New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 4976313	39 (0.660)	4 (0.070)	4/240	NT	8.3%	coding (458/1155 nt)	flgJ	peptidoglycan hydrolase FlgJ
	?	NC_002947	= 4976408	52 (0.940)					coding (363/1155 nt)	flgJ	peptidoglycan hydrolase FlgJ

CAGGCCGTTGTCCGGCACGGCGAAGGCCTTGGCTACTGCCTGACCGTCACGGGCAGGCACGGCGGCGTTATTGGCAGTTTCCGCCGACGGCACGATACCGGCCAACAGGCGGTCGGTGAGTTTGCTTGGCAGGGCCAGGCGCCGCGCGTTGAGTGCAGCAACGTCGTTGCGCGTAGCGGACGAGGCCATGGCATGCGCTGGCTCCGCCACCTTGTTGCCCCACAATGCCGGGCCACCGCTATCGACGCGCGGGAACGGGCTGGTATTGATCGACGCACTGCGGCCCTTGGTC  >  NC_002947/4976165‑4976456                                                                                                                                                     |                                                                                                                                                cAGGCCGTTGTCCGGCACGGCGAAGGCCTTGGCTACTGCCTGACCGTCACGGGCAGGCACGGCGGCGTTATTGGCAGTTTCCGCCGACGGCACGATACCGGCCAACAGGCGGTCGGTGAGTTTGCTTGGCAGGGCCAGGCGCCGCGCGT                                                                                                                                                 <  3:78449‑M1/149‑1 (MQ=255)  aGGCCGTTGTCCGGCACGGCGAAGGCCTTGGCTACTGCCTGACCGTCACGGGCAGGCACGGCGGCGTTATTGGCAGTTTCCGCCGACGGCACGATACCGGCCAACAGGCGGTCGGTGAGTTTGCTTGGCAGGGCCAGGCGCCGCGCGtt                                                                                                                                                >  5:76388/1‑149 (MQ=255)    gCCGTTGTCCGGCACGGCGAAGGCCTTGGCTACTGCCTGACCGTCACGGGCAGGCACGGCGGCGTTATTGGCAGTTTCCGCCGACGGCACGATACCGGCCAACAGGCGGTCGGTGAGTTTGCTTGGCAGGGCCAGGCGCCGCGCGtt                                                                                                                                                >  5:321454/1‑147 (MQ=255)        ttGTCCGGCACGGCGAAGGCCTTGGCTACTGCCTGACCGTCACGGGCAGGCACGGCGGCGTTATTGGCAGTTTCCGCCGACGGCACGATACCGGCCAACAGGCGGTCGGTGAGTTTGCTTGGCAGGGCCAGGCGCCGCGCGTTGAGTgc                                                                                                                                          <  5:197066/149‑1 (MQ=255)              ggCACGGCGAAGGCCTTGGCTACTGCCTGACCGTCACGGGCAGGCACGGCGGCGTTATTGGCAGTTTCCGCCGACGGCACGATACCGGCCAACAGGCGGTCGGTGAGTTTGCTTGGCAGGGCCAGGCGCCGCGCGTTGAGTGCAGCAAc                                                                                                                                    <  8:74639/149‑1 (MQ=255)                  cGGCGAAGGCCTTGGCTACTGCCTGACCGTCACGGGCAGGCACGGCGGCGTTATTGGCAGTTTCCGCCGACGGCACGATACCGGCCAACAGGCGGTCGGTGAGTTTGCTTGGCAGGGCCAGGCGCCGCGCGTTGAGTGCAGCAAcgtcg                                                                                                                                <  1:314998/149‑1 (MQ=255)                  cGGCGAAGGCCTTGGCTACTGCCTGACCGTCACGGGCAGGCACGGCGGCGTTATTGGCAGTTTCCGCCGACGGCACGATACCGGCCAACAGGCGGTCGGTGAGTTTGCTTGGCAGGGCCAGGCGCCGCGCGTTGAGTGCAGCAAcgtcg                                                                                                                                <  3:19979/149‑1 (MQ=255)                     cGAAGGCCTTGGCTACTGCCTGACCGTCACGGGCAGGCACGGCGGCGTTATTGGCAGTTTCCGCCGACGGCACGATACCGGCCAACAGGCGGTCGGTGAGTTTGCTTGGCAGGGCCAGGCGCCGCGCGTTGa                                                                                                                                              >  1:175908/1‑132 (MQ=255)                      gAAGGCCTTGGCTACTGCCTGACCGTCACGGGCAGGCACGGCGGCGTTATTGGCAGTTTCCGCCGACGGCACGATACCGGCCAACAGGCGGTCGGTGAGTTTGCTTGGCAGGGCCAGGCGCCGCGCGTTGAGTGCAGCAACGTCGTTgc                                                                                                                            <  3:108827/149‑1 (MQ=255)                        aGGCCTTGGCTACTGCCTGACCGTCACGGGCAGGCACGGCGGCGTTATTGGCAGTTTCCGCCGACGGCACGATACCGGCCAACAGGCGGTCGGTGAGTTTGCTTGGCAGGGCCAGGCGCCGCGCGTTGAGTGCAGCAACGTCGTTgcgc                                                                                                                          <  3:301555/149‑1 (MQ=255)                        aGGCCTTGGCTACTGCCTGACCGTCACGGGCAGGCACGGCGGCGTTATTGGCAGTTTCCGCCGACGGCACGATACCGGCCAACAGGCGGTCGGTGAGTTTGCTTGGCAGGGCCAGGCGCCGCGCGTTGAGTGCAGCAACGTCGTTgcgc                                                                                                                          <  6:364212/149‑1 (MQ=255)                        aGGCCTTGGCTACTGCCTGACCGTCACGGGCAGGCACGGCGGCGTTATTGGCAGTTTCCGCCGACGGCACGATACCGGCCAACAGGCGGTCGGTGAGTTTGCTTGGCAGGGCCAGGCGCCGCGCGTTGAGTGCAGCAACGTCGTTgcgc                                                                                                                          <  4:235019/149‑1 (MQ=255)                            cTTGGCTACTGCCTGACCGTCACGGGCAGGCACGGCGGCGTTATTGGCAGTTTCCGCCGACGGCACGATACCGGCCAACAGGCGGTCGGTGAGTTTGCTTGGCAGGGCCAGGCGCCGCGCGTTGAGTGCAGCAACGTCGTTGCGCGTAg                                                                                                                      >  5:187354/1‑149 (MQ=255)                               ggCTACTGCCTGACCGTCACGGGCAGGCACGGCGGCGTTATTGGCAGTTTCCGCCGACGGCACGATACCGGCCAACAGGCGGTCGGTGAGTTTGTTTGGCAGGGCCAGGCGCCGCGCGTTGAGTGCAGCAACGTCGTTGCGCGTAGCg                                                                                                                    <  2:311922/148‑1 (MQ=255)                                    cTGCCTGACCGTCACGGGCAGGCACGGCGGCGTTATTGGCAGTTTCCGCCGACGGCACGATACCGGCCAACAGGCGGTCGGTGAGTTTGCTTGGCAGGGCCAGGCGCCGCGCGTTGAGTGCAGCAACGTCGTTGCGCGTAGCGGACGa                                                                                                               <  6:321454/148‑1 (MQ=255)                                       ccTGCCCGTGACGGTCAGGCACGGCGGCGTTATTGGCAGTTTCCGCCGACGGCACGATACCGGCCAACAGGCGGTCGGTGAGTTTGCTTGGCAGGGCCAGGCGCCGCGCGTTGAGTGCAGCAACGTCGTTGCGCGTAGCGGACGAGGc                                                                                                            >  4:117582/1‑148 (MQ=255)                                       ccTGACCGTCACGGGCAGGCACGGCGGCGTTATTGGCAGTTTCCGCCGACGGCACGATACCGGCCAACAGGCGGTCGGTGAGTTTGCTTGGCAGGGCCAGGCGCCGAGCGTTGAGTGCAGCAACGTCGTTGCGCGTAGCGGACGAGGc                                                                                                            >  5:357786/1‑148 (MQ=255)                                       ccTGACCGTCACGGGCAGGCACGGCGGCGTTATTGGCAGTTTCCGCCGACGGCACAATACCGGCCAACAGGCGGTCGGTGAGTTTGCTTGGCAGGGCCAGGCGCCGCGCGTTGAGTGCAGCAACGTCGTTGCGCGTAGCGGACGAgg                                                                                                             <  7:131579/147‑1 (MQ=255)                                       ccTGACCGTCACGGGCAGGCACGGCGGCGTTATTGGCAGTTTCCGCCGACGGCACAATACCGGCCAACAGGCGGTCGGTGAGTTTGCTTGGCAGGGCCAGGCGCCGCGCGTTGAGTGCAGCAACGTCGTTGCGCGTAGCGGACGAgg                                                                                                             >  8:131579/1‑147 (MQ=255)                                        cTGACCGTCACGGGCAGGCACGGCGGCGTTATTGGCAGTTTCCGCCGACGGCACGATACCGGCCAACAGGCGGTCGGTGAGTTTGCTTGGCAGGGCCAGGCGCCGCGCGTTGAGTGCAGCAACGTCGTTGCGCGTAGCGGACGAGGCCa                                                                                                          >  4:36002/1‑149 (MQ=255)                                        cTGACAGTCACGGGCAGGCACGGCGGCGTTATTGGCAGTTTCCGCCGACGGCACGATACCGGCCAACAGGCGGTCGGTGAGTTTGCTTGGCAGGGCCAGGCGCCGCGCGTcgatagcggtggcccggcattgtggggcaacaaggtggc                                                                                                          >  5:230165‑M1/1‑110 (MQ=255)                                           aCCGTCCCGGCCTGGCACGGCGGCGTTATTGGCAGTTTCCGCCGACGGCACGATACCGGCCAACAGGCGGTCGGTGAGTTTGCTTGGCAGGGCCAGGCGCCGCGCGTTGAGTGCAGCAACGTCGTTGCGCGTAGCGGACGAGGCCATg                                                                                                        <  1:166896/148‑1 (MQ=255)                                            ccGTCACGGGCAGGCACGGCGGCGTTATTGGCAGTTTCCGCCGACGGCACGATACCGGCCAACAGGCGGTCGGTGAGTTTGCTTGGCAGGGCCAGGCGCCGCGCGTTGAGTGCAGCAACGTCGTTGCGCGTAGCGGACGAGGCCATgg                                                                                                       >  3:229593/1‑148 (MQ=255)                                             cGTCACGGGCAGGCACGGCGGCGTTATTGGCAGTTTCCGCCGACGGCACGATACCGGCCAACAGGCGGTCGGTGAGTTTGCTTGGCAGGGCCAGGCGCCGCGCGTTGAGTGCAGCAACGTCGTTGCGCGTAGCGGACGAGGCCATGGCa                                                                                                     >  6:140208/1‑149 (MQ=255)                                                         gcaCGGCGGCGTTATTGGCAGTTTCCGCCGACGGCACGATACCGGCCAACAGGCGGTCGGTGAGTTTGCTTGGCAGGGCCAGGCGCCGCGCGTTGAGTGCAGCAACGTCGTTGCGCGTAGCGGACGAGGCCATGGCATGCGCTGGCTcc                                                                                         <  6:76388/149‑1 (MQ=255)                                                                   gTTATTGGCAGTTTCCGCCGACGGCACGATACCGGCCAACAGGCGGTCGGTGAGTTTGCTTGGCAGGGCCAGGCGCCGCGCGTTGAGTGCAGCAACGTCGTTGCGCGTAGCGGACGAGGCCATGGCATGCGCTGGCTCCGCCACCttgt                                                                               <  6:187354/149‑1 (MQ=255)                                                                    ttATTGGCAGTTTCCGCCGACGGCACGATACCGGCCAACAGGCGGTCGGTGAGTTTGCTTGGCAGGGCCAGGCGCCGCGCGTTGAGTGCAGCAACGTCGTTGCGCGTAGCGGACGAGGCCATGGCATGCGCTGGCTCCGCCACCttgtt                                                                              >  3:116643/1‑149 (MQ=255)                                                                    ttATTGGCAGTTTCCGCCGACGGCACGATACCGGCCAACAGGCGGTCGGTGAGTTTGCTTGGCAGGGCCAGGCGCCGCGCGTTGAGTGCAGCAACGTCGTTGCGCGTAGCGGACGAGGCCATGGCATGCGCTGGCTCCGCCACCttgtt                                                                              >  1:377945/1‑149 (MQ=255)                                                                                  cgccgACGGCACGATACCGGCCAACAGGCGGTCGGTGAGTTTGCTTGGCAGGTCCAGGCGCCGCGCGTTGAGTGCAGCAACGTCGTTGCGCGTAGCGGACGAGGCCATGGCATGCGCTGGCTCCGCCACCTTGTTGCCCCACAATGCCg                                                                <  8:67471/149‑1 (MQ=255)                                                                                          gCACGATACCGGCCAACAGGCGGTCGGTGAGTTTGCTTGGCAGGGCCAGGCGCCGCGCGTTGAGTGCAGCAACGTCGTTGCGCGTAGCGGACGAGGCCATGGCATGCGCTGGCTCCGCCACCTTGTTGCCCCACAATGCCGGGCCACCg                                                        <  4:229593/149‑1 (MQ=255)                                                                                            aCGATACCGGCCAACAGGCGGTCGGTGAGTTTGCTTGGCAGGGCCAGGCGCCGCGCGTcgatagcggtggcccggcattgtggggcaacaaggtggcggagccagcgcatgccatggcctcgtccgctacgcgcaacgacgttgctgca                                                      >  2:369974‑M1/1‑58 (MQ=255)                                                                                            aCGATACCGGCCAACAGGCGGTCGGTGAGTTTGCTTGGCAGGGCCAGGCGCCGCGCGTTGAGTGCAGCAACGTCGTTGCGCGTAGCGGACGAGGCCATGGCATGCGCTGGCTCCGCCACCTTGTTGCCCCACAATGCCGGGCCACCGCt                                                      <  7:318494/149‑1 (MQ=255)                                                                                             cGATACCGGCCAACAGGCGGTCGGTGAGTTTGCTTGGCAGGGCCAGGCGCCGCGCGTTGAGTGCAGCAACGTCGTTGCGCGTAGCGGACGAGGCCATGGCATGCGCTGGCTCCGCCACCTTGTTGCCCCACAATGCCGGGCCACCGCTa                                                     <  5:140208/149‑1 (MQ=255)                                                                                                      ccAACAGGCGGTCGGTGAGTTTGCTTGGCAGGGCCAGGCGCCGCGCGTTGAGTGCAGCAACGTCGTTGCGCGTAGCGGACGAGGCCATGGCATGCGCTGGCTCCGCCACCTTGTTGCCCCACAATGCCGGGCCACCGCTATCGacgcgc                                            <  1:154241‑M2/149‑7 (MQ=255)                                                                                                       cAACAGGCGGTCGGTGAGTTTGCTTGGCAGGGCCAGGCGCCGCGCGTcgatagcggtggcccggcattgtggggcaacaaggtggcggagccagcgcatgccatggcctcgtccgctacgcgcaacgacgttgctgcactcaacgcgcg                                           <  6:230165‑M1/149‑103 (MQ=255)                                                                                                        aaCAGGCGGTCGGTGAGTTTGCTTGGCAGGGCCAGGCGCCGCGCGTcgatagcggtggcccggcattgtggggcaacaaggtggcggagccagcgcatgccatggcctcgtccgctacgcgcaacgacgttgctgcactcaacgcgcgg                                          <  1:369974‑M1/149‑104 (MQ=255)                                                                                                        aaCAGGCGGTCGGTGAGTTTGCTTGGCAGGGCCAGGCGCCGCGCGTTGAGTGCAGCAACGTCGTTGCGCGTAGCGGACGAGGCCATGGCATGCGCTGGCTCCGCCACCTTGTTGCCCCACAATGCCGGGCCACCGCTATCGacgcgcgg                                          <  1:377610‑M2/149‑9 (MQ=255)                                                                                                          cAGGCGGTCGGTGAGTTTGCTTGGCAGGGCCAGGCGCCGCGCGTTGAGTGCAGCAACGTCGTTGCGCGTAGCGGACGAGGCCATGGCATGCGCTGGCTCCGCCACCTTGTTGCCCCACAATGCCGGGCCACCGCTATCGACGCGCggg                                         >  8:111659/1‑148 (MQ=255)                                                                                                             gCGGTCGGTGAGTTTGCTTGGCAGGGCCAGGCGCCGCGCGTTGAGTGCAGCAACGTCGTTGCGCGTAGCGGACGAGGCCATGGCATGCGCTGGCTCCGCCACCTTGTTGCCCCACAATGCCGGGCCACCGCTATCGACGCGCGGGAACg                                     >  8:325496/1‑149 (MQ=255)                                                                                                                gtcggtGAGTTTGCTTGGCAGGGCCAGGCGCCGCGCGTTGAGTGCAGCAACGTCGTTGCGCGTAGCGGACGAGGCCATGGCATGCGCTGGCTCCGCCACCTTGTTGCCCCACAATGCCGGGCCACCGCTATCGACGCGCGGGAACGGGc                                  <  2:377945/149‑1 (MQ=255)                                                                                                                     tGAGTTTGCTTGGCAGGGCCAGGCGCCGCGCGTTGAGTGCAGCAACGTCGTTGCGCGTAGCGGACGAGGCCATGGCATGCGCTGGCTCCGCCACCTTGTTGCCCCACAATGCCGGGCCACCGCTATCGACGCGCGGGAACGGGCTGGTa                             >  4:176711/1‑149 (MQ=255)                                                                                                                     tGAGTTTGCTTGGCAGGGCCAGGCGCCGCGCGTTGAGTGCAGCAACGTCGTTGCGCGTAGCGGACGAGGCCATGGCATGCGCTGGCTCCGCCACCTTGTTGCCCCACAATGCCGGGCCACCGCTATCGACGCGCGGGAACGGGCTGGTa                             >  7:63653/1‑149 (MQ=255)                                                                                                                            gCTTGGCAGGGCCAGGCGCCGCGCGTTGAGTGCAGCAACGTCGTTGCGCGTAGCGGACGAGGCCATGGCATGCGCTGGCTCCGCCACCTTGTTGCCCCACAATGCCGGGCCACCGCTATCGACGCGCGGGAACGGGCTGGTATTGATc                       >  8:152419/1‑148 (MQ=255)                                                                                                                             cTTGGCAGGGCCAGGCGCCGCGCGGTGAGGGCAGCAACGTCGTTGCGCGTAGCGGACGAGGCCATGGCATGCGCTGGCTCCGCCACCTTGTTGCCCCACAATGCCGGGCCACCGCTATCGACGCGCGGGAACGGGCTGGTATTGATCGa                     <  7:163760/149‑1 (MQ=255)                                                                                                                                ggCAGGGCCAGGCGCCGCGCGTTGAGTGCAGCAACGTCGTTGCGCGTAGCGGACGAGGCCATGGCATCCGCTGGCTCCGCCACATTGTTGCCCAACAATGCAGGGCCACCGCTATCGACGCGCGGGAACGGGCTGGAATTGATCTACg                   >  6:357279/1‑148 (MQ=255)                                                                                                                                 gCAGGGCCAGGCGCCGCGCGTTGAGTGCAGCAACGTCGTTGCGCGTAGCGGACGAGGCCATGGCATGCGCTGGCTCCGCCACCTTGTTGCCCCACAATGCCGGGCCACCGCTATCGACGCGCGGGAACGGGCTGGTATTGATCGACGCa                 <  6:357786/149‑1 (MQ=255)                                                                                                                                     ggCCAGGCGCCGCGCGTTGAGTGCAGCAACGTCGTTGCGCGTAGCGGACGAGGCCATGGCATGCGCTGGCTCCGCCACCTTGTTGCCCCACAATGCCGGGCCACCGCTATCGACGCGCTGGAACGGGCTGGTATTGATCGACGCACTGc             <  5:357279/149‑1 (MQ=255)                                                                                                                                              ccgcGCGTcgatagcggtggcccggcattgtggggcaacaaggtggcggagccagcgcatgccatggcctcgtccgctacgcgcaacgacgttgctgcactcaacgcgcggcgcctggccctgccaagcaaactcaccgaccgcctgtt    <  1:377610‑M1/149‑142 (MQ=255)                                                                                                                                              ccgcGCGTTGAGTGCAGCAACGTCGTTGCGCGTAGCGGACGAGGCCATGGCATGCGCTGGCTCCGCCACCTTGTTGCCCCACAATGCCGGGCCACCGCTATCGacgcgcggcgcctggccctgccaagcaaactcaccgaccgcctgtt    <  1:369974‑M2/149‑47 (MQ=255)                                                                                                                                               cgcgcgTTGAGTGCAGCAACGTCGTTGCGCGTAGCGGACGAGGCCATGGCATGCGCTGGCTCCGCCACCTTGTTGCCCCACAATGCCGGGCCACCGCTATCGacgcgcggcgcctggccctgccaagcaaactcaccgaccgcctgttg   <  6:230165‑M2/149‑48 (MQ=255)                                                                                                                                                gcgcgTcgatagcggtggcccggcattgtggggcaacaaggtggcggagccagcgcatgccatggcctcgtccgctacgcgcaacgacgttgctgcactcaacgcgcggcgcctggccctgccaagcaaactcaccgaccgcctgttgg  <  1:154241‑M1/149‑144 (MQ=255)                                                                                                                                                gcgcgTTGAGTGCAGCAACGTCGTTGCGCGTAGCGGACGAGGCCATGGCATGCGCTGGCTCCGCCACCTTGTTGCCCCACAATGCCGGGc                                                             <  3:88439/90‑1 (MQ=255)                                                                                                                                                gcgcgTTGAGTGCAGCAACGTCGTTGCGCGTAGCGGACGAGGCCATGGCATGCGCTGGCTCCGCCACCTTGTTGCCCCACAATGCCGGGc                                                             >  4:88439/1‑90 (MQ=255)                                                                                                                                                     |                                                                                                                                                CAGGCCGTTGTCCGGCACGGCGAAGGCCTTGGCTACTGCCTGACCGTCACGGGCAGGCACGGCGGCGTTATTGGCAGTTTCCGCCGACGGCACGATACCGGCCAACAGGCGGTCGGTGAGTTTGCTTGGCAGGGCCAGGCGCCGCGCGTTGAGTGCAGCAACGTCGTTGCGCGTAGCGGACGAGGCCATGGCATGCGCTGGCTCCGCCACCTTGTTGCCCCACAATGCCGGGCCACCGCTATCGACGCGCGGGAACGGGCTGGTATTGATCGACGCACTGCGGCCCTTGGTC  >  NC_002947/4976165‑4976456

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.