Table 3 Differences between the assemblies. This table lists all 23 differences between our assembly and the existing Illumina assembly. The validation results when taking the FES into account are also given

1355

1355

Insertion in cp_2320 (61 bp)

Yes

-

LSCR

1426

1361

Substitution (1 bp)

Yes

-

LSCR

1430

1365

Insertion in cp_2320 (1 bp)

Yes

-

LSCR

12,633

12,567

Insertion in cp_2320 (1 bp)

Yes

-

LSCR

29,255

29,188

Deletion in cp_2320 (5 bp)

Yes

-

LSCR

35,514

35,452

Deletion in cp_2320 (2 bp)

Yes

-

LSCR

45,756

45,696

Substitution (1 bp)

Yes

-

LSCR

45,773

45,713

Deletion in cp_2320 (1 bp)

Yes

-

LSCR

45,776

45,717

Deletion in cp_2320 (1 bp)

Yes

-

LSCR

45,780

45,722

Deletion in cp_2320 (1 bp)

Yes

-

LSCR

51,980

51,923

Deletion in cp_2320 (4 bp)

Yes

-

LSCR

56,686

56,633

Deletion in cp_2320 (1 bp)

Yes

accD

LSCR

60,118

60,066

Insertion in cp_2320 (2 bp)

Yes

cemA

LSCR

63,266

63,212

Substitution (1 bp)

Yes

psbL

LSCR

84,321

84,267

Insertion in cp_2320 (1 bp)

Yes

-

IR 1

96,607

96,552

Deletion in cp_2320 (6 bp)

Yes

-

IR 1

100,122

100,073

Deletion in cp_2320 (1 bp)

No

-

IR 1

111,817

111,769

Substitution 6 bp (1 bp)

Yes

-

SSCR

111,858

111,810

Insertion in cp_2320 (45 bp)

Yes

ccsA

SSCR

114,513

114,420

Substitution (1 bp)

Yes

ndhD

SSCR

117,806

117,713

Deletion in cp_2320 (1 bp)

Yes

ndhA^a

SSCR

136,237

136,145

Deletion in cp_2320 (6 bp)

Yes

-

IR 2

148,514

148,428

Insertion in cp_2320 (1 bp)

Yes

-

IR 2