New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	4911617 =	39 (0.920)	4 (0.100)	4/246	NT	9.4%	coding (95/1197 nt)	cycH	cytochrome c‑type biogenesis protein
	?	NC_002947	4911645 =	40 (0.990)					coding (67/1197 nt)	cycH	cytochrome c‑type biogenesis protein

CCTTCGGTATCGGCCAGCAGCTCGCGGGCAGCCTCGTCCCGGCCCCTAGCCATCTGCGCCTCATCGAGCACACCGGCGGCTTGTTGGGCCCCCAGTTCGGCGACACGTTCCTGGTAAAGGGCCACGTTCAAGGCCGTGCGGTCTTCTTCCTGC‑TGGCGACGGCGGCCACGCAGGATCGGGAGCAGCAAAAAGCTGAGGGCAGCGAGCAGCAGAAGGCCCGCGCTAAGCCAGAATTCAATCATGGGTCTGTTCTTTTTCCAGCAGTTTGGCGAGACGCTCGCGTTCTTCGGCA  >  NC_002947/4911470‑4911761                                                                                                                                                    |                                                                                                                                                  ccTTCGGTATCGGCCAGCAGCTCGCGGGCAGCCTCGTCCCGGCCCCTAGCCATCTGCGCCTCATCGAGCACACCGGCGGCTTGTTGGGCCCCCAGTTCGGCGACACGTTCCTGGTAAAGGGCCACGTTCAAGGCCGTGCGGTCttcttc                                                                                                                                                  <  6:44043/149‑1 (MQ=255)  cTTCGGTATCGGCCAGCAGCTCGCGGGCAGCCTCGTCCCGGCCCCTAGCCATCTGCGCCTCATCGAGCACACCGGCGGCTTGTTGGGCCCCCAGTTCGGCGACACGTTCCTGGTAAAGGGCCACGTTCAAGGCCGTGCGGTCTTCTTcc                                                                                                                                                 >  7:210898/1‑149 (MQ=255)    ggccgtgcagggcgccgatgagttgtctgccgaagaacgcgagcgtctcgccaaactgctggaaaaagaacagacccatgattgaattctggcttagcgcgggccttatgctgctcgctgccctcagctttttgctgctcccgaTCctg                                                                                                                                               <  1:88542‑M1/5‑1 (MQ=255)          gcagggcgccgatgagttgtctgccgaagaacgcgagcgtctcgccaaactgctggaaaaagaacagacccatgattgaattctggcttagcgcgggccttctgctgctcgctgccctcagctttttgctgctcccgaTCCTGC‑TGGc                                                                                                                                         <  2:130008‑M1/10‑1 (MQ=255)            ggCCAGCAGCTCGCGGGCAGCCTCGTCCCGGCCCCTAGCCATCTGCGCCTCATCGAGCACACCGGCGGCTTGTTGGGCCCCCAGTTGGGCGACACGTTCCTGGTAAAGGGCCACGTTCAAGGCCGTGCGGTCTTCTTCCTGC‑TGGCGa                                                                                                                                       <  8:210898/148‑1 (MQ=255)                 gcagcTCGCGGGCAGCCTCGTCCCGGCCCCTAGCCATCTGCGCCTCATCGAGCACACCGGCGGCTTGTTGGGCCCCCAGTTCGGCGACACGTTCCTGGTAAAGGGCCACGTTCAAGGCCGTGCGGTCTTCTTCCTGC‑TGGCGAcggcgg                                                                                                                                 <  3:15927/149‑1 (MQ=255)                          gggCAGCCTCGTCCCGGCCCCTAGCCATCTGCGCCTCATCGAGCACACCGGCGGCTTGTTGGGCCCCCAGTTCGGCGACACGTTCCTGGTAAAGGGCCACGTTCAAGGCCGTGCGGTCTTCTTCCTGC‑TGGCGACGGCGGCCACGCAg                                                                                                                         >  2:10205/1‑148 (MQ=255)                           ggCAGCCTCGTCCCGGCCCCTAGCCATCTGCGCCTCATCGAGCACACCGGCGGCTTGTTGGGCCCCCAGTTCGGCGACACGTTCCTGGTAAAGGGCCACGTTCAAGGCCGTGCGGTCTTCTTCCTGC‑TGGCGACGGCGGCCACGc                                                                                                                           >  2:120587/1‑145 (MQ=255)                           ggCAGCCTCGTCCCGGCCCCTAGCCATCTGCGCCTCATCGAGCACACCGGCGGCTTGTTGGGCCCCCAGTTCGGCGACACGTTCCTGGTAAAGGGCCACGTTCAAGGCCGTGCGGTCTTCTTCCTGC‑TGGCGACGGCGGCCACGc                                                                                                                           <  1:120587/145‑1 (MQ=255)                             tctgccgaagaacgcgagcgtctcgccaaactgctggaaaaagaacagacccatgattgaattctggcttagcgcgggccttctgctgctcgctgccctcagctttttgctgctcccgaTCCTGC‑TGGCGACGGCGGCCACGCAGGAt                                                                                                                      >  1:130008‑M1/120‑148 (MQ=255)                                         ggCCCCTAGCCATCTGCGCCTCATCGAGCACACCGGCGGCTTGTTGGGCCCCCAGTTCGGCGACACGTTCCTGGTAAAGGGCCACGTTCAAGGCCGTGCGGTCTTCTTCCTGC‑TGGCGACGGCGGCCACGCAGGATCGGGAGCAGCaa                                                                                                          >  6:266578/1‑148 (MQ=255)                                             ccTAGCCATCTGCGCCTCATCGAGCACACCGGCGGCTTGTTGGGCCCCCAGTTCGGCGACACGTTCCTGGTAAAGGGCCACGTTCAAGGCCGTGCGGTCTTCTTCCTGC‑TGGCGACGGCGGCCACGCAGGATCGGGAGCAGCAAAAAGc                                                                                                     >  3:59434/1‑149 (MQ=255)                                                 gCCATCTGCGCCTCATCGAGCACACCGGCGGCTTGTTGGGCCCCCAGTTCGGCGACACGTTCCTGGTAAAGGGCCACGTTCAAGGCCGTGCGGTCTTCTTCCTGC‑TGGCGACGGCGGCCACGCAGGATCGGGAGCAGCAAAAAGCTGa                                                                                                  <  1:10205/148‑1 (MQ=255)                                                    aTCTGCGCCTCATCGAGCACACCGGCGGCTTGTTGGGCCCCCAGTTCGGCGACACGTTCCTGGTAAAGGGCCACGTTCAAGGCCGTGCGGTCTTCTTCCTGC‑TGGCGACGGCGGCCACGCAGGATCGGGAGCAGCAAAAAGCTGAggg                                                                                               >  5:250919/1‑148 (MQ=255)                                                         cgcgTCATCGAGCACACCGGCGGCTTGTTGGGCCCCCAGTTCGGCGAGACGTTCCTGGTAAAGGGCCACGTTCAAGGCCGTGCGGTCTTCTTCCTGC‑TGGCGACGGCTGCCACGCAGGATCGGGAGCAGCAAAAAGCTGAGGGCAGCGa                                                                                         <  1:159038/149‑1 (MQ=255)                                                           ccTCATCGAGCACACCGGCGGCTTGTTGGGCCCCCAGTTCGGCGACACGTTCCTGGTAAAGGGCCACGTTCAAGGCCGTGCGGTCTTCTTCCTGC‑TGGCGACGGCGGCCACGCAGGATCGGGAGCAGCAAAAAGCTGAGGGCAGCGag                                                                                        >  6:56883/1‑148 (MQ=255)                                                                ggaaaaagaacagacccatgattgaattctggcttagcgcgggccttctgctgctcgctgccctcagctttttgctgctcccgaTCCTGC‑TGGCGACGGCGGCCACGCAGGATc                                                                                                                     >  7:142502‑M1/85‑114 (MQ=255)                                                                ggaaaaagaacagacccatgattgaattctggcttagcgcgggccttctgctgctcgctgccctcagctttttgctgctcccgaTCCTGC‑TGGCGACGGCGGCCACGCAGGATc                                                                                                                     <  8:142502‑M1/30‑1 (MQ=255)                                                                   aGCACACCGGCGGCTTGTTGGGCCCCCAGTTCGGCGACACGTTCCTGGTAAAGGGCCACGTTCAAGGCCGTGCGGTCTTCTTCCTGC‑TGGCGACGGCGGCCACGCAGGATCGGGAGCAGCAAAAAGCTGAGGGCAGCGAGCAGCAGAAg                                                                               <  5:266578/149‑1 (MQ=255)                                                                          cggcggCTTGTTGGGCCCCCAGTTCGGCGACACGTTCCTGGTAAAGGGCCACGTTCAAGGCCGTGCGGTCTTCTTCCTGC‑TGGCGACGGCGGCCACGCAGGATCGGGAGCAGCAAAAAGCTGAGGGCAGCGAGCAGCAGAAGGCCcgcg                                                                        >  7:214632/1‑149 (MQ=255)                                                                                cTTGTTGGGCCCCCAGTTCGGCGACACGTTCCTGGTAAAGGGCCACGTTCAAGGCCGTGCGGTCTTCTTCCTGC‑TGGCGACGGCGGCCACGCAGGATCGGGAGCAGCAAAAAGCTGAGGGCAGCGAGCAGCAGAAGGCCCGCGCTAAGc                                                                  >  1:20466/1‑149 (MQ=255)                                                                                      gggCCCCCAGTTCGGCGACACGTTCCTGGTAAAGGGCCACGTTCAAGGCCGTGCGGTCTTCTTCCTGC‑TGGCGACGGCGGCCACGCAGGATCGGGAGCAGCAAAAAGCTGAGGGCAGCGAGcagcag                                                                                  <  6:50477/127‑1 (MQ=255)                                                                                      gggCCCCCAGTTCGGCGACACGTTCCTGGTAAAGGGCCACGTTCAAGGCCGTGCGGTCTTCTTCCTGC‑TGGCGACGGCGGCCACGCAGGATCGGGAGCAGCAAAAAGCTGAGGGCAGCGAGcagcag                                                                                  >  5:50477/1‑127 (MQ=255)                                                                                      gggCCCCCAGTTCGGCGACACGTTCCTGGTAAAGGGCCACGTTCAAGGCCGTGCGGTCTTCTTCCTGC‑TGGCGACGGCGGCCACGCAGGATCGGGAGCAGCAAAAAGCTGAGGGCAGCGAGCAGCAGAAGGCCCGCGCTAAGCCa                                                                <  8:32717/145‑1 (MQ=255)                                                                                      gggCCCCCAGTTCGGCGACACGTTCCTGGTAAAGGGCCACGTTCAAGGCCGTGCGGTCTTCTTCCTGC‑TGGCGACGGCGGCCACGCAGGATCGGGAGCAGCAAAAAGCTGAGGGCAGCGAGCAGCAGAAGGCCCGCGCTAAGCCa                                                                >  7:32717/1‑145 (MQ=255)                                                                                          ccccAGTTCGGCGACACGTTCCTGGTAAAGGGCCACGTTCAAGGCCGTGCGGTCTTCTTCCTGC‑TGGCGACGGCGGCCACGCAGGATCGGGagcag                                                                                                             >  7:225347/1‑96 (MQ=255)                                                                                          ccccAGTTCGGCGACACGTTCCTGGTAAAGGGCCACGTTCAAGGCCGTGCGGTCTTCTTCCTGC‑TGGCGACGGCGGCCACGCAGGATCGGGagcag                                                                                                             <  8:225347/96‑1 (MQ=255)                                                                                          ccccAGTTCGGCGACACGTTCCTGGTAAAGGGCCACGTTCAAGGCCGTGCGGTCTTCTTCCTGC‑TGGCGACGGCGGCCACGCAGGATCGGGAGCGGCAAAAAGCTGAGGGCAGCGAGCAGCAGAAGGCCCGCGCTAAGCCAGAATTCaa                                                        <  3:217181/149‑1 (MQ=255)                                                                                          ccccAGTTCGGCGACACGTTCCTGGTAAAGGGCCACGTTCAAGGCCGTGCGGTCTTCTTCCTGC‑TGGCGACGGCGGCCACGCAGGATCGGGAGCAGCAAAAAGCTGAGGGCAGCGAGCAGCAGAAGGCCCGCGCTAAGCCAGAATTCaa                                                        >  2:221528/1‑149 (MQ=255)                                                                                             cAGTTCGGCGACACGTTCCTGGTAAAGGGCCACGTTCAAGGCCGTGCGGTCTTCTTCCTGC‑TGGCGACGGCGGCCACGCAGGATCGGGAGCAGCAAAAAGCTGAGGGCAGCGAGCAGCAGaa                                                                                >  7:173396/1‑122 (MQ=255)                                                                                             cAGTTCGGCGACACGTTCCTGGTAAAGGGCCACGTTCAAGGCCGTGCGGTCTTCTTCCTGC‑TGGCGACGGCGGCCACGCAGGATCGGGAGCAGCAAAAAGCTGAGGGCAGCGAGCAGCAGaa                                                                                <  8:173396/122‑1 (MQ=255)                                                                                                 tCGGCGACACGTTCCTGGTAAAGGGCCACGTTCAAGGCCGTGCGGTCTTCTTCCTGC‑TGGCGACGGCGGCCACGCAGGATCGGGAGCAGCAAAAAGCTGAGGGCAGCGAGCAGCAGAAGGCCCGCGCTAAGCCAGAATTCAATCATgg                                                  <  1:221528/148‑1 (MQ=255)                                                                                                    gCGACACGTTCCTGGTAAAGGGCCACGTTCAAGGCCGTGCGGTCTTCTTCCTGC‑TGGCGACGGCGGCCACGCAGGATCGGGAGCAGCAAAAAGCTGAGGGCAGCGAGCAGCAGAAGGCCCGCGCTAAGCCAGAATTCAATCATGGGTCt                                              >  6:3634/1‑149 (MQ=255)                                                                                                         acGTTCCTGGTAAAGGGCCACGTTCAAGGCCGTGCGGTCTTCTTCCTGC‑TGGCGACGGCGGCCACGCAGGATCGGGAGCAGCAAAAAGCTGAGGGCAGCGAGCAGCAGAAGGCCCGCGCTAAGCCAGAATTCAATCATGGGTCTGTTCt                                         >  5:39568/1‑149 (MQ=255)                                                                                                           gTTCCTGGTAAAGGGCCACGTTCAAGGCCGTGCGGTCTTCTTCCTGC‑TGGCGACGGCGGCCACGCAGGATCGGGAGCAGCAAAAAGCTGAGGGCAGCGAGCAGCAGAAGGCCCGCGCTAAGCCAGAATTCAATCATGGGTCTGTTCttt                                       <  6:250919/149‑1 (MQ=255)                                                                                                               cTGGTAAAGGGCCACGTTCAAGGCCGTGCGGTCTTCTTCCTGC‑TGGCGACGGCGGCCACGCAGGATCGGGAGCAGCAAAAAGCTGAGGGCAGCGAGCAGCAGAAGGCCCGCGCTAAGCCAGAATTCAATCATGGGTCTGTTCTTTTTc                                    <  2:20466/148‑1 (MQ=255)                                                                                                                tGGTAAAGGGCCACGTTCAAGGCCGTGCGGTCTTCTTCCTGC‑TGGCGACGGCGGCCACGCAGGATCGGGAGCAGCAAAAAGCTGAGGGCAGCGAGCAGCAGAAGGCCCGCGCTAAGCCAGAATTCAATCATGGGTCTGTACTTTTTc                                    >  5:51653/1‑147 (MQ=255)                                                                                                                        ggCCACGATCAAGGCCGTGAGGTCTTCTTCCTGC‑AGGCGACGGCGGCCACGCAGGATCGGGAGCAGCAAAAAGCTGAGGGCAGCCAGCAGCAGAAGGCCCGCGCTAAGCCAGAATTCAATCATGGGTCTGTTCATATTCcagcataatg                          >  2:224613/1‑144 (MQ=255)                                                                                                                          ccACGTTCAAGGCCGTGCGGTCTTCTTCCTGC‑TGGCGACGGCGGCCACGCAGGATCGGGAGCAGCAAAAAGCTGAGGGCAGCGAGCAGCAGAAGGCCCGCGCTAAGCCAGAATTCAATCATGGGTCTGTTCTTTTTCCAGCAGTTTGGc                        <  8:214632/149‑1 (MQ=255)                                                                                                                               tcagctttttgctgctcccgaTCCTGCGTGGCCGCCGTCGCCA‑GCAGGATCGGGAGCAGCAAAAAGCTGAGGGCAGCGAGCAGCAGAAGGCCCGCGCTAAGCCAGAATTCAATCATGGGTCTGTTCTTTTTCCAGCAGTTTGGCGAGAc                   <  2:15237‑M1/128‑1 (MQ=255)                                                                                                                                    ggCCGTGCGGTCTTCTTCCTGC‑TGGCGACGGCGGCCACGCAGGATCGGGAGCAGCAAAAAGCTGAGGGCAGCGAGCAGCAGAAGGCCCGCGCTAAGCCAGAATTCAATCATGGGTCTGTTCTTTTTCCAGCAGTTTGGCGAGACGCTcg              >  3:245420/1‑149 (MQ=255)                                                                                                                                              tcttctTCCTGC‑TGGCGACGGCGGCCACGCAGGATGGGGAGCAGCAAAAAGCTGAGGGCAGCGAGCAGCAGAAGGCCCGCGCTAAGCCAGAATTCAATCATGGGTCTGTTCTTTTTCCAGCAGTTTGGCGAGACGCTCGCGTTCTTCgg    <  4:59434/149‑1 (MQ=255)                                                                                                                                              tcttctTCCTGC‑TGGCGACGGCGGCCACGCAGGATCGGGAGCAGCAAAAAGCTGAGGGCAGCGAGCAGCAGAAGGCCCGCGCTAAGCCTGAATTCAATCATGGGTCTGTTCTTTTTCCAGCAGTTTGGCGAGACGCTCGCGTTCTTCgg    >  1:112439/1‑149 (MQ=255)                                                                                                                                              tcttctTCCTGC‑TGGCGACGGCGGCCACGCAGGATCGGGAGCAGCAAAAAGCTGAGGGCAGCGAGCAGCAGAAGGCCCGCGCTAAGCCAGAATTCAATCATGGGTCTGTTCTTTTTCCAGCAGTTTGGCgag                     <  2:131358/132‑1 (MQ=255)                                                                                                                                              tcttctTCCTGC‑TGGCGACGGCGGCCACGCAGGATCGGGAGCAGCAAAAAGCTGAGGGCAGCGAGCAGCAGAAGGCCCGCGCTAAGCCAGAATTCAATCATGGGTCTGTTCTTTTTCCAGCAGTTTGGCgag                     >  1:131358/1‑132 (MQ=255)                                                                                                                                              tcttctTCCTGC‑TGGCGACGGCGGCCACGCAGGATCGGGAGCAGCAAAAAGCTGAGGGCAGCGAGCAGCAGAAGGCCCGCGCTAAGCCAGAATTCAATCATGGGTCTGTTCTTTTTCCAGCAGTTTGGCGAGACGCTCGCGTTCTTCgg    <  5:3634/149‑1 (MQ=255)                                                                                                                                              tcttctTAGTGC‑TGGAGACGGCGGACACTATGGATCGGTTCTAGCATAAAGCTGAGTGCAGCGAGCAGCTGAAGGCCCGCGCTAAGCCAGATTTCAATCATGGGTCTGTTCTTTTTCCAGCAGTTTGGCGAGACGCTCGCGTTCTTCgg    <  1:224613/149‑1 (MQ=255)                                                                                                                                              ccttcttCCTGC‑TGGCGACGGCGGCCACGCAGGATCGGGAGCAGCAAAAAGCTGAGTGCAGGGAGCAGCAGAAGGCCCGCGCTAAGCCTGAATTCAATCATGGGTCTGTTCTTTTTCCAGCAGTTTGGCGAGACGCTCGCGTTCTTCg     <  2:112439/147‑1 (MQ=255)                                                                                                                                                ttcttcCTGC‑TGGCGACGTGTGCGACGCAGGATCGGGAGCAGCAAAATGCTGAGGGCAGCGAGAAGAAGTAGGCCCGCTCTAAGCCAGAATTCAATCATGGGTCTGTTGTTTTTCCAGCAGTTTGGCGAGACGCTCGAGTTCTTCGGct  <  2:124094/149‑2 (MQ=255)                                                                                                                                                ttcttcCTGC‑TGGCGACGGCGGGCACGCAGGATCGGGAGCAGCAAAAAGCTGAGGGCAGCGAGCAGCAGAAGGCCCGCGCTAAGCCAGAATTCAATCATGGGTCTGTTCTTTTTCCAGCAGTTTGGCGAGACGCTCGCGTTCTTCgg    >  7:169500/1‑147 (MQ=255)                                                                                                                                                ttcttcCTGC‑TGGCGACGGCGGCCACGCAGGATCGGGAGCAGCAAAAAGCTGAGGGCAGCGAGCAGCAGAAGGCCCGCGCTAAGCCAGAATTCAATCATGGGTCTGTTCTTTTTCCAGCAGTTTGGCGAGACGCTcgc             <  4:165325/138‑1 (MQ=255)                                                                                                                                                ttcttcCTGC‑TGGCGACGGCGGCCACGCAGGATCGGGAGCAGCAAAAAGCTGAGGGCAGCGAGCAGCAGAAGGCCCGCGCTAAGCCAGAATTCAATCATGGGTCTGTTCTTTTTCCAGCAGTTTGGCGAGACGCTcgc             >  3:165325/1‑138 (MQ=255)                                                                                                                                                    |                                                                                                                                                  CCTTCGGTATCGGCCAGCAGCTCGCGGGCAGCCTCGTCCCGGCCCCTAGCCATCTGCGCCTCATCGAGCACACCGGCGGCTTGTTGGGCCCCCAGTTCGGCGACACGTTCCTGGTAAAGGGCCACGTTCAAGGCCGTGCGGTCTTCTTCCTGC‑TGGCGACGGCGGCCACGCAGGATCGGGAGCAGCAAAAAGCTGAGGGCAGCGAGCAGCAGAAGGCCCGCGCTAAGCCAGAATTCAATCATGGGTCTGTTCTTTTTCCAGCAGTTTGGCGAGACGCTCGCGTTCTTCGGCA  >  NC_002947/4911470‑4911761

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ 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.