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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