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Table 1 Characterization of the genetic heterogeneity Sites and SNP in large gene families

From: GenHtr: a tool for comparative assessment of genetic heterogeneity in microbial genomes generated by massive short-read sequencing

Maq

Chrom Position

Genotype profile at selected loci of SRX007711

Genotype profile at selected loci of FPR3757

Read Depth

SRX007711 Mean Phred Values

Max Phred Value

Functional Description

 

I. Heterogeneity sites that passed the SNPfilter and have an average of per-base Phred value greater than 13

*

778416

T:6 G:140

G:37

6

31.5

40

sulfatase family protein

*

2512836

C:7 G:115

G:37

8

31.25

40

sensor histidine kinase

*

107624

A:5 C:110

C:37

5

29.8

40

hypothetical protein

*

435033

T:5 G:98

G:37

5

28.2

38

hypothetical protein

*

1021087

T:5 G:151

G:37

5

26.2

40

lipoate-protein ligase A family protein

*

1662849

A:5 C:134

C:37

6

24.66

40

penicillin-binding protein 3

*

2648343

A:5 C:192

C:37

5

24.6

40

drug transporter phosphotransferase system, glucose-

*

2674216

A:5 C:170

C:37

5

24.6

40

specific IIABC component

*

1542366

T:6 G:129

G:37

6

24.5

40

hypothetical protein lantibiotic epidermin biosynthesis

*

1950547

A:5 C:164

C:37

5

23.4

40

protein EpiC

*

105211

A:6 G:132

G:37

8

20.3

40

hypothetical protein

*

1857182

A:14 G:85

G:37

14

19.42

40

hypothetical protein

phiSLT ORF2067-like protein, phage

*

1558524

T:5 G:56

G:37

7

17.57

40

tail tape measure protein

phi77 ORF014-like protein, phage anti-

*

2122182

C:122 G:6

C:37

6

17.28

38

repressor protein

*

1383603

A:5 G:128

G:37

5

15.8

20

oxacillin resistance-related FmtC protein

  

(A:2) T:5

    

lactose phosphotransferase system

*

2333470

C:164

C:37

7

15.28

40

repressor

       

putative fibronectin/fibrinogen binding

*

1206348

A:1 T:6 G:145

G:37

7

14.71

25

protein

  

A:153 (T:1)

     

*

2262790

G:6

A:37

7

13.14

29

cation efflux family protein

 

II. Heterogeneity sites that did not pass the SNPfilter but have an average per base Phred value greater than 13

 

1180638

T:5 G:97

G:37

5

40

40

cell division protein ftsA

       

2-oxoglutarate dehydrogenase E1

 

1437922

C:149 G:5

C:37

5

39.2

40

component

 

2212436

A:5 C:107

C:37

5

37.8

40

thiamine-phosphate pyrophosphorylase

 

257712

T:5 G:101

G:37

5

35.6

40

sensor histidine kinase family protein

 

861340

A:9 C:136

C:49

10

34

40

clumping factor A

       

acetyl-CoA carboxylase, biotin carboxyl

 

1714319

T:6 C:95

C:37

6

34

40

carrier protein

 

1252956

T:9 G:125

G:37

9

33

40

DNA topoisomerase I

       

lantibiotic epidermin leader peptide

 

1948255

A:5 C:169

C:37

5

32.8

40

processing serine protease EpiP

 

955972

A:5 C:145

C:37

5

32.6

40

Hypothetical protein

 

2123183

A:25 X:29

A:37

29

31.44

40

putative phage transcriptional regulator

 

2638027

A:5 C:112

C:36

5

31

40

gluconate kinase

 

1829558

T:5 G:118

G:37

5

30.8

40

septation ring formation regulator EzrA

       

putative maltose ABC transporter,

 

247386

A:5 C:163

C:37

5

30.4

40

maltose-binding protein

 

2262622

C:5 G:156

G:37

5

30.4

40

cation efflux family protein

 

344352

C:460 G:7

C:131

8

29.5

40

Hypothetical protein

 

346978

C:383 G:7

C:113

8

29.5

40

Hypothetical protein

 

472492

T:5 G:194

G:37

5

29.4

40

Hypothetical protein

 

2175831

A:585 G:8

A:229

9

28

40

5 S ribosomal RNA

 

1753468

C:96 G:5

C:37

5

27.2

40

Hypothetical protein

 

1503664

A:113 T:6

A:37

6

27.16

40

Hypothetical protein

 

617974

A:374 T:5

A:99

5

26.2

38

sdrD protein

 

154794

A:5 C:136

C:37

5

25.6

40

Fe/Mn family superoxide dismutase

 

1943616

C:5 G:110

G:37

5

25.2

32

serine protease SplA

 

2064321

C:113 G:6

C:37

6

24.8

40

Hypothetical protein

 

910508

A:177 T:6

A:37

7

24

40

lipoyl synthase

       

5-methyltetrahydropteroyltriglutamate--

 

408863

T:6 G:160

G:37

6

23.16

40

homocysteine S-methyltransferase

 

2417570

A:5 G:109

G:37

5

22.8

39

Na+/H+ antiporter NhaC

       

glycerol uptake operon antiterminator

 

1311574

A:5 C:181

C:37

5

22.6

40

regulatory protein

       

capsular polysaccharide biosynthesis

 

175115

X:6 G:136

G:37

6

21.33

40

protein Cap5B

 

2775087

A:14 T:107

T:49

14

20.4

29

clumping factor B

 

2678195

A:5 G:92

G:37

5

19.4

27

LysR family transcriptional regulator

 

451366

C:5 G:119

G:37

5

19.2

33

Superantigen-like protein 5

 

1633215

A:5 C:83

C:37

5

18.4

28

putative traG membrane protein

 

2114835

A:6 C:136

C:37

7

17.14

27

phiPVL ORF046-like protein

 

1859648

C:5 X:1 G:121

G:37

6

16

24

FtsK/SpoIIIE family protein

 

467549

A:89 T:23

A:58

23

15.56

40

Staphylococcal tandem lipoprotein

 

2123177

A:57 X:5

A:37

5

15.4

21

putative phage transcriptional regulator

 

36501

A:29 G:391

G:192

29

15.13

40

putative transposase

 

1857109

A:162 G:12

A:37

12

14

40

hypothetical protein

 

950365

A:5 C:113

C:37

5

13.8

17

Exonuclease RexB

 

801123

T:5 G:91

G:37

5

13.4

28

transferrin receptor

 

2481059

T:5 G:148

G:37

5

13.4

21

response regulator protein

 

1545118

A:15 T:109

T:37

15

13.2

40

putative lipoprotein

 

IV. Heterogeneity sites at RNA genes that pass the SNPfileter when single RNA genes were used as reference sequence.

*

1997102

A:69 T:13

A:37

13

7.0

30

Leu tRNA

 

1996261

T:7 C:76

C:55

8

14.25

30

Met tRNA

*

1961354

T:12 C:25

C:55

12

20.16

40

Met tRNA

 

517898

T:581 C:8

T:231

8

31.37

40

5 S ribosomal RNA

*

556291

T:560 C:16

T:225

16

20.56

40

5 S ribosomal RNA

 

561501

T:580 C:8

T:229

8

31.37

40

5 S ribosomal RNA

 

1997607

A:569 G:8

A:218

8

31.37

40

5 S ribosomal RNA

 

2292385

A:549 G:8

A:218

8

31.37

40

5 S ribosomal RNA

 

516288

A:34 G:408

G:185

34

14.11

40

23 S ribosomal RNA

 

517172

T:6 G:495

G:185

6

13.83

26

23 S ribosomal RNA

 

559891

A:34 G:408

G:185

34

14.1

40

23 S ribosomal RNA

 

560775

T:6 G:495

G:185

6

13.83

26

23 S ribosomal RNA

 

1998333

A:6 C:495

C:185

6

13.8

26

23 S ribosomal RNA

 

1999217

T:34 C:408

C:185

34

14.11

40

23 S ribosomal RNA

 

2176557

A:6 C:495

C:185

6

13.83

26

23 S ribosomal RNA

 

2177441

T:34 C:408

C:185

34

14.1

40

23 S ribosomal RNA

 

2293111

A:6 C:495

C:185

6

13.83

26

23 S ribosomal RNA