199 (53,651) 51,635 (1) 199/53,651 0.2 7/53,915 0.01
lp56 (52,971) 241248 51,105 50,156/52,909 95 2,152/52,909 4 1 (65) 51,105 (52,578) 837/53,318 1.6 7/53,318 0.01
lp38 (38,829) 241249 37,824 37,356/38,823 96 1,429/38,823 3 54 (38,821) 37,454 (6) 176/38,821 0.45 1/38,821 0.002
cp32-1 (30,750) 241247 67,311 20,520/21,493 95 663/21,493 3 36,733 (1) 57,597 (21,458) 2694/60,973b 4.4   
lp17 (16,821) ch_216a 16,238 16,067/16,821 96 751/16,821 4 42 (1) 16,111 (16,821) 80/16,989 0.47 0/16,989 0.0
lp28-1 (28,155) ch_17a 15,787 15,638/16,873 93 1,117/16,873 6 1 (1866) 15,785 (18,709) 1911/19,082 10.0 171/21,885 0.78
lp36 (36,849) ch_474a 34,829 34,690/36,856 94 2,094/36,856 5 1 (8) 34,777 (36,848) 281/36,856 0.7 0/36,856 0.0
cp32-3 (30,223) ch_176a 30,596 23,314/24,600 95 1,195/24,600 4 7187 (5629) 30,596 (30,223) 286/31,974 0.9 2/30,223 0.006
cp32-4 (30,299) ch_152a 22,112 21,907/23,209 94 1,105/23,209 4 1 (4046) 22,111 (27,247) 339/27,247 1.2 3/27,247 0.01
cp32-9 (30,651) ch_212a 28,699 17,790/19,416 92 1,325/19,416 6 1 (11,245) 18,100 (30,651) 491/30,651 2.7 2/30,651 0.006
cp32-2 ch_293a 18,058 nd nd nd nd nd nd 181/18,058b 1.0   
  1. aunassembled trimmed reads
  2. baligned to Pacific Bioscience SMRT sequence unitig4 (cp32-1 fused plasmid) and unitig6 (cp32-2), respectively