New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	3576788 =	NA (NA)	91 (1.390)	64/292	0.0	95.8%	intergenic (+10/‑55)	yrhA/insA	pseudogene, interrupted by IS1E/IS1 repressor TnpA
	?	CP009273	= 3649852	4 (0.060)					coding (249/333 nt)	hdeA	stress response protein acid‑resistance protein

CTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAGCGCT  >  CP009273/3576644‑3576930                                                                                                                                                 |                                                                                                                                               ctctCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGa                                                                                                                                            >  1:509951/1‑149 (MQ=255)  tctcGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGAt                                                                                                                                           <  1:1117870/149‑1 (MQ=255)      gATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGACCAAGTAAAAATCTCATAAACCCTGATCTACAAGAACGGTTAGTGAACGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGAtgctg                                                                                                                                       <  1:261989/149‑1 (MQ=255)      gATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATCATGATGATTTCATACGCACTGGTCTAGAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGa                                                                                                                                            <  2:129/144‑1 (MQ=255)       aTTCCAGAACCTTCAGTTAAAAACCTTTTTTTTTTTTTTTTATTCTATAGAAATAATGATGATTTCATAAACCCTGATCTAGAAGAACGGTTGCTGATCGGGGATTATAGCATTTCAATTTTTACTTATGACATTTAAGGTGAt                                                                                                                                           >  2:591950/1‑144 (MQ=255)       aTTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGAtgctgc                                                                                                                                      >  1:889552/1‑149 (MQ=255)            aGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATTAATTTTATAGAAATAATTATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGAtgctgc                                                                                                                                      <  2:377772/144‑1 (MQ=255)            aGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATCTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACAGTAAAGGTGAtgctgc                                                                                                                                      <  2:63412/144‑1 (MQ=255)                 cTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTg                                                                                                                            >  1:119039/1‑149 (MQ=255)                    cAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGAACTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGTTGATGCCGCCAACTTAc                                                                                                                              >  2:448865/1‑144 (MQ=255)                     aGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACt                                                                                                                             >  2:946202/1‑144 (MQ=255)                      gTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTg                                                                                                                            <  2:941222/144‑1 (MQ=255)                       ttAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGGTTTAg                                                                                                                      >  1:945224/1‑149 (MQ=255)                         aaaaaCCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAgtg                                                                                                                    >  1:1013615/1‑149 (MQ=255)                          aaaaCCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATATACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATGAAAGGTGAGGCTGCCAACTTACTGATTTAgggt                                                                                                                   >  1:97577/1‑149 (MQ=255)                           aaaCCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTa                                                                                                                       <  2:683236/144‑1 (MQ=255)                           aaaCCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTa                                                                                                                       <  2:599754/144‑1 (MQ=255)                                   ttGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTatta                                                                                                               <  2:888519/144‑3 (MQ=255)                                      ccGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTAGGATgg                                                                                                            >  2:198748/1‑144 (MQ=255)                                                 ttttATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAAATTTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTc                                                                                            <  1:215569/149‑1 (MQ=255)                                                    tataGAAATAATGATGATTTCATAAACCCTGAGCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGc                                                                                              <  2:507752/144‑1 (MQ=255)                                                      taGAAATAATGATGATTTGATATAGGCTGATCTACCAGAACGGTTAGTGATCGGGGATTAGAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTc                                                                                            <  2:931865/144‑1 (MQ=37)                                                                gatgatTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGttt                                                                             <  1:878676/149‑1 (MQ=255)                                                                  tgatTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCt                                                                           <  1:861122/149‑1 (MQ=255)                                                                               ccTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCcct                                                              >  1:351611/1‑149 (MQ=255)                                                                                 tGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCcctcc                                                            >  1:360188/1‑149 (MQ=255)                                                                                 tGATCTACAAGAACGGGTAGTGATCGGGGCTTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTCGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCcctcc                                                            >  1:704411/1‑149 (MQ=255)                                                                                     cTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGtt                                                        >  1:115515/1‑149 (MQ=255)                                                                                      tACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTc                                                       <  1:656625/149‑1 (MQ=255)                                                                                        cAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAg                                                     <  1:1030731/149‑1 (MQ=255)                                                                                          cgAACGGTTAGTGAGCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGtt                                                        <  2:907768/143‑1 (MQ=255)                                                                                           gAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTCTTc                                                       >  2:352934/1‑144 (MQ=255)                                                                                             aCGGTTAGTGGTCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGAGTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAg                                                     <  2:1748/144‑1 (MQ=255)                                                                                                     tGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTTAGGTGCTCCAGTGGCTTCTGCTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGAc                                             >  2:274974/1‑144 (MQ=255)                                                                                                     ggATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGGGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGggt                                        <  1:44540/148‑1 (MQ=255)                                                                                                      gaacgaggATTATAGCATTACAATGTTTACTGATGACATTAATGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACg                                            >  2:858279/7‑144 (MQ=17)                                                                                                        tCGGGGATTATAGCATTTCAATATGTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTCGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCCGTTCAGCTACTGACggg                                          <  2:754684/144‑1 (MQ=255)                                                                                                          ggggATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGc                                   <  1:1120422/149‑1 (MQ=255)                                                                                                          ggggATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGc                                   <  1:519033/149‑1 (MQ=255)                                                                                                           gggATTATAGCATTGCAATATTTACTTATGGCGTTAAAGGTGATGCTGCCAACCTACTGATTTAGTGTATGATGGGGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGggtg                                       <  2:869390/144‑1 (MQ=17)                                                                                                              aTTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGgtggtg                                    >  2:198511/1‑144 (MQ=255)                                                                                                               ttATAGAATTTCAATATTTACTTATGACATTAATGGTGATGCTGCCAACTTACTGACTTAGTGTATGATGGTTTTTTTGACGTGCTCCAGTGGGTTCTGTTTATATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGc                                   <  2:5800/144‑1 (MQ=17)                                                                                                                tataGCATTTCAATATGTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACg                             <  1:979996/149‑1 (MQ=255)                                                                                                                 ataGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACgg                            <  1:1004498/149‑1 (MQ=255)                                                                                                                  taGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGtt                                >  2:686129/1‑143 (MQ=255)                                                                                                                  taGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACAGACGGGGTGGTGCGTAGCGGc                           >  1:22279/1‑149 (MQ=255)                                                                                                                   agtaTTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTTATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTaa                               <  2:733331/141‑1 (MQ=255)                                                                                                                   aGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTaa                               <  2:930231/144‑1 (MQ=255)                                                                                                                     cATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCCACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGGGCTGCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCGGCTACTGACGGGGTGGCGCGTAACg                             >  2:524/1‑144 (MQ=17)                                                                                                                          cAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTACGTGACGGCgaa                        >  2:162755/1‑144 (MQ=255)                                                                                                                            atttttACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAg                      <  2:812622/141‑1 (MQ=255)                                                                                                                              atTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTTTGATGGTGATTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGCTGGTGCGTAACGGCAAAGGCAccgcc               >  1:650737/1‑149 (MQ=255)                                                                                                                               tttACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCAccgccg              <  1:282427/149‑1 (MQ=255)                                                                                                                                ttACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCAcc                  <  2:865782/144‑1 (MQ=255)                                                                                                                                   cTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGTTGCTTTAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCAccgcc               >  2:430067/1‑144 (MQ=255)                                                                                                                                    ttATGACATTAAAGGTGATGCTGCAAACTTACTGATTTAGTGTATGAGGGTGTTTTTGAGGTACTCCAGTGACTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCAgcgccc              >  2:117447/1‑143 (MQ=14)                                                                                                                                      aTGACATTACAGGTGATGCTGCCCACTTACTGATTTAGTGTCTGCTGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCCGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCa       <  1:932288/149‑1 (MQ=11)                                                                                                                                           aTTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAGCGCt  >  1:470686/1‑149 (MQ=33)                                                                                                                                               aaGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAgcgc   <  2:974586/144‑1 (MQ=11)                                                                                                                                                 |                                                                                                                                               CTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAGCGCT  >  CP009273/3576644‑3576930

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ 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.