New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 2786752	50 (0.850)	3 (0.050)	3/238	NT	6.4%	intergenic (‑84/‑238)	alx/ahpC	alkaline‑induced transporter/peroxiredoxin/alkylhydroperoxide reductase small subunit
	?	NC_002947	= 2786780	42 (0.760)					intergenic (‑112/‑210)	alx/ahpC	alkaline‑induced transporter/peroxiredoxin/alkylhydroperoxide reductase small subunit

CAGCCACAACCAGGCGCTGGTACCGAGGACAGGTGTTGTGAGGAATGATTGCAGAGCTGTCATGAGCCCCTCCTTGAATGTCGACGTTGCAAGGCAACAGTGATCCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGTTTGCCCGTGATACCGAATGGGGAGCTGTTACATTTCTTTGCCAGTGCAGAGTTCAGGTCCGCAATCCTTTGCTCAGCCCGTTCCCTTCTATTAAATAACCCCAGTTATAGCCAAAACC  >  NC_002947/2786606‑2786892                                                                                                                                                   |                                                                                                                                             cAGCCACAACCAGGCGCTGGTACCGAGGACAGGTGTTGTGAGGAATGATTGCAGAGCTGTCATGAGCCCCTCCTTGAATGTCGACGTTGCAAGGCAACAGTGATCCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACAt                                                                                                                                            >  2:18855/1‑149 (MQ=255)   gCCACAACCAGGCGCTGGTACCGAGGACAGGTGTTGTGAGGAATGATTGCAGAGCTGTCATGAGCCCCTCCTTGAATGTCGACGTTGCAAGGCAACAGTGATCCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACATgg                                                                                                                                          <  6:111117/149‑1 (MQ=255)    ccACAACCAGGCGCTGGTACCGAGGACAGGTGTTGTGAGGAATGATTGCAGAGCTGTCATGAGCCCCTCCTTGAATGTCGACGTTGCAAGGCAACAGTGATCCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACATggg                                                                                                                                         >  6:312017/1‑149 (MQ=255)         aCCAGGCGCTGGTACCGAGGACAGGTGTTGTGAGGAATGATTGCAGAGCTGTCATGAGCCCCTCCTTGAATGTCGACGTTGCAAGGCAACAGTGATCCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGa                                                                                                                                    <  1:278635/149‑1 (MQ=255)            aGGCGCTGGTACCGAGGACAGGTGTTGTGAGGAATGATTGCAGAGCTGTCATGAGCCCCTCCTTGAATGTCGACGTTTCAAGGCAACAGTGATCAGACATGGCGGCTTGGCAGCCGTCAGAGGGTCCCGGTATCACATGGGCTTGAGCg                                                                                                                                 <  7:290618/149‑1 (MQ=255)                   ggTACCGAGGACAGGTGTTGTGAGGAATGATTGCAGAGCTGTCATGAGCCCCTCCTTGAATGTCGACGTTGCAAGGCAACAGTGATCCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGAccc                                                                                                                          >  4:375045/1‑149 (MQ=255)                       ccGAGGACAGGTGTTGTGAGGAATGATTGCAGAGCTGTCATGAGCCCCTCCTTGAATGTCGACGTTGCAAGGCAACAGTGATCCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGttt                                                                                                                      >  1:340199/1‑149 (MQ=255)                         gAGGACAGGTGTTGTGAGGAATGATTGCAGAGCTGTCATGAGCCCCTCCTTGAATGTCGACGTTGCAAGGCAACAGTGATCCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGTTTGc                                                                                                                    <  8:28846/149‑1 (MQ=255)                          aGGACAGGTGTTGTGAGGAATGATTGCAGAGCTGTCATGAGCCCCTCCTTGAATGTCGACGTTGCAAGGCAACAGTGATCCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGTTTGcc                                                                                                                   <  2:340199/149‑1 (MQ=255)                                    ttgtGAGGAATGATTGCAGAGCTGTCATGAGCCCCTCCTTGAATGTCGACGTTGCAAGGCAACAGTGATCCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACgggcaaacgggtctacgctcaagcccatgtgataccg                                                                                                         <  5:312021‑M1/149‑38 (MQ=255)                                       tgAGGAATGATTGCAGAGCTGTCATGAGCCCCTCCTTGAATGTCGACGTTGCAAGGCAACAGTGATCCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGTTTGCCCGTGATACCGAAt                                                                                                      >  6:106298/1‑149 (MQ=255)                                           gAATGATTGCAGAGCTGTCATGAGCCCCTCCTTGAATGTCGACGTTGCAAGGCAACAGTGATCCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGAc                                                                                                                            >  4:155581/1‑123 (MQ=255)                                           gAATGATTGCAGAGCTGTCATGAGCCCCTCCTTGAATGTCGACGTTGCAAGGCAACAGTGATCCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGAc                                                                                                                            <  3:155581/123‑1 (MQ=255)                                           gAATGATTGCAGAGCTGTCATGAGCCCCTCCTTGAATGTCGACGTTGCAAGGCAACAGTGATCCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGTTTGCCCGTGATACCGAATggg                                                                                                   >  3:325425/1‑148 (MQ=255)                                           gAATGATTGCAGAGCTGTCATGAGCCCCTCCTTGAATGTCGACGTTGCAAGGCAACAGTGATCCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGTTTGCCCGTGATACCGAATggcg                                                                                                  >  8:277123/1‑147 (MQ=255)                                             aTGATTGCAGAGCTGTCATGAGCCCCTCCTTGAATGTCGACGTTGCAAGGCAACAGTGATCCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGTTTGCCCGTGATACCGAATGGGGAg                                                                                                <  5:312017/149‑1 (MQ=255)                                                     agagCTGTCATGAGCCCCTCCTTGAATGTCGACGTCGCAAGGCAACAGTGATCCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGTTTGCCCGTGATACCGAATGGGGAGCTGTTACa                                                                                        <  6:288787/149‑1 (MQ=255)                                                       agCTGTCATGAGCCCCTCCTTGAATGTCGACGTTGCAAGGCAACAGTGATCCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGTTTGCCCGTGATACCGAATGGGGAGCTGTTACAtt                                                                                      >  7:112663/1‑149 (MQ=255)                                                            tCATGAGCCCCTCCTTGAATGTCGACGTTGCAAGGCAACAGTGATCCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGTTTGCCCGTGATACCGAATGGGGAGCTGTTACATTTCttt                                                                                 <  2:68162/149‑1 (MQ=255)                                                                     cctcctTGAATGTCGACGTTGCAAGGCAACAGTGATCCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGTTTGCCCGTGATACCGAATGGGGAGCTGTTACATTTCTTTGCCAGTg                                                                          >  8:126536/1‑147 (MQ=255)                                                                      ctcctTGAATGTCGACGTTGCAAGGCAACAGTGATCCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGtt                                                                                                                       >  6:208677/1‑101 (MQ=255)                                                                      ctcctTGAATGTCGACGTTGCAAGGCAACAGTGATCCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGtt                                                                                                                       <  5:208677/101‑1 (MQ=255)                                                                      ctcctTGAATGTCGACGTTGCAAGGCAACAGTGATCCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGTTTGCCCGTGATACCGAATGGGGAGCTGTTACATTTCTTTGCCAGTGCag                                                                       <  7:180259/149‑1 (MQ=255)                                                                       tcctTGAATGTCGACGTTGCAAGGCAACAGTGATCCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGTTTGCCCGTGATACCGAATGGGGAGCTGTTACATTTCTTTGCCAGTGCa                                                                        >  1:100199/1‑147 (MQ=255)                                                                         ctTGAATGTCGACGTTGCAAGGCAACAGTGATCCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGTTTGCCCGTGATACCGAATGGGGAGCTGTTACATTTCTTTGCCAGTGCaga                                                                      <  7:126536/147‑1 (MQ=255)                                                                             aaTGTCGACGTTGCAAGGCAACAGTGATGCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGTGCGTTGAGCCGTTTGCGCGTGATAGCGAATGGGGAGCTGTTACATTTCTTTGCCAGTGCAGAGTTCAg                                                                <  1:18855/149‑1 (MQ=255)                                                                                gTCGACGTTGCAAGGCAACAGTGATCCGACATGGCGGCTTGACAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGTTTGCCCGTGATACCGAATg                                                                                                     >  7:177549/1‑109 (MQ=255)                                                                                gTCGACGTTGCAAGGCAACAGTGATCCGACATGGCGGCTTGACAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGTTTGCCCGTGATACCGAATg                                                                                                     <  8:177549/109‑1 (MQ=255)                                                                                   gACGTTGCAAGGCAACAGTGATCCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGt                                                                                                                        <  7:133054/87‑1 (MQ=255)                                                                                   gACGTTGCAAGGCAACAGTGATCCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGt                                                                                                                        >  8:133054/1‑87 (MQ=255)                                                                                       ttGCAAGGCAACAGTGATCCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGTTTGCCCGTGATACCGAATGGGGAGCTGTTACATTTCTTTGACAGTGCAGAGTTCAGGTCCGCAATc                                                      >  4:228243/1‑149 (MQ=255)                                                                                            aGGCAACAGTGATCCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGTTTGCCCGTGATACCGAATGGGGAGCTGTTACATTTCTTTGCCAGTGCAGAGTTCAGGTCCGCAATCCTTTg                                                 <  7:277123/149‑1 (MQ=255)                                                                                             ggCAACAGTGATCCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGTTTGCCCGTGATACCGAATGGGGAGCTGTTACATTTCTTTGCCAGTGCAGAGTTCAGGTcc                                                            >  5:292861/1‑137 (MQ=255)                                                                                             ggCAACAGTGATCCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGTTTGCCCGTGATACCGAATGGGGAGCTGTTACATTTCTTTGCCAGTGCAGAGTTCAGGTcc                                                            <  6:292861/137‑1 (MQ=255)                                                                                              gCAACAGTGATCCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACgggcaaacgggtctacgctcaagcccat                                                                                                                  <  4:102432‑M1/82‑29 (MQ=255)                                                                                              gCAACAGTGATCCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACgggcaaacgggtctacgctcaagcccat                                                                                                                  >  3:102432‑M1/1‑54 (MQ=255)                                                                                                aaCAGTGATCCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGTTTGCCCGTGATACCGAATGGGGAGCTGTTACATTTCTTTGCCAGTGCAGAGTTCAGGTCCGCAATCCTTTGCt                                               >  4:188079/1‑147 (MQ=255)                                                                                                    gTGATCCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGTTTGCCCGTGATACCGAATGGGGAGCTGTTACATTTCTTTGCCAGTGCAGAGTTCAGGTCCGCAATCCTTTGCTCAGc                                           >  2:145683/1‑147 (MQ=255)                                                                                                       aTCCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGTTTGCCCGTGATACCGAATGGGGAGCTGTTACATTTCTTTGCCAGTGCAGAGTTCAGGTCCGCAATCCTTTGCTCAGCCCGtt                                      <  8:112663/149‑1 (MQ=255)                                                                                                       aTCCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGTTTGCCCGTGATACCGAATGGGGAGCTGTTACATTTCTTTGCCAGTGCAGAGTTCAGGTCCGCAATCCTTTGCTCAGCCCGtt                                      >  8:342405/1‑149 (MQ=255)                                                                                                       aTCCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGTTTGCCCGTGATACCGAATGGGGAGCTGTTACATTTCTTTGCCAGTGCAGAGTTCAGGTCCGCAATCCTTTGCTCAGCCCGtt                                      <  5:106298/149‑1 (MQ=255)                                                                                                       aTCCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGTTTGCCCGTGATACCGAATGGGGAGCTGTTACATTTCTTTGCCAGTGCAGAGTTCAGGTCCGCAATCCTTTGCTCAGCCCGtt                                      >  4:144490/1‑149 (MQ=255)                                                                                                        tCCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGTTTGCCCGTGATACCGAATGGGGAGCTGTTACATTTCTTTGCCAGTGCAGAGTTCAGGTCCGCAATCCTTTGCTCAGCCCGTTc                                     <  4:325425/149‑1 (MQ=255)                                                                                                         ccGCCATGGCGGCTTGGCATCCGTCATACGGGCCCGGTATCACATGGGCTTGAGCGTAGTCCCGTTTGCCCGTGATACCGAATGGGGAGCTGTTACATTTCTTTGCCAGTGCAGAGTTCAGGTCCGCAATCCTTTGCTCAGCCCGTTcc                                    <  4:68048/149‑1 (MQ=255)                                                                                                         ccGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGTTTGCCCGTGATACCGAATGGGGAGCTGTTACATTTCTTTGCCAGTGCAGAGTTCAGGTCCGCAATCCTTTGCTCAGCCCGTTcc                                    >  4:365784/1‑149 (MQ=255)                                                                                                           gACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGTTTGCCCGTGATACCGAATGGGGAGCTGTTACATTTCTTTGCCAGTGCAGAGTTCAGGTCCGCAATCCTTTGCTCAGCCCGTTCCCt                                  >  4:191601/1‑149 (MQ=255)                                                                                                             cATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGTTTGCCCTTGATACCGAATGGGGAGCTGTTACATTTCTTTGCCAGTGCAGAGTTCAGGTCCGCAATCCTTTGCTCAGCCCGTTCCCTTc                                <  2:100199/149‑1 (MQ=255)                                                                                                                   ggcTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGTTTGCCCGTGATACCGAATGGGGAGCTGTTACATTTCTTTGCCAGTGCAGAGTTCAGGTCCGCAATCCTTTGCTCAGc                                           <  7:183254/132‑1 (MQ=255)                                                                                                                   ggcTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGTTTGCCCGTGATACCGAATGGGGAGCTGTTACATTTCTTTGCCAGTGCAGAGTTCAGGTCCGCAATCCTTTGCTCAGc                                           >  8:183254/1‑132 (MQ=255)                                                                                                                   ggcTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGTTTGCCCGTGATACCGAATGGGGAGCTGTTACATTTCTTTGCCAGTGCAGAGTTCAGGTCCGCAATCCTTTGCTCAGCCCGTTCCCTTCTATTa                           >  7:145246/1‑148 (MQ=255)                                                                                                                          cAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGTTTGCCCGTGATACCGAATGGGGAGCTGTTACATTTCTTTGCCAGTGCAGAGTTCAGGTCCGCAATCCTTTGCTCAGCCCGTTCCCTTCTATTAAATAAccc                   >  4:74761/1‑149 (MQ=255)                                                                                                                           aGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGTTTGCCCGTGATACCGAATGGGGAGCTGTTACATTTCTTTGCCAGTGCAGAGTTCAGGTCCGCAATCCTTTGCTCAGCCCGTTCCCTTCTATTAAATAAcccc                  <  3:375045/149‑1 (MQ=255)                                                                                                                            gCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGTTTGCCCGTGATACCGAATGGGGAGCTGTTACATTTCTTTGCCAGTGCAGAGTTCAGGTCCGCAATCCTTTGCTCAGCCCGTTCCCTTCTATTAAATAACCCCa                 <  1:145683/149‑1 (MQ=255)                                                                                                                                    agGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGTTTGCCCGTGATACCGAATGGGGAGCTGTTACATTTCTTTGCCAGTGCAGAGTTCAGGTCCGCAATCCTTTGCTCAGCCCGTTCCCTTCTATTAAATAACCCCAGTTATAGc         >  6:350643/1‑149 (MQ=255)                                                                                                                                          ccGGTATCACATGGGCTTGAGCGTAGACCCGTTTGCCCGTGATACCGAATGGGGAg                                                                                                >  4:187781/1‑56 (MQ=255)                                                                                                                                          ccGGTATCACATGGGCTTGAGCGTAGACCCGTTTGCCCGTGATACCGAATGGGGAg                                                                                                <  3:187781/56‑1 (MQ=255)                                                                                                                                           cGGTATCACATGGGCTTGAGCGTAGACCCGTTTGCCCgtgataccgggcccctctgacggctgccaagccgccatgtcggatcactgttgccttgcaacgtcgacattcaaggaggggctcatgacagctctgcaatcattcctcacaa  <  5:312021‑M2/149‑113 (MQ=255)                                                                                                                                                   |                                                                                                                                             CAGCCACAACCAGGCGCTGGTACCGAGGACAGGTGTTGTGAGGAATGATTGCAGAGCTGTCATGAGCCCCTCCTTGAATGTCGACGTTGCAAGGCAACAGTGATCCGACATGGCGGCTTGGCAGCCGTCAGAGGGGCCCGGTATCACATGGGCTTGAGCGTAGACCCGTTTGCCCGTGATACCGAATGGGGAGCTGTTACATTTCTTTGCCAGTGCAGAGTTCAGGTCCGCAATCCTTTGCTCAGCCCGTTCCCTTCTATTAAATAACCCCAGTTATAGCCAAAACC  >  NC_002947/2786606‑2786892

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.