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

2694/60,973^b

4.4

lp17 (16,821)

ch_216^a

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_17^a

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_474^a

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_176^a

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_152^a

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_212^a

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_293^a

18,058

nd

nd

nd

nd

nd

nd

181/18,058^b

1.0