New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 728713	28 (0.650)	6 (0.150)	5/240	NT	18.9%	coding (199/963 nt)	rluD	23S rRNA pseudouridine(1911/1915/1917) synthase
	?	NC_002947	= 728729	25 (0.610)					coding (215/963 nt)	rluD	23S rRNA pseudouridine(1911/1915/1917) synthase

CCAACGCCTCGACCAGGTCGCCGCCCAATTGTTCGCCGAGTACTCGCGTTCGCGGCTAACTTCGTGGATCAAAGAGGGCCGCCTGACGGTCGATGGTGCAGTCGTGCGCCCTCGAGACCTTGTTCATGGTGGCTCTCAGCTTGCCCTGGAGGCCGAACAAGAGGCCCAGGGCGAGTGGATCGCAGAAGATATCGAACTGGATATCGTCTACGAAGACGACCACATCCTGGTGATCAACAAGCCTGCCGGGCTGGTTGTGCACCCGGCGGCCGGGCATGCCAGCGGCACCCTGCTCAAC  >  NC_002947/728565‑728862                                                                                                                                                     |                                                                                                                                                      ccAACGCCTCGACCAGGTCGCCGCCCAATTGTTCGCCGAGTACTCGCGTTCGCGGCTAACTTCGTGGATCAAAGAGGGCCGCCTGACGGTCGATGGTGCAGTCGTGCGCCCTCGAGACCTTGTTCATGGTGGCTCTCAGCTTGCCCTGGg                                                                                                                                                      >  2:984055‑M1/1‑149 (MQ=255) ccAACGCCTCGACCAGGTCGCCGCCCAATTGTTCGCCGAGTACTCGCGTTCGCGGCTAACTTCGTGGATCAAAGAGGGCCGCCTGACGGTCGATGGTGCAGTCGTGCGCCCTCGAGACCTTGTTCATGGTGGCTCTCAGCTTGCCCTGGg                                                                                                                                                      >  2:984039‑M1/1‑149 (MQ=255) ccAACGCCTCGACCAGGTCGCCGCCCAATTGTTCGCCGAGTACTCGCGTTCGCGGCTAACTTCGTGGATCAAAGAGGGCCGCCTGACGGTCGATGGTGCAGTCGTGCGCCCTCGAGACCTTGTTCATGGTGGCTCTCAGCTTGCCCTGGa                                                                                                                                                      <  2:948135/150‑1 (MQ=255)  cAACGCCTCGACCAGGTCGCCGCCCAATTGTTCGCCGAGTACTCGCGTTCGCGGCTAACTTCGTGGATCAAAGAGGGCCGCCTGACGGTCGATGGTGCAGTCGTGCGCCCTCGAGACCTTGTTCATGGTGGCTCTCAGCTTGCCCTGGAg                                                                                                                                                     >  1:1114331/1‑150 (MQ=255)    aCGCCTCGACCAGGTCGCCGCCCAATTGTTCGCCGAGTACTCGCGTTCGCGGCTAACTTCGTGGATCAAAGAGGGCCGCCTGACGGTCGATGGTGCAGTCGTGCGCCCTCGAGACCTTGTTCATGGTGGCTCTCAGCTTGCCCTGGAGGc                                                                                                                                                   <  2:326051/150‑1 (MQ=255)        cTCGACCAGGTCGCCGCCCAATTGTTCGCCGAGTACTCGCGTTCGCGGCTAACTTCGTGGATCAAAGAGGGCCGCCTGACGGTCGATGGTGCAGTCGTGCGCCCTCGAGACCTTGTTCATGGTGGCTCTCAGCTTGCCCTGGAGGc                                                                                                                                                   <  1:1061038/146‑1 (MQ=255)        cTCGACCAGGTCGCCGCCCAATTGTTCGCCGAGTACTCGCGTTCGCGGCTAACTTCGTGGATCAAAGAGGGCCGCCTGACGGTCGATGGTGCAGTCGTGCGCCCTCGAGACCTTGTTCATGGTGGCTCTCAGCTTGCCCTGGAGGc                                                                                                                                                   >  2:1061038/1‑146 (MQ=255)            aCCAGGTCGCCGCCCAATTGTTCGCCGAGTACTCGCGTTCGCGGCTAACTTCGTGGATCAAAGAGGGCCGCCTGACGGTCGATGGTGCAGTCGTGCGCCCTCGAGACCTTGTTCATGGTGGCTCTCAGCTTGCCCTGGAGGCCGAACAag                                                                                                                                           <  2:670845/150‑1 (MQ=255)             ccAGGTCGCCGCCCAATTGTTCGCCGAGTACTCGCGTTCGCGGCTAACTTCGTGGATCAAAGAGGGCCGCCTGACGGTCGATGGTGCAGTCGTGCGCCCTCGAGACCTTGTTCATGGTGGCTCTCAGCTTGCCCTGGAAGCCGAACAaga                                                                                                                                          <  2:1043767/150‑1 (MQ=255)                 gTCGCCGCCCAATTGTTCGCCGAGTACTCGCGTTCGCGGCTAACTTCGTGGATCAAAGAGGGCCGCCTGACGGTCGATGGTGCAGTCGTGCGCCCTCGAGACCTTGTTCATGGTGGCTCTCAGCTTGCCCTGGAGGCCGAACAAGAGGCc                                                                                                                                      <  1:213301‑M2/150‑2 (MQ=255)                   cgccgcCCAATTGTTCGCCGAGTACTCGCGTTCGCGGCTAACTTCGTGGATCAAAGAGGGCCGCCTGACGGTCGATGGTGCAGTCGTGCGCCCTCGAGACCTTGTTCATGGTGGCTCTCAGCTTGCCCTGGAGGCCGAACAAGAGGCcca                                                                                                                                    >  1:1101054‑M2/1‑147 (MQ=255)                     ccgccCAATTGTTCGCCGAGTACTCGCGTTCGCGGCTAACTTCGTGGATCAAAGAGGGCCGCCTGACGGTCGATGGTGCAGTCGTGCGCCCTCGAGACCTTGTTCATGGTGGCTCTCAGCTTGCCCTGGAGGCCGAACAAGAGGCccagg                                                                                                                                  >  1:788015‑M2/1‑145 (MQ=255)                                            tCGCGTTCGCGGCTAACTTCGTGGATCAAAGAGGGCCGCCTGACGGTCGATGGTGCAGTCGTGCGCCCTCGAGACCTTGTTCATGGTGGCTCTCAGCTTGCCCTGGAGGCCGAACAAGAgg                                                                                                                                        >  1:598154/1‑121 (MQ=255)                                            tCGCGTTCGCGGCTAACTTCGTGGATCAAAGAGGGCCGCCTGACGGTCGATGGTGCAGTCGTGCGCCCTCGAGACCTTGTTCATGGTGGCTCTCAGCTTGCCCTGGAGGCCGAACAAGAgg                                                                                                                                        <  2:598154/121‑1 (MQ=255)                                            tCGCGTTCGCGGCTAACTTCGTGGATCAAAGAGGGCCGCCTGACGGTCGATGGTGCAGTCGTGCGCCCTCGAGACCTTGTTCATGGTGGCTCTCAGCTTGCCCTGGAGGCCGAACAAGAGGCCCAGGGCGAGTGGATCGCAGAAGATATc                                                                                                           >  2:1048420/1‑150 (MQ=255)                                            tCGCGTTCGCGGCTAACTTCGTGGATCAAAGAGGGCCGCCTGACGGTCGATGGTGCAGTCGTGCGCCCTCGAGACCTTGTTCATGGTGGCTCTCAGCTTGCCCTGGAGGCCGAACAAGAGGCCCAGGGCGAGTGGATCGCAGAAGATATc                                                                                                           >  2:921374/1‑150 (MQ=255)                                              gcgTTCGCGGCTAACTTCGTGGATCAAAGAGGGCCGCCTGACGGTCGATGGTGCAGTCGTGCGCCCTCGAGACCTTGTTCATGGTGGCTCTCAGCTTGCCCTGGAGGCCGAACAAGAGGCCCAGGGCGAGTGGATCGCAGAAGATATCGa                                                                                                         >  2:847420/1‑150 (MQ=255)                                               cgTTCGCGGCTAACTTCGTGGATCAAAGAGGGCCGCCTGACGGTCGATGGTGCAGTCGTGCGCCCTCGAGACCTTGTTCATGGTGGCTCTCAGCTTGCCCTGGgcctcttgttcggcctccagggcaagctgagagccaccatgaacaag                                                                                                        <  1:984055‑M1/150‑48 (MQ=255)                                               cgTTCGCGGCTAACTTCGTGGATCAAAGAGGGCCGCCTGACGGTCGATGGTGCAGTCGTGCGCCCTCGAGACCTTGTTCATGGTGGCTCTCAGCTTGCCCTGGgcctcttgttcggcctccagggcaagctgagagccaccatgaacaag                                                                                                        <  1:984039‑M1/150‑48 (MQ=255)                                                  tCGCGGCTAACTTCGTGGATCAAAGAGGGCCGCCTGACGGTCGATGGTGCAGTCGTGCGCCCTCGAGACCTTGTTCATGGTGGCTCTCAGCTTGCCCTGGAGGCCGAACAAGAGGCCCAGGGCGAGTGGATCGCAGAAGATATCGAACTg                                                                                                     <  1:1048420/150‑1 (MQ=255)                                                   cgcgGCTAACTTCGTGGATCAAAGAGGGCCGCCTGACGGTCGATGGTGCAGTCGTGCGCCCTCGAGACCTTGTTCATGGTGGCTCTCAGCTTGCCCTGGAGGCCGAACAAGAGGCCCAGGGCGAGTGGATCGCAGAAGATATCGAACTgg                                                                                                    <  1:783723/150‑1 (MQ=255)                                                    gcgGCTAACTTCGTGGATCAAAGAGGGCCGCCTGACGGTCGATGGTGCAGTCGTGCGCCCTCGAGACCTTGTTCATGGTGGCTCTCAGCTTGCCCTGGAGGCCGAACAAGAGGCCCAGGGCGAGTGGATCGCAGAAGATATCGAACTGGa                                                                                                   >  2:3914/1‑150 (MQ=255)                                                        cTAACTTCGTGGATCAAAGAGGGCCGCCTGACGGTCGATGGTGCAGTCGTGCGCCCTCGAGACCTTGTTCATGGTGGCTCTCAGCTTGCCCTGGAGGCCGAACAAGAGGCCCAGGGCGAGTGGATCGCAGAAGATATCGAACTGGATATc                                                                                               <  2:1114331/150‑1 (MQ=255)                                                            cTTCGTGGATCAAAGAGGGCCGCCTGACGGTCGATGGTGCAGTCGTGCGCCCTCGAGACCTTGTTCATGGTGGCTCTCAGCTTGCCCTGGAGGCCGAACAAGAGGCCCAGGGCGAGTGGATCGCAGAAGATATCGAACTGGATATCGTCt                                                                                           >  1:1090068/1‑150 (MQ=255)                                                                gTGGATCAAAGAGGGCCGCCTGACGGTCGATGGTGCAGTCGTGCGCCCTCGAGACCTTGTTCATGGTGGCTCTCAGCTTGCCCTGGAGGCCGAACAAGAGGCCCAGGGCGAGTGGATCGCAGAAGATATCGAACTGGATATCGTCTACGa                                                                                       >  2:1026173/1‑150 (MQ=255)                                                                 tGGATCAAAGAGGGCCGCCTGACGGTCGATGGTGCAGTCGTGCGCCCTCGAGACCTTGTTCATGGTGGCTCTCAGCTTGCCCTGGAGGCCGAACAAGAGGCCCAGGGCGAGTGGATCGCAGAAGATATCGAACTGGATATCGTCTACGaa                                                                                      <  2:170919/150‑1 (MQ=255)                                                                        aaGAGGGCCGCCTGACGGTCGATGGTGCAGTCGTGCGCCCTCGAGACCTTGTTCATGGTGGCTCTCAGCTTGCCCTGGgcctcttgttcggcctccagggcaagctgaga                                                                                                                       <  2:129942‑M1/110‑33 (MQ=255)                                                                        aaGAGGGCCGCCTGACGGTCGATGGTGCAGTCGTGCGCCCTCGAGACCTTGTTCATGGTGGCTCTCAGCTTGCCCTGGAGGCCGAACAAGAGGCCCAGGGCGAGTGGATCGCAGAAGATATCGAACTGGATATCGTCTACGAAGACGAcc                                                                               <  1:742691/150‑1 (MQ=255)                                                                        aaGAGGGCCGCCTGACGGTCGATGGTGCAGTCGTGCGCCCTCGAGACCTTGTTCAGGGTGGCTCTCAGCTTGCCCTGGgcctcttgttcggcctccagggcaagctgaga                                                                                                                       >  1:129942‑M1/1‑78 (MQ=255)                                                                                  ccTGACGGTCGATGGTGCAGTCGTGCGCCCTCGAGACCTTGTTCATGGTGGCTCTCAGCTTGCCCTGGAGGCCGAACAAGAGGCCCAGGGCGAGTGGATCGCAGAAGATATCGAACTGGATATCGTCTACGAAGACGACCACATCCTGGt                                                                     <  2:1096834/150‑1 (MQ=255)                                                                                   cTGACGGTCGATGGTGCAGTCGTGCGCCCTCGAGACCTTGTTCATGGTGGCTCTCAGCTTGCCCTGGAGGCCGAACAAGAGGCCCAGGGCGAGTGGATCGCAGAAGATATCGAACTGGATATCGTCTACGAAGACGACCACATCCTGGTg                                                                    <  2:1103086/150‑1 (MQ=255)                                                                                      aCGGTCGATGGTGCAGTCGGGCGCCCTCGAGACCTTGTTCATGGTGGCTCTCAGCTTGCCCTGGAGGCCGAACAAGAGGCCCAGGGCGAGTGGATCGCAGAATATATCGAACTGGATATCGTCTACGAAGACGACCACATCCTGGTGATc                                                                 <  2:213301/150‑1 (MQ=255)                                                                                                 tGCAGTCGTGCGCCCTCGAGACCTTGTTCATGGTGGCTCTCAGCTTGCCCTGGAGGCCGAACAAGAGGCCCAGGGCGAGTGGATCGCAGAAGATATCGAACTGGATATCGTCTACGAAGACGACCACATCCTGGTGATCAACAAGCCTGc                                                      >  2:977913/1‑150 (MQ=255)                                                                                                 tGCAGTCGTGCGCCCTCGAGACCTTGTCCATGGTGGCGCTCAGCGCGCCCTGGCGGCCGAACAGGAGGCCCAGGGCGAGTGCATCGCAGACGATAACGAACTGGATATCGTCTACGAAGACGGCGCCATCCTGGTCCTCAACACGCCTGc                                                      >  2:388427/1‑150 (MQ=255)                                                                                                           cgcCCTCGAGACCTTGTTCATGGTGGCTCTCAGCTTGCCCTGGAGGCCGAACAAGAGGCCCAGGGCGAGTGGATCGCAGAAGATATCGAACTGGATATCGTCTACGAAGACGACCACATCCTGGTGATCAACAAGCCTGTCGGGCTGGtt                                            <  1:3914/150‑1 (MQ=255)                                                                                                                tCGAGACCTTGTTCATGGTGGCTCTCAGCTTGCCCTGGAGGCCGAACAAGAGGCCCAGGGCGAGTGGATCGCAGAAGATATCGAACTGGATATCGTCTACGAAGACGACCACATCCTGGTGATCAACAAGCCTGCCGGGCTGGTTGTGCa                                       <  1:847420/150‑1 (MQ=255)                                                                                                                      ccTTGTTCATGGTGGCTCTCAGCTTGCCCTGGAGGCCGAACAAGAGGCCCAGGGCGAGTGGATCGCAGAAGATATCGAACTGGATATCGTCTACGAAGACGACCACATCCTGGTGATCAACAAGCCTGCCGGGCTGGTTGTGCACCcggc                                 <  1:977913/150‑1 (MQ=255)                                                                                                                       cTTGTTCATGGTGGCTCTCAGCTTGCCCTGGAGGCCGAACAAGAGGCccagggcaagctgagagccaccatgaacaaggtctcgagggcgcacgactgcaccatcgaccgtcaggcggccctctttgatccacgaagttagccgcgaacg                                <  1:984039‑M2/150‑104 (MQ=255)                                                                                                                       cTTGTTCATGGTGGCTCTCAGCTTGCCCTGGAGGCCGAACAAGAGGCccagggcaagctgagagccaccatgaacaaggtctcgagggcgcacgactgcaccatcgaccgtcaggcggccctctttgatccacgaagttagccgcgaacg                                <  1:984055‑M2/150‑104 (MQ=255)                                                                                                                              aTGGTGGCTCTCAGCTTGCCCTGGgcctcttgttcgg                                                                                                                                          <  2:236435‑M1/37‑14 (MQ=255)                                                                                                                              aTGGTGGCTCTCAGCTTGCCCTGGgcctcttgttcgg                                                                                                                                          >  1:236435‑M1/1‑24 (MQ=255)                                                                                                                                ggtggGTCATAGCTGGCCCGTGATGCTGAACTAGAGGCCCAGGGCGAGTGGATCGCAGAAGATATCGAACTGGATATCGTCTACGAAGACGACCACATCCTGGTGATCAACAAGCCTGCCGGGCTGGTTGTGCACCCGGCGGCCGGGCAt                       <  2:341072/150‑1 (MQ=255)                                                                                                                                      tctcAGCTTGCCCTGGAGGCCGAACAAGAGGCccagggcaagctgagagccaccctgaacaaggtctcgagggcgcacgactgcaccatcgaccgtcaggcggccctctt                                                         >  1:129942‑M2/1‑32 (MQ=255)                                                                                                                                      tctcAGCTTGCCCTGGAGGCCGAACAAGAGGCccagggcaagctgagagccaccatgaacaaggtctcgagggcgcacgactgcaccatcgaccgtcaggcggccctctt                                                         <  2:129942‑M2/110‑79 (MQ=255)                                                                                                                                      tctcAGCTTGCCCTGGAGGCCGAACAAGAGGCCCAGGGCGAGTGGATCGCAGAAGATATCGAACTGGATATCGTCTACGAAGACGACCACATCCTGGTGATCAACAAGCCTGCCGGGCTGGTTGTGCACCCGGCGGCCGGGCATGCCAGc                 >  2:720054/1‑150 (MQ=255)                                                                                                                                          aGCTTGCCCTGGAGGCCGAACAAGAGGCCCAGGGCGAGTGGATCGCAGAAGATATCGAACTGGATATCGTCTACGAAgacg                                                                                  >  1:671583/1‑81 (MQ=255)                                                                                                                                          aGCTTGCCCTGGAGGCCGAACAAGAGGCCCAGGGCGAGTGGATCGCAGAAGATATCGAACTGGATATCGTCTACGAAgacg                                                                                  <  2:671583/81‑1 (MQ=255)                                                                                                                                             ttGCCCTGGAGGCCGAACAAGAGGCCCAGGGCGAGTGGATCGCAGAAGATATCGAACTGGATATCGTCTACGAAGACGACCACATCCTGGTGATCAACAAGCCTGCCGGACGGGTTGTGCACCCGGCGGCCGGGCATGCCAGCGGCAccc          >  1:364761/1‑150 (MQ=255)                                                                                                                                                 ccTGGgcctcttgttcggcctccagggcaagctgagagccaccatgaacaaggtctcgagggcgcacgactgcaccatcgaccgtcaggcggccctctttgatccacgaagttagccgcgaacgcgagtactcggcgaacaattgggcgg      >  1:788015‑M1/1‑5 (MQ=255)                                                                                                                                                 ccTGGAGGCCGAACAAGAGGCCCAGGGCGAGTGGATCGCAGAAGATATCGAACTGGATATCGTCTACGAAGACGACCACATCCTGGTGATCAACAAGCCTGCCGGGCTGGTTGTGCACCCGGCGGCCGGGCATGCCAGCGGCACCCTGCt      >  2:743181/1‑150 (MQ=255)                                                                                                                                                   tGGgcctcttgttcggcctccagggcaagctgagagccaccatgaacaaggtctcgagggcgcacgactgcaccatcgaccgtcaggcggccctctttgatccacgaagttagccgcgaacgcgagtactcggcgaacaattgggcggcg    >  1:1101054‑M1/1‑3 (MQ=255)                                                                                                                                                     ggcctcttgttcggcctccagggcaagctgagagccaccatgaacaaggtctcgagggcgcacgactgcaccatcgaccgtcaggcggccctctttgatccacgaagttagccgcgaacgcgagtactcggcgaacaattgggcggcgac  <  1:213301‑M1/150‑150 (MQ=255)                                                                                                                                                     |                                                                                                                                                      CCAACGCCTCGACCAGGTCGCCGCCCAATTGTTCGCCGAGTACTCGCGTTCGCGGCTAACTTCGTGGATCAAAGAGGGCCGCCTGACGGTCGATGGTGCAGTCGTGCGCCCTCGAGACCTTGTTCATGGTGGCTCTCAGCTTGCCCTGGAGGCCGAACAAGAGGCCCAGGGCGAGTGGATCGCAGAAGATATCGAACTGGATATCGTCTACGAAGACGACCACATCCTGGTGATCAACAAGCCTGCCGGGCTGGTTGTGCACCCGGCGGCCGGGCATGCCAGCGGCACCCTGCTCAAC  >  NC_002947/728565‑728862

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