New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 5746768	49 (0.930)	4 (0.080)	4/234	NT	8.0%	coding (1262/1422 nt)	PP_5043	PhoPQ‑activated pathogenicity‑like protein
	?	NC_002947	= 5746784	45 (0.900)					coding (1246/1422 nt)	PP_5043	PhoPQ‑activated pathogenicity‑like protein

CCCTGATCCGCTGGTGGATGCTCAGGATAAGTCTGCGGCAAAACGCTGACCGGGCTGGTGACAACGAAACCATCAGCAAACCGCGCCTCTACGAACCGCGCCTGCCAGCCTTGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCATGGCGGAAGTCCCGATCCAAGGGGTTAGCCGCAGTCCATACCTTCACTGCTACAGGCATTTCCGAAAGCCGTACCAGCACATGCGCAGCTCCTTCGCCCGGAGCC  >  NC_002947/5746639‑5746932                                                                                                                                                  |                                                                                                                                                      cccTGATCCGCTGGTGGATGCTCAGGATAAGTCTGCGGCAAAACGCTGACCGGGCTGGTGACAACGAAACCATCAGCAAACCGCGCCTCTACGAACCGCGCCTGCCAGCCTTGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTCactg                                                                                                                                                   <  1:973004‑M2/150‑5 (MQ=255) cccTGATCCGCTGGTGGATGCTCAGGATAAGTCTGCGGCAAAACGCTGACCGGGCTGGTGACAACGAAACCATCAGCAAACCGCGCCTCTACGAACCGCGCCTGCCAGCCTTGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTCactg                                                                                                                                                   <  2:757355‑M2/150‑5 (MQ=255)          gCTGGTGGATGCTCAGGATAAGTCTGCGGCAAAACGCTGACCGGGCTGGTGACAACGAAACCATCAGCAAACCGCGCCTCTACGAACCGCGCCTGCCAGCCTTGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTCactggg                                                                                                                                                 >  1:1162868‑M2/1‑137 (MQ=255)          gCTGGTGGATGCTCAGGATAAGTCTGCGGCAAAACGCTGACCGGGCTGGTGACAACGAAACCATCAGCAAACCGCGCCTCTACGAACCGCGCCTGCCAGCCTTGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTCactggg                                                                                                                                                 <  2:1162868‑M2/143‑7 (MQ=255)              gtggATGCTCAGGATAAGTCTGCGGCAAAACGCTGACCGGGCTGGTGACAACGAAACCATCAGCAAACCGCGCCTCTACGAACCGCGCCTGCCAGCCTTGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTCACTGGGGATGATCGTCt                                                                                                                                      <  1:973188/150‑1 (MQ=255)                        aGGATAAGTCTGCGGCAAAACGCTGACCGGGCTGGTGACAACGAAACCATCAGCAAACCGCGCCTCTACGAACCGCGCCTGCCAGCCTTGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTCACTGGGGATGATCGTCTGCGATGTGTa                                                                                                                            <  1:767465/150‑1 (MQ=255)                             aagcatGCGGCAAAACGCTGACCGGGCTGGTGACAACGAAACCATCAGCAAACCGCGCCTCTACGAACCGCGCCTGCCAGCCTTGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTa                                                                                                                      <  1:704014/145‑1 (MQ=255)                                  tGCGGCAAAACGCTGACCGGGCTGGTGACAACGAAACCATCAGCAAACCGCGCCTCTACGAACCGCGCCTGCCAGCCTTGCGCCGGCGGCGCCCAGTCAAGGCTGAACGGCGGACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCg                                                                                                                 >  1:374214/1‑150 (MQ=255)                                        aaaaCGCTGACCGGGCTGGTGACAACGAAACCATCAGCAAACCGCGCCTCTACGAACCGCGCCTGCCAGCCTTGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCa                                                                                                           >  1:873625/1‑150 (MQ=255)                                        aaaaCGCTGACCGGGCTGGTGACAACGAAACCATCAGCAAACCGCGCCTCTACGAACCGCGCCTGCCAGCCTTGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTAACTGGGGATGATCGTATGCAAAGCGTAGC‑GTACGCCGCatgaa                                                                                                           >  2:227339/1‑146 (MQ=255)                                           aCGCTGACCGGGCTGGTGACAACGAAACCATCAGCAAACCGCGCCTCTACGAACCGCGCCTGCCAGCCTTGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCATgg                                                                                                        <  1:757355/150‑1 (MQ=255)                                            cGCTGACCGGGCTGGTGACAACGAAACCATCAGCAAACCGCGCCTCTACGAACCACGCCTGCCAGCCTTGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCATGGc                                                                                                       <  2:750231/150‑1 (MQ=255)                                             gCTGACCGGGCTGGTGACAACGAAACCATCAGCAAACCGCGCCTCTACGAACCGCGCCTGCCAGCCTTGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCATGGCg                                                                                                      >  2:1338650/1‑150 (MQ=255)                                              cTGACCGGGCTGGTGACAACGAAACCATCAGCAAACCGCGCCTCTACGAACCGCGCCTGCCAGCCTTGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCATGGCgg                                                                                                     <  2:833428/150‑1 (MQ=255)                                                    gggCTGGTGACAACGAAACCATCAGCAAACCGCGCCTCTACGAACCGCGCCTGCCAGCCTTGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCATGGCGGAAGTcc                                                                                               <  2:864658/150‑1 (MQ=255)                                                       cTGGTGACAACGAAACCATCAGCAAACCGCGCCTCTACGAACCGCGCCTGCCAGCCTTGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCATGGCGGAAGTCCCGa                                                                                            <  1:495834/150‑1 (MQ=255)                                                           tGACAACGAAACCATCAGCAAACCGCGCCTCTACGAACCGCGCCTGCCAGCCTTGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCATGGCGGAAGTCCCGa                                                                                            <  2:1001173/146‑1 (MQ=255)                                                           tGACAACGAAACCATCAGCAAACCGCGCCTCTACGAACCGCGCCTGCCAGCCTTGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCATGGCGGAAGTCCCGa                                                                                            >  1:1001173/1‑146 (MQ=255)                                                             aCAACGAAACCATCAGCAAACCGCGCCTCTACGAACCGCGCCTGCCAGCCTTGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCATGGTGGAAGTCCCGATCCAAg                                                                                      <  1:1300065/150‑1 (MQ=255)                                                               aaCGAAACCATCAGCAAACCGCGCCTCTACGAACCGCGCCTGCCAGCCTTGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCATgg                                                                                                        <  2:64582/130‑1 (MQ=255)                                                               aaCGAAACCATCAGCAAACCGCGCCTCTACGAACCGCGCCTGCCAGCCTTGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCATgg                                                                                                        >  1:64582/1‑130 (MQ=255)                                                                aCGAAACCATCAGCAAACCGCGCCTCTACGAACCGCGCCTGCCAGCCTTGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCATGGCGGAAGTCCCGATCCAAgggg                                                                                   >  1:270412/1‑150 (MQ=255)                                                                       cATCAGCAAACCTCCCCTCTACGAACCGCCCCTTCCAGCCTTGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCATGGCGGAAGTCCCGATCCAAGGGGTTAGCCg                                                                            >  2:797935/1‑150 (MQ=255)                                                                       cATCAGCAAACCGCGCCTCTACGAACCGCGCCTGCCAGCCTTGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCATGGCGGAAGTCCCGATCCAAGGGGTTAGCCg                                                                            <  1:1042988/150‑1 (MQ=255)                                                                            gCAAACCGCGCCTCTACGAACCGCGCCTGCCAGCCTTGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCATGGCGGAAGTCCCGATCCAAGGGGTTAGCCGCAGTc                                                                       >  1:1168252/1‑150 (MQ=255)                                                                              aaaCCGCGCCTCTACGAACCGCGCCTGCCAGCCTTGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTCACTGGGgatga                                                                                                                                            >  1:628122/1‑80 (MQ=255)                                                                              aaaCCGCGCCTCTACGAACCGCGCCTGCCAGCCTTGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTCACTGGGgatga                                                                                                                                            <  2:628122/80‑1 (MQ=255)                                                                               aaCCGCGCCTCTACGAACCGCGCCTGCCAGCCTTGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCATGGCGGAAGTCCCGATCCAAGGGGTTAGCCGCAGTCCAt                                                                    <  2:1168252/150‑1 (MQ=255)                                                                                   gcgcCTCTACGAACCGCGCCTGCCAGCCTTGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCATGGCGGAAGTCCCGATCCAAGGGGTTAGCCGCAGTCCATACCt                                                                >  2:1236434/1‑150 (MQ=255)                                                                                       ctctACGAACCGCGCCTGCCAGCCTTGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCTTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCATTGCGGAAGTCCCGATCCAAGGGGTTATCCGCAGTCCATACCTTCAc                                                            <  2:408010/150‑1 (MQ=255)                                                                                        tctACGAACCGCGCCTGCGAGCCTTGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCATGGCGGAAGTCCCGATCCAAGGGGTTAGCCGCAGTCCATACCTTCACt                                                           >  1:48754/1‑150 (MQ=255)                                                                                          gtagaggcgcgCCTGCCAGCCTTGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCATGGCGGAAGTCCCGATCCAAGGGGTTAGCCGCAGTCCATACCTTCACTGc                                                         <  1:561472/143‑1 (MQ=255)                                                                                             gAACCGCGCCTGCCAGCCTTGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCATGGCGGaa                                                                                                   <  2:967629/105‑1 (MQ=255)                                                                                             gAACCGCGCCTGCCAGCCTTGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCATGGCGGaa                                                                                                   >  1:967629/1‑105 (MQ=255)                                                                                              aaCCGCGCCTGCCATCCTTGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCATGGCGGAAGTCCCGATCCAAGGGGTTAGCCGCAGTCCATACCTACACTGCTACa                                                     <  2:80294/150‑1 (MQ=255)                                                                                                  gcgcCTGCCAGCCTTGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCATGGCGGAAGTCCCGATCCAAGGGGTTAGCCGCAg                                                                         <  1:508723/126‑1 (MQ=255)                                                                                                  gcgcCTGCCAGCCTTGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCATGGCGGAAGTCCCGATCCAAGGGGTTAGCCGCAg                                                                         >  2:508723/1‑126 (MQ=255)                                                                                                           aGCCTTGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCATGGCGGAAGTCCCGATCCAAGGGGTTAGCCGCAGTCCATACCTTCACTGCTACAGGCATTTCCGaaa                                        <  2:908457/150‑1 (MQ=255)                                                                                                            gCCTTGCGCCGGCGGCGCCTACTCAAGGCTGCTCGCTGCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCTGGCATGGCGGAAGTCCCGATCCAATGGGTTAGTCGCAGTCCATACCTTCCCTGCTACAGGCATTTCCGAAAg                                       <  1:227339/150‑1 (MQ=255)                                                                                                              cTTGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCATGGCGGAAGTCCCGATCCAAGGGGTTAGCCGCAGTCCATACCTTCACTGCTACAGGCATTTCCGAAAGcc                                     >  2:493228/1‑150 (MQ=255)                                                                                                              cTTGCGCCGGAGGAGGCCAGTCAAGGCGGAACGCCTCACTGGAAATCGTAAGC‑GCGCAGTCTGGCGGTGCCCTGACGGCATGGCGGAAGTCCCGATCCAAGGGGTTAGCAGCAGTCCATACCTTCACTGCTACAGGCATTTCCGAAAGcc                                     <  1:1236434/150‑1 (MQ=255)                                                                                                               ttGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTCactgggcgctgccggcgcccaggttgcaggcgcggttggtagaggcgcggtttgctgatggtttcgttgtcaccagcccggtcagcgttttgccgcagacttatcctgagcatc                                     <  1:1243905‑M2/150‑115 (MQ=255)                                                                                                               ttGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCATGGCGGAAGTCCCGATCCAAGGGGTTAGCCGCAGTCCATACCTTCACTGCTACAGGCATTTCCGAAAGc                                      <  1:741790/148‑1 (MQ=255)                                                                                                               ttGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCATGGCGGAAGTCCCGATCCAAGGGGTTAGCCGCAGTCCATACCTTCACTGCTACAGGCATTTCCGAAAGc                                      >  2:741790/1‑148 (MQ=255)                                                                                                                  ggcCGGCGGCGCCCAGTCAAGGCTGAACGCCTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCATGGCGGAAGTCCCGATCCAAGGGGTTAGCCGCAGTCCATCCCTTCACTGCTACAGGCATTTCCGAAAGCCGTAc                                 <  2:63795/149‑1 (MQ=255)                                                                                                                    ccGGCGGCGCCCAGTCAAGGCTGAACGCCTCactgggcgccgccggcgcaaggctggcaggcgcggttcgtagaggcgcggtttgctgatggtttcgttgtcacca                                                                            <  2:509269‑M2/106‑76 (MQ=255)                                                                                                                    ccGGCGGCGCCCAGTCAAGGCTGAACGCCTCactgggcgccgccggcgcaaggctggcaggcgcggttcgtagaggcgcggtttgctgatggtttcgttgtcacca                                                                            >  1:509269‑M2/1‑31 (MQ=255)                                                                                                                          gcgcCCAGTCAAGGCTGAACGCCTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCATGGCGGAAGTCCCGATCCAAGGGGTTAGCCGCAGTCCATACCTTCACTGCTACAGGCATTTCCGAAAGCCGTACCAGCACAt                         <  2:973004/150‑1 (MQ=255)                                                                                                                            gcCCAGTCAAGGCTGAACGCCTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCATGGCGGAAGTCCCGATCCAAGGGGTTAGCCGCAGTCCATACCTTCACTGCTACAGGCATTTCCGAAAGCCGTACCAGCACATgc                       >  2:1184626/1‑150 (MQ=255)                                                                                                                             cccTGTCAAGGCCAAACGCCTCCCTGGGAATGACCGTGTGCTTTGTGTAAC‑GTACCCCGCAGGCATGGCGGAAGTCCCGATCCAAGGGGTTAGCCGCAGTCCATACCTTCACTGCTACAGGCATTTCCGAAAGCCGTACCAGCACATgcg                      <  2:374214/150‑1 (MQ=255)                                                                                                                                aGTCAAGGCTGAACGCCTCactgggcgccgccggcgcaaggctggcaggcgcggttcgtagaggcgcggtttgctgatggtttcgttgtcaccagcccggtcagcgttttgccgcagacttatcctgagcatccaccagcggatcagggg                    >  2:1243905‑M2/1‑19 (MQ=255)                                                                                                                                aGTCAAGGCTGAACGCCTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCATGGCGGAAGTCCCGATCCAAGGGGTTAGCAGCAGTCCATACCTTAACCAGATCGGGCATGTCCGAAAGCCGTACCAGCACATGCGCAg                   >  2:474076/1‑150 (MQ=255)                                                                                                                                 gTCAAGGCTGAACGCCTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCATGGCGGAAGTCCCGATCCAAGGGGTTAGcc                                                                             <  1:1272336/91‑1 (MQ=255)                                                                                                                                 gTCAAGGCTGAACGCCTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCATGGCGGAAGTCCCGATCCAAGGGGTTAGcc                                                                             >  2:1272336/1‑91 (MQ=255)                                                                                                                                 gTCAAGGCTGAACGCCTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCATGGCGGAAGTCCCGATCCAAGGGGTTAGCCGCAGTCCATACCTTCACTGCTACAGGCATTTCCGAAAGCCGTACCAGCACATGCGCAGc                  <  2:1423709/150‑1 (MQ=255)                                                                                                                                                cTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCATGGCGGAAGTCCCGATCCAAGGGGTTAGCCGCAGTCCATACCTTCACTGCTACAGGCATTTCCGAAAGCCGTACCAGCACATGCGCAGCTCCTTCGCCCGGAGc   >  1:293051/1‑150 (MQ=255)                                                                                                                                                cTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCATGGCGGAAGTCCCGATCCAAGGGGTTAGCCGCAGTCCATACCTTCACTGCTACAGGCATTTCCGAAAGCCGTACCAGCACATGCGCAGCTCCTTCGCCCGGAGc   <  1:493228/150‑1 (MQ=255)                                                                                                                                                 tCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCATGGCGGAAGTCCCGATCCAAGGGGTTAGCCGCAGTCAATACCTTCACTGCTACAGGCATTTCCGAAATCCGTACCACCACATACCCAGCTCCTTCGCCCGGacca  >  2:179783/1‑147 (MQ=255)                                                                                                                                                  |                                                                                                                                                      CCCTGATCCGCTGGTGGATGCTCAGGATAAGTCTGCGGCAAAACGCTGACCGGGCTGGTGACAACGAAACCATCAGCAAACCGCGCCTCTACGAACCGCGCCTGCCAGCCTTGCGCCGGCGGCGCCCAGTCAAGGCTGAACGCCTCACTGGGGATGATCGTCTGCGATGTGTAGC‑GTACCCCGCAGGCATGGCGGAAGTCCCGATCCAAGGGGTTAGCCGCAGTCCATACCTTCACTGCTACAGGCATTTCCGAAAGCCGTACCAGCACATGCGCAGCTCCTTCGCCCGGAGCC  >  NC_002947/5746639‑5746932

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ 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.