New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	5244966 =	42 (0.800)	4 (0.080)	4/246	NT	8.7%	coding (373/834 nt)	hmgR	Hmg transcriptional repressor
	?	NC_002947	5245022 =	43 (0.840)					coding (429/834 nt)	hmgR	Hmg transcriptional repressor

GGGGCGCGAGGCATTGCGGGTGGGGCTGGCGGCGCTGGGCAGCATCGATGTGCTGAAGGTGGCGGCGATGCCGTTGTCGCAGTTGCGAGATGAGCTCAACGAAAGCTGCTTCATCGCCGTGTGGGGCAACCAGGGGGCCACGGTGGTAAGCATCGAACCTGCCGTGCGCGCGGTCACCGTGGTGACCCAGATCGGTTCGGTGCTGCCGTTGCTCAGTTCGTCCACCGGGCTGGTATTCGCCGCCTACCTGCCCGAGCGAGAAACCCAGGAGCTGCGCGACAGGGAACTGGCCGCTTT  >  NC_002947/5244818‑5245114                                                                                                                                                     |                                                                                                                                                     ggggCGCGAGGCATTGCGGGTGGGGCTGGCGGCGCTGGGCAGCATCGATGTGCTGAAGGTGGCGGCGATGCCGTTGTCGCAGTTGCGAGATGAGCTCAACGAAAGCTGCTTCATCGCCGTGTGGGGCAACCAGGGGGCCACGGTGGTaa                                                                                                                                                      <  3:287774/149‑1 (MQ=255)  cccttttcgcggatgccggccagcagtgtgtgatagtcactggcggtttgttgcaaagcggccagttccctgtcgcgcagctcctgggtttctcgctcgggcaggtaggcggcgaataccagcccggtggacgaactgagcaacggcag                                                                                                                                                     <  5:296423‑M1/2‑1 (MQ=255)       cgAGGCATTGCGGTGGGGGCTGGCGGCTCTGGGCAGCATCGATGTGCTGAAGGTGGCGGCGATGCCGTTGTCGCAGTTGCGATATGAGCTCAACGAAAGCTGCTTCATCGCCGTGTGGGGCAACCAGGGGGCCACGGTGGTAAGCATCg                                                                                                                                                <  8:132578/149‑1 (MQ=255)                gCGGGTGGGGCTGGCGGCGCTGGGCAGCATCGATGTGCTGAAGGTGGCGGCGATGCCGTTGTCGCAGTTGCGAGATGAGCTCAACGAAAGCTGCTTCATCGCCGTGTGGGGCAACCAGGGGGCCACGGTGGTAAGCATCGAACCTGcc                                                                                                                                        <  6:36960/148‑1 (MQ=255)                              tgtgatagtcactggcggtttgttgcaaagcggccagttccctgtcgcgcagctaatgggtttctcgctcgggcaggtagtcgtcgaataccagcacggtggacgaactgagcaacggcAGCATCGAACCTGCCGTGCGCGCGGTCAcc                                                                                                                         <  3:273632‑M1/30‑1 (MQ=255)                                 cacTGGGCAGCATCGATGTGCTGAAGGTGGCGGCGATGCCGTTGTCGCAGTTGCGAGATGAGCTCAACGAAAGCTGCTTCATCGCCGTGTGGGGCAACCAGGGGGCCACGGTGGTAAGCATCGAACCTGCCGTGCGCGCGGTCACCgtg                                                                                                                      <  5:306611/147‑1 (MQ=255)                                        cagcaTCGATGTGCTGAAGGTGGCGGCGATGCCGTTGTCGCAGTTGCGAGATGAGCTCAACGAAAGCTGCTTCATCGCCGTGTGGGGCAACCAGGGGGCCACGGTGGTAAGCATCGAACCTGcc                                                                                                                                        <  6:70510/124‑1 (MQ=255)                                        cagcaTCGATGTGCTGAAGGTGGCGGCGATGCCGTTGTCGCAGTTGCGAGATGAGCTCAACGAAAGCTGCTTCATCGCCGTGTGGGGCAACCAGGGGGCCACGGTGGTAAGCATCGAACCTGcc                                                                                                                                        >  5:70510/1‑124 (MQ=255)                                          gcaTCGATGTGCTGAAGGTGGCGGCGATGCCGTTGTCGCAGTTGCGAGATGAGCTCAACGAAAGCTGCTTCATCGCCGTGTGGGGCAACCAGGGGGCCACGGTGGAAAGCATCGAACCTGCCGTGCGCGCGGTCACCGTGGTGACCCAg                                                                                                             <  4:116237/149‑1 (MQ=255)                                             tCGATGTGCTGAAGGTGGCGGCGATGCCGTTGTCGCAGTTGCGAGATGAGCTCAACGAAAGCTGCTTCATCGCCGTGTGGGGCAACCAGGGGGCCACGGTGGTAAGCATCGAACCTGCCGTGCGCGCGGTCACCGTGGTGACCCAGAtc                                                                                                          <  6:182434/149‑1 (MQ=255)                                                 tgtgCTGAAGGTGGCGGCGATGCCGTTGTCGCAGTTGCGAGATGAGCTCAACGAAAGCTGCTTCATCGCCGTGTGGGGCAACCAGGGGGCCACGGTGGTAAGCATCGAACCTGCCGTGCGCGCGGTCACCGTGGTGACCCAGAtcggtt                                                                                                      <  5:193442/149‑1 (MQ=255)                                                     cTGAAGGTGGCGGCGATGCCGTTGTCGCAGTTGCGAGATGAGCTCAACGAAAGCTGCTTCATCGCCGTGTGGGGCAACCAGGGGGCCACGGTGGTaa                                                                                                                                                      <  3:117326/97‑1 (MQ=255)                                                     cTGAAGGTGGCGGCGATGCCGTTGTCGCAGTTGCGAGATGAGCTCAACGAAAGCTGCTTCATCGCCGTGTGGGGCAACCAGGGGGCCACGGTGGTaa                                                                                                                                                      >  4:117326/1‑97 (MQ=255)                                                      tGAAGGTGGCGGCGATGCCGTTGTCGCAGTTGCGAGATGAGCTCAACGAAAGCTGCTTCATCGCCGTGTGGGGCAACCAGGGGGCCACGGTGGTAAGCATCGAACCTGCCGTGCGCGCGGTAACCGTGGTGACCCAGATCGGTTCGGtg                                                                                                 >  8:124927/1‑149 (MQ=255)                                                              gccagttccctgtcgctcagctcctgggtttctcgctcgggcaggtaggcggcgaataccagcccggtggacgaactgagccacggcAGCATCGAACCTGCCGTGCGCGCGGTCACCGTGGTGACCCAGATCGGTTCGGTGCTGCCGtt                                                                                         >  4:273632‑M1/88‑149 (MQ=255)                                                                        cGTTGTCGCAGTTGCGAGATGAGCTCAACGAAAGCTGCTTCATCGCCGTGTGGGGCAACCAGGGGGCCACGGTGGTAAGCATCGAATCTGCCGTGCGCGCGGTCACCGTGGTGACCCAGATCGGTTCGGTGCTGCCGTTGCTCAGTTCg                                                                               >  5:149819/1‑149 (MQ=255)                                                                        cGTTGTCGCAGTTGCGAGATGAGCTCAACGAAAGCTGCTTCATCGCCGTGTGGGGCAACCAGGGGGCCACGGTGGTAAGCATCGAACCTGCCGTGCGCGCGGTCACCGTGGTGACCCAGATCGGTTCGGTGCTGCCGTTGCTCAGTTCg                                                                               >  3:305544/1‑149 (MQ=255)                                                                             tCGCAGTTGCGAGATGAGCTCAACGAAAGCTGCTTCATCGCCGTGTGGGGCAACCAGGGGGCCACGGTGGTAAGCATCGAACCTGCCGTGCGCGCGGTCACCGTGGTGACCCAGATCGGTTCGGtgct                                                                                               <  7:162528/128‑1 (MQ=255)                                                                             tCGCAGTTGCGAGATGAGCTCAACGAAAGCTGCTTCATCGCCGTGTGGGGCAACCAGGGGGCCACGGTGGTAAGCATCGAACCTGCCGTGCGCGCGGTCACCGTGGTGACCCAGATCGGTTCGGtgct                                                                                               >  8:162528/1‑128 (MQ=255)                                                                                     gCGAGATGAGCTCAACGAAAGCTGCTTCATCGCCGTGTGGGGCAACCAGGGGGCCACGGTGGTAAGCATCGAACCTGCCGTGCGCGCGGTCACCGTGGTGACCCAGATCGGTTCGGTGCTGCCGTTGCTCAGTTCGTCCACCGGGCTgg                                                                  >  8:77724/1‑149 (MQ=255)                                                                                       gagaTGAGCTCAACGAAAGCTGCTTCATCGCCGTGTGGGGCAACCAGGGGGCCACGGTGGTAAGCATCGAATCTGCCGTGCGCGCGGTCACCGTGGTGACCCAGATCGGTTCGGTGCTGCCGTTGCTCAGTTCGTCCACCGGGCTGGTa                                                                <  6:149819/149‑1 (MQ=255)                                                                                         gaTGAGCTCAACGAAAGCTGCTTCATCGCCGTGTGGGGCAACCAGGGGGCCACGGTGGTAAGCATCGAACCTGCCGTGCGCGCGGTCACCGTGGTGACCCAGATCGGTTCGGTGCTGCCGTTGCTCAGTTCGTCCACCGGGc                                                                     <  7:182249/142‑1 (MQ=255)                                                                                         gaTGAGCTCAACGAAAGCTGCTTCATCGCCGTGTGGGGCAACCAGGGGGCCACGGTGGTAAGCATCGAACCTGCCGTGCGCGCGGTCACCGTGGTGACCCAGATCGGTTCGGTGCTGCCGTTGCTCAGTTCGTCCACCGGGc                                                                     >  8:182249/1‑142 (MQ=255)                                                                                            gAGCTCAACGAAAGCTGCCTCATCGCCGTGTGGGGCAACCAGGGGGCCACGGTGGTAAGCATCGAACCTGCCGTGCGCGCGGTCACCGTGGTGACCCAGATCGGTTCGGTGCTGCCGTTGCTCAGTTCGTCCACCGGGCTGGTATTcgc                                                           >  1:245548/1‑149 (MQ=255)                                                                                                 ctcgggcaggtaggcggcgaataccagcccggtggacgaactgagcaacggcAGCATCGAACCTGCCGTGCGCGCGGTCACCGTGGTGACCCAGATCGGTTCGGTGCTGCCGTTGCTCAGTTCg                                                                               >  7:3073‑M1/53‑124 (MQ=255)                                                                                                 ctcgggcaggtaggcggcgaataccagcccggtggacgaactgagcaacggcAGCATCGAACCTGCCGTGCGCGCGGTCACCGTGGTGACCCAGATCGGTTCGGTGCTGCCGTTGCTCAGTTCg                                                                               <  8:3073‑M1/72‑1 (MQ=255)                                                                                                   aCGAAAGCTGCTTCATCGCCGTGTGGGGCAACCAGGGGGCCACGGTGGTAAGCATCGAACCTGCCGTGCGCGCGGTCACCGTGGTGACCCAGATCGGTTCGGTGCTGCCGTTGCTCAGTTCGTCCACCGGGCTGGTATTCGCCGCCTAc                                                    >  4:259741/1‑149 (MQ=255)                                                                                                   aCGAAAGCTGCTTCATCGCCGTGTGGGGCAACCAGGGGGCCACGGTGGTAAGCATCGAACCTGCCGTGCGCGCGGTCACCGTGGTGACCCAGATCGGTTCGGTGCTGCCGTTGCTCAGTTCGTCCACCGGGCTGGTATTCGCCGCCTAc                                                    <  3:259741/149‑1 (MQ=255)                                                                                                     gAAAGCTGCTTCATCGCCGTGTGGGGCAACCAGGGGGCCACGGTGGTAAGCATCGAACCTGCCGTGCGCGCGGTCACCGTGGTGACCCAGATCGGTTCGGTGCTGCCGTTGCTCAGTTCGTCCACCGGGCTGGTa                                                                <  5:291400/135‑1 (MQ=255)                                                                                                     gAAAGCTGCTTCATCGCCGTGTGGGGCAACCAGGGGGCCACGGTGGTAAGCATCGAACCTGCCGTGCGCGCGGTCACCGTGGTGACCCAGATCGGTTCGGTGCTGCCGTTGCTCAGTTCGTCCACCGGGCTGGTa                                                                >  6:291400/1‑135 (MQ=255)                                                                                                           tgctTCATCGCCGTGTGGGGCAACCAGGGGGCCACGGTGGTAAGCATCGAACCTGCCGTGCGCGCGGTCACCGTGGTGACCCAGATCGGTTCGGTGCTGCCGTTGCTCAGTTCGTCCACCGGGCTGGTATTCGCCGCCTACCTGccc                                              >  7:191228/1‑147 (MQ=255)                                                                                                            gctTCATCGCCGTGTGGGGCAACCAGGGGGCCACGGTGGTAAGCATCGAACCTGCCGTGCGCGCGGTCACCGTGGTGACCCAGATCGGTTCGGTGCTGCCGTTGCTCAGTTCGTCCACCGGGCTGGTATTCGCCGCCTACCTGCCcgag                                           >  8:191618/1‑149 (MQ=255)                                                                                                             ctTCATCGCCGTGTGGGGCAACCAGGGGGCCACGGTGGCAAGCATCGAACCTGCCGTGCGCGCGGTCACCGTGGTGACCCAGATCGGTTCGGTGCTGCCGTTGCTCAGTTCGTCCACCGGGCAGGTAGGCGGCGAATACCAGCCcggt                                           <  7:258825/148‑3 (MQ=255)                                                                                                             cctCATCGCCGTGTGGGGCAACCAGGGGGCCACGGTGGTAAGCATCGAACCTGCCGTGCGCGCGGTCACCGTGGTGACCCAGATCGGTTCGGTGCTGCCGTTGCTCAGTTCGTCCACCGGGCTGGTATTCGCCGCCTACCTGCCcgagc                                          <  2:245548/147‑1 (MQ=255)                                                                                                                    gCCGTGTGGGGCAACCAGGGGGCCACGGTGGTAAGCATCGAACCTGCCGTGCGCGCGGTCACCGTGGTGACCCAGATCGGTTCGGTGCTGCCGTTGCTCAGTTCGTCCACCGGGCTGGTATTCGCCGCCTACCTGCCcgag                                           <  1:91154/141‑1 (MQ=255)                                                                                                                    gCCGTGTGGGGCAACCAGGGGGCCACGGTGGTAAGCATCGAACCTGCCGTGCGCGCGGTCACCGTGGTGACCCAGATCGGTTCGGTGCTGCCGTTGCTCAGTTCGTCCACCGGGCTGGTATTCGCCGCCTACCTGCCcgag                                           >  2:91154/1‑141 (MQ=255)                                                                                                                            gggCAACCAGGGGGCCACGGTGGTAAGCATCGAACCTGCCGTGCGCGCGGTCACCgtg                                                                                                                      <  3:33908/58‑1 (MQ=255)                                                                                                                            gggCAACCAGGGGGCCACGGTGGTAAGCATCGAACCTGCCGTGCGCGCGGTCACCgtg                                                                                                                      >  4:33908/1‑58 (MQ=255)                                                                                                                             ggCAACCAGGGGGCCACGGTGGTAAGCATCGAACCTGCCGTGCGCGCGGTCACCGTGGTGACCCAGATCGGTTCGGTGCTGCCGTTGCTCAGTTCGTCCACCGGGCTGGTATTCGCCGCCTACCTGCCCGAGCGAGAAACCCAGGAGCt                          >  1:89056/1‑149 (MQ=255)                                                                                                                              gCAACCAGGGGGCCACGGTGGTAAGCATCGAACCTGCCGTGCGCGCGGTCACCGTGGTGACCCAGATCGGTTCGGTGCTGCCGTTGCTCAGTTCGTCCACCGGGCTGGTATTCGCCGCCTACCTGCCcgagcgag                                       >  8:312792/1‑135 (MQ=255)                                                                                                                              gCAACCAGGGGGCCACGGTGGTAAGCATCGAACCTGCCGTGCGCGCGGTCACCGTGGTGACCCAGATCGGTTCGGTGCTGCCGTTGCTCAGTTCGTCCACCGGGCTGGTATTCGCCGCCTACCTGCCcgagcgag                                       <  7:312792/135‑1 (MQ=255)                                                                                                                                aaCCAGGGGGCCACGGTGGTAAGCATCGAACCTGCCGTGCGCGCGGTCACCGTGGTGACCCAGATCGGTTCGGTGCTGCCGTTGCTCAGTTCGTCCACCGGGCTg                                                                   >  5:264352/1‑105 (MQ=255)                                                                                                                                aaCCAGGGGGCCACGGTGGTAAGCATCGAACCTGCCGTGCGCGCGGTCACCGTGGTGACCCAGATCGGTTCGGTGCTGCCGTTGCTCAGTTCGTCCACCGGGCTg                                                                   <  6:264352/105‑1 (MQ=255)                                                                                                                                aaCCAGGGGGCCACGGTGGTAAGCATCGAACCTGCCGTGCGCGCGGTCACCGTGGTGACCCAGATCGGTTCGGTGCTGCCGTTGCTCAGTTCGTCCACCGGGCTGGTATTCGCCGCCTACCTGCCCGAGCGAGAAACCCAGGAGCTgcg                       >  8:39317/1‑149 (MQ=255)                                                                                                                                   cAGGGGGCCACGGTGGTAAGCATCGAACCTGCCGTGCGCGCGGTCACCGTGGTGACCCAGATCGGTTCGGTGCTGCCGTTGCTCAGTTCGTCCACCGGGCTGGTATTCGCCGCCTACCTGCCCGAGCGAGAAACCCAGGAGCTGCGCGa                    >  5:74228/1‑149 (MQ=255)                                                                                                                                    aGGGGGCCACGGTGGTAAGCATCGAACCTGCCGTGCGCGCGGTCACCGTGGTGACCCAGATCGGTTCGGTGCTGCCGTTGCTCAGTTCGTCCACCGGGCTGGTATTCGCCGCCTACCTGCCCGAGCGAGAAACCCAGGAGCTGCGCGa                    >  2:203633/1‑148 (MQ=255)                                                                                                                                    aGGGGGCCACGGTGGTAAGCATCGAACCTGCCGTGCGCGCGGTCACCGTGGTGACCCAGATCGGTTCGGTGCTGCCGTTGCTCAGTTCGTCCACCGGGCTGGTATTCGCCGCCTACCTGCCCGAGCGAGAAACCCAGGAGCTGCGCGAc                   <  1:203633/149‑1 (MQ=255)                                                                                                                                            aCGGTGGTAAGCATCGAACCTGCCGTGCGCGCGGTCACCGTGGTGACCCAGATCGGTTCGGTGCTGCCGTTGCTCAGTTCGTCCACCGGGCTGGTATTCGCCGCCTACCTGCCCGAGCGAGAAACCCAGGAGCTGCGCGACAGGGAACt           <  7:124927/149‑1 (MQ=255)                                                                                                                                               gtggtAAGCATCGAACCTGCCGTGCGCGCGGTCACCGTGGTGACCCAGATCGGTTCGGTGCTGCCGTTGCTCAGTTCGTCCACCGGGCTGGTATTCGCCGCCTACCTGCCCGAGCGAGAAACCCAGGAGCTGCGCGACAGGGAACTGGc        <  7:77724/149‑1 (MQ=255)                                                                                                                                               gtggtAAGCATCGAACCTGCCGTGCGCGCGGTCACCGTGGTGACCCAGATCGGTTCGGTGCTGCCGTTGCTCAGTTCGTCCACCGGGCTGGTATTCGCCGCCTACCTGCCCGAGCGAGAAACCCAGGAGCTGCGCGACAGGGAACTGGc        <  8:191228/149‑1 (MQ=255)                                                                                                                                                   tAAGCATCGAACCTGCCGTGCGCGCGGTCACCGTGGTGACCCAGATCGGTTCGGTGCTGCCGTTGCTCAGTTCGTCCACCGGGCTGGTATTCGCCGCCTACCTGCCCGAGCGAGAAACCCAGGAGCTGCGCGACAGGGAACTGGCCGCt    >  6:296423/1‑149 (MQ=255)                                                                                                                                                     AGCATCGAACCTGCCGTGCGCGCGGTCACCGTGGTGACCCAGATCGGTTCGGTGCTGCCGTTGCTCAGTTCGTCCACCGGGCTGGTATTCGCCGCCTACCTGCCCGAGCGAGAAACCCAGGAGCTGCGCGACAGGGAACTGGCCGCttt  >  4:305544‑M1/1‑149 (MQ=255)                                                                                                                                                     |                                                                                                                                                     GGGGCGCGAGGCATTGCGGGTGGGGCTGGCGGCGCTGGGCAGCATCGATGTGCTGAAGGTGGCGGCGATGCCGTTGTCGCAGTTGCGAGATGAGCTCAACGAAAGCTGCTTCATCGCCGTGTGGGGCAACCAGGGGGCCACGGTGGTAAGCATCGAACCTGCCGTGCGCGCGGTCACCGTGGTGACCCAGATCGGTTCGGTGCTGCCGTTGCTCAGTTCGTCCACCGGGCTGGTATTCGCCGCCTACCTGCCCGAGCGAGAAACCCAGGAGCTGCGCGACAGGGAACTGGCCGCTTT  >  NC_002947/5244818‑5245114

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.