New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 288413	40 (0.530)	4 (0.060)	3/242	NT	9.2%	coding (750/759 nt)	yagI	CP4‑6 prophage; putative DNA‑binding transcriptional regulator
	?	NC_000913	= 288439	42 (0.600)					coding (724/759 nt)	yagI	CP4‑6 prophage; putative DNA‑binding transcriptional regulator

GCTGTCGGACGACTACATCGGCGGGCGCGGCTTCTTCACCGGCGCGTTTGTGGGCCTGCACTGCGAGGACATCAGCGGCGACGGCTGCTACGCGGACTTCGACTACTTCACCTACGAGCCGGTCTAACGGCTCAGGCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGCCCGGCCTGCTGAAGCTGCTCGCGGAAATTAGCCAGCTCCGCGTCGTCCACGCGGGAGGTCAGCGTCGACAGGCTCAGGGCGGCGATGACGCGGGACTCGTGGTTCCACACCGGCACCGCCA  >  NC_000913/288273‑288561                                                                                                                                             |                                                                                                                                                     gCTGTCGGACGACTACATCGGCGGGCGCGGCTTCTTCACCGGCGCGTTTGTGGGCCTGCACTGCGAGGACATCAGCGGCGACGGCTGCTACGCGGACTTCGACTACTTCACCTACGAGCCGGTCTAACGGCTCAGGCCGGGTAGCCCAg                                                                                                                                              >  3:118395/1‑149 (MQ=255)       ggACGACTACATCGGCGGGCGCGGCTTCTTCACCGGCGCGTTTGTGGGCCTGCACTGCGGGGACATCAGCGGCGACGGCTGCTACGCGGACTTCGACTACTTCACCTACGAGCCGGTCTAACGGCTCAGGCCGGGTAGCCCAgcgcgcg                                                                                                                                        >  1:138019/1‑149 (MQ=255)            acTACATCGGCGGGCGCGGCTTCTTCACCGGCGCGTTTGTGGGCCTGCACTGCGAGGACATCAGCGGCGACGGCTGCTACGCGGACTTCGACTACTTCACCTACGAGCCGGTCTAACGGCTCAGGCCGGGTAGCCCAGCGCGCGCgaga                                                                                                                                   >  4:546903/1‑149 (MQ=255)                  tCGGCGGGCGCGGCTTCTTCACCGGCGCGTTTGTGGGCCTGCACTGCGAGGACATCAGCGGCGACGGCTGCTACGCGGACTTCGACTACTTCACCTACGAGCCGGTCTAACGGCTCAGGCCGGGTAGCCCAGCGCGCGCGAGAGCGCGa                                                                                                                             <  3:483627/149‑1 (MQ=255)                    ggcgggcgCGGCTTCTTCACCGGCGCGTTTGTGGGCCTGCACTGCGAGGACATCAGCGGCGACGGCTGCTACGCGGACTTCGACTACTTCACCTACGAGCCGGTCTAACGGCTCAGGCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGc                                                                                                                           >  4:18743‑M2/1‑148 (MQ=255)                      cgggcgCGGCTTCTTCACCGGCGCGTTTGTGGGCCTGCACTGCGAGGACATCAGCGGCGACGGCTGCTACGCGGACTTCGACTACTTCACCTACGAGCCGGTCTAACGGCTCAGGCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGccc                                                                                                                         >  1:418256‑M2/1‑146 (MQ=255)                          cgcgGCTTCTTCACCGGCGCGTTTGTGGGCCTGCACTGCGAGGACATCAGCGGCGACGGCTGCTACGCGGACTTCGACTACTTCACCTACGAGCCGGTCTAACGGCTCAGGCCGGGctcgcgctctcgcgcgcgctgggctacccggcc                                                                                                                     <  4:525004‑M1/149‑34 (MQ=255)                           gcgGCTTCTTCACCGGCGCGTTTGTGGGCCTGCACTGCGAGGACATCAGCGGCGACGGCTGCTACGCGGACTTCGACTACTTCACCTACGAGCCGGTCTAACGGCTCAGGCCGGGctcgcgctctcgcgcgcgctgggctacccggcct                                                                                                                    <  1:180638‑M1/149‑35 (MQ=255)                           gcgGCTTCTTCACCGGCGCGTTTGTGGGCCTGCACTGCGAGGACATCAGCGGCGACGGCTGCTACGCGGACTTCGACTACTTCACCTACGAGCCGGTCTAACGGCTCAGGCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGcccggcct                                                                                                                    >  1:531755‑M2/1‑141 (MQ=255)                               cttcttCACCGGCGCGTTTGTGGGCCTGCACTGCGAGGACATCAGCGGCGACGGCTGCTACGCGGACTTCGACTACTTCACCTACGAGCCGGTCTAACGGCTCAGGCCGGGTAGCCCATCGCGCTCGAGAGCGCGGGCCCGGCctgctg                                                                                                                >  3:358930/1‑149 (MQ=255)                                   ttcACCGGCGCGTTTGTGGGCCTGCACTGCGAGGACATCAGCGGCGACGGCTGCTACGCGGACTTCGACTACTTCACCTACGAGCCGGTCTAACGGCTCAGGCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGCCCGGCCTGCTGAAgc                                                                                                            >  3:618111/1‑149 (MQ=255)                                    tcACCGGCGCGTTTGTGGGCCTGCACTGCGAGGACATCAGCGGCGACGGCTGCTACGCGGACTTCGACTACTTCACCTACGAGCCGGTCTAACGGCTCAGGCCGGGctcgcgctctcgcgcgcgctgggctacccggcc                                                                                                                     <  4:414346‑M1/139‑34 (MQ=255)                                    tcACCGGCGCGTTTGTGGGCCTGCACTGCGAGGACATCAGCGGCGACGGCTGCTACGCGGACTTCGACTACTTCACCTACGAGCCGGTCTAACGGCTCAGGCCGGGctcgcgctctcgcgcgcgctgggctacccggcc                                                                                                                     >  3:414346‑M1/1‑106 (MQ=255)                                            gcgTTTGTGGGCCTGCACTGCGAGGACATCAGCGGCGACGGCTGCTACGCGGACTTCGACTACTTCACCTACGAGCCGGTCTAACGGCTCAGGCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGCCCGGCCTGCTGAAGCTGCTCGCgg                                                                                                   <  4:209231/149‑1 (MQ=255)                                                ttGTGGGCCTGCACTGCGAGGACATCAGCGGCGACGGCTGCTACGCGGACTTCGACTACTTCACCTACGAGCCGGTCTAACGGCTCAGGCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGCCCGGCCTGCTGAAGCTGCTCGCGGAAAt                                                                                               <  4:115710/149‑1 (MQ=255)                                                  gtgGGCCTGCACTGCGAGGACATCAGCGGCGACGGCTGCTACGCGGACTTCGACTACTTCACCTACGAGCCGGTCTAACGGCTCAGGCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGCCCGGCCTGCTGAAGCTGCTCGCGGAAATTa                                                                                             <  4:118395/149‑1 (MQ=255)                                                  gtgGGCCTGCACTGCGAGGACATCAGCGGCGACGGCTGCTACGCGGACTTCGACTACTTCACCTACGAGCCGGTCTAACGGCTCAGGCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGCCCGGCCTGCTGAAGCTGCTCGCGGAAATTa                                                                                             <  1:555995/149‑1 (MQ=255)                                                  gtgGGCCTGCACTGCGAGGACATCAGCGGCGACGGCTGCTACGCGGACTTCGACTACTTCACCTACGAGCCGGTCTAACGGCTCAGGCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGCCCGGCCTGCTGAAGCTGCTCGCGGAAATTa                                                                                             <  2:426649/149‑1 (MQ=255)                                                       ccTGCACTGCGAGGACATCAGCGGCGACGGCTGCTACGCGGACTTCGACTACTTCACCTACGAGCCGGTCTAACGGCTCAGGCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGCCCGGCCTGCTGAAGCTGCTCGCGGAAATTAGCCAg                                                                                        >  1:212708/1‑149 (MQ=255)                                                        cTGCACTGCGAGGACACCAGCGGCGACGGCTGCTACGCGGACTTCGACTACTTCGCCTGCGAGCCGGTCTAACGGCTCAGGCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGCCCGGCTTGCTGAAGCTGCTCGCGGAAATTAGCCAGc                                                                                       <  4:680379/149‑1 (MQ=255)                                                           cACTGCGAGGACATCAGCGGCGACGGCTGCTACGCGGACTTCGACTACTTCACCTACGAGCCGGTCTAACGGCTCAGGCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGCCCGGCCTGCTGAAGCTGCTCGCGGAAATTAGCCAGCTcc                                                                                    >  1:431240/1‑149 (MQ=255)                                                              tGCGAGGACATCAGCGGCGACGGCTGCTACGCGGACTTCGACTACTTCACCTACGAGCCGGTCTAACGGCTCAGGCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGCCCGGCCTGCTGAAGCTGCTCGCGGAAATTAGCCAGCTCcgc                                                                                  <  4:66697/148‑1 (MQ=255)                                                              tGCGAGGACATCAGCGGCGACGGCTGCTACGCGGACTTCGACTACTTCACCTACGAGCCGGTCTAACGGCTCAGGCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGCCCGGCCTGCTGAAGCTGCTCGCGGAAATTAGCCAGCTCcgc                                                                                  >  3:66697/1‑148 (MQ=255)                                                               gCGAGGACATCAGCGGCGACGGCTGCTACGCGGACTTCGACTACTTCACCTACGAGCCGGTCTAACGGCTCAGGCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGCCCGGCCTGCTGAAGCTGCTCGCGGAAATTAGCCAGCTCCGcgt                                                                                >  1:74436/1‑149 (MQ=255)                                                                  aGGACATCAGCGGCGACGGCTGCTACGCGGACTTCGACTACTTCACCTACGAGCCGGTCTAACGGCTCAGGCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGCCCGGCCTGCTGAAgct                                                                                                           <  4:642861/119‑1 (MQ=255)                                                                  aGGACATCAGCGGCGACGGCTGCTACGCGGACTTCGACTACTTCACCTACGAGCCGGTCTAACGGCTCAGGCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGCCCGGCCTGCTGAAgct                                                                                                           >  3:642861/1‑119 (MQ=255)                                                                          aGCGGCGACGGCTGCTACGCGGACTTCGACTACTTCACCTACGAGCCGGTCTAACGGCTCAGGCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGCCCGGCCTGCTGAAGCTGCTCGCGGAAATTAGCCAGCTCCGCGTCGTCCACGCgg                                                                     <  2:74436/149‑1 (MQ=255)                                                                             ggcgACGGCTGCTACGCGGACTTCGACTACTCCACCTACGAGCCGGTCTAACGGCTCAGGCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGCCCGGCCTGCTGAAGCTGCTCGCGGAAATTAGCCAGCTCCGCGTGGACGACGCggagc                                                                  <  2:212708/149‑4 (MQ=255)                                                                                   ggCTGCTACGCGGACTTCGACTACTTCACCTACGAGCCGGTCTAACGGCTCAGGCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGCCCGGCCTGCTGAAGCTGCTCGCGGAAATTAGCCAGCTCCGCGTCGTCCACGCGGGAGGTCAGc                                                            >  3:437146/1‑149 (MQ=255)                                                                                            gcgGACTTCGACTACTTCACCTACGAGCCGGTCTAACGGCTCAGGCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGCCCGGCCTGCTGAAGCTGCTCGCGGAAATTAGCCAGCTCCGCGTCGTCCACGCGGGAGGTCAGCGTCGACAgg                                                   >  1:125675/1‑149 (MQ=255)                                                                                            gcgGACTTCGACTACTTCACCTACGAGCCGGTCTAACGGCTCAGGCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGCCCGGCCTGCTGAAGCTGCTCGCGGAAATTAGCCAGCTCCGCGTCGTCCACGCGGGAGGTCAGCGTCGACAgg                                                   >  2:600014/1‑149 (MQ=255)                                                                                                aCTTCGACTACTTCACCTACGAGCCGGTCTAACGGCTCAGGCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGCCCGGCCTGCTGAAGCTGCTCGCGGAAATTAGCCAGCTCCGCGTCGTCCACGCGGGAGGTCAGCGTCGACAGGCTCa                                               >  4:415182/1‑149 (MQ=255)                                                                                                  ttCGACTACTTCACCTACGAGCCGGTCTAACGGCTCAGGCCGGGTa                                                                                                                                                    <  3:579326/46‑1 (MQ=255)                                                                                                  ttCGACTACTTCACCTACGAGCCGGTCTAACGGCTCAGGCCGGGTa                                                                                                                                                    >  4:579326/1‑46 (MQ=255)                                                                                                         actTCACCTACGAGCCGGTCTAACGGCTCAGGCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGCCCGGCCTGCTGAAGCTGCTCGCGGAAATTAGCCAGCTCCGCGTCGTCCACGCGGGAGGTCAGCGTCGACAGGCTCAGGGCGGCGa                                      <  2:138019/149‑1 (MQ=255)                                                                                                          ctTCACCTACGAGCCGGTCTAACGGCTCAGGCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGCCCGGCCTGCTGAAGCTGCTCGCGGAAATTAGCCAGCTCCGCGTCGTCCACGCGGGAGGTCAGCGTCGACAGGCTCAGGGCGGCGAt                                     <  3:15950/149‑1 (MQ=255)                                                                                                           ttCACCTACGAGCCGGTCTAACGGCTCAGGCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGCCCGGCCTGCTGAAGCTGCTCGCGGAAATTAGCCAGCTCCGCGTCGTCCACGCGGGAGGTCAGCGTCGACAGGCTCAGGGCGGCGATg                                    >  2:591243/1‑149 (MQ=255)                                                                                                           ttCACCTACGAGCCGGTCTAACGGCTCAGGCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGCCCGGCCTGCTGAAGCTGCTCGCGGAAATTAGCCAGCTCCGCGTCGTCCACGCGGGAGGTCAGCGTCGACAGGCTCAGGGCGGCGATg                                    >  2:617950/1‑149 (MQ=255)                                                                                                           ttCACCTACGAGCCGGTCTAACGGCTCAGGCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGCCCGGCCTGCTGAAGCTGCTCGCGGAAATTAGCCAGCTCCGCGTCGTCCACGCGGGAGGTCAGCGTCGACAGGCTCAGGGCGGCGATg                                    >  2:550680/1‑149 (MQ=255)                                                                                                                   cGAGCCGGTCTAACGGCTCAGGCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGCCCGGCCTGCTGAAGCTGCTCGCGGAAATTAGCCAGCTCCGCGTCGTCCACGCGGGAGGTCAGCGTCGACAGGCTCAGGGCGGCGATGACGCGGGa                            <  2:125675/149‑1 (MQ=255)                                                                                                                      gCCGGTCTAACGGCTCAGGCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGCCCGGCCTGCTGAAGCTGCTCGCGGAAATTAGCCAGCTCCGCGTCGTCCACGCGGGAGGTCAGCGTCGACAGGCTCAGGGCGGCGATGACGCGGGACTc                         >  2:689407/1‑149 (MQ=255)                                                                                                                      gCCGGTCTAACGGCTCAGGCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGCCCGGCCTGCTGAAGCTGCTCGCGGAAATTAGCCAGCTCCGCGTCGTCCACGCGGGAGGTCAGCGTCGACAGGCTCAGGGCGGCGATGACGCGGGACTc                         >  2:691561/1‑149 (MQ=255)                                                                                                                          gTCTAACGGCTCAGGCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGCCCGGCCTGCTGAAGCTGCTCGCGGAAATTAGCCAGCTCCGCGTCGTCCACGCGGGAGGTCAGCGTCGACAGGCTCAGGGCGGCGATGAc                                  >  2:401916/1‑136 (MQ=255)                                                                                                                          gTCTAACGGCTCAGGCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGCCCGGCCTGCTGAAGCTGCTCGCGGAAATTAGCCAGCTCCGCGTCGTCCACGCGGGAGGTCAGCGTCGACAGGCTCAGGGCGGCGATGAc                                  <  1:401916/136‑1 (MQ=255)                                                                                                                             tAACGGCTCAGGCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGCCCGGCCTGCTGAAGCTGCTCGCGGAAATTAGCCAGCTCCGCGTCGTCCACGCGGGAGGTCAGc                                                            <  4:573732/107‑1 (MQ=255)                                                                                                                             tAACGGCTCAGGCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGCCCGGCCTGCTGAAGCTGCTCGCGGAAATTAGCCAGCTCCGCGTCGTCCACGCGGGAGGTCAGc                                                            >  3:573732/1‑107 (MQ=255)                                                                                                                               aCGGCTCAGGCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGCCCGGCCTGCTGAAGCTGCTCGCGGAAATTAGCCAGCTCCGCGTCGTCCACGCGGGAGGTCAGCGTCGACAGGCTCAGGGCGGCGATGACGCGGGACTCGTGGTTCca                >  3:327833/1‑149 (MQ=255)                                                                                                                                  gCTCAGGCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGCCCGGCCTGCTGAAGCTGCTCGCGGAAATTAGCCAGCTCCGCGTCGTCCACGCGGGAGGTCAGCGTCGACAGGCTCAGGGCGGCGATGACGCGGGACTCGTGGTTCCacac             >  1:527674/1‑149 (MQ=255)                                                                                                                                    tCAGGCCGGGTAGCCCAGCCCGCGCGAGAGCGCGAGCCCGGCCTGCTGAAGCAGCTCGCGGAAATTAGCCAGCTCCGCGTCGTCCACGCGGGAGGTAAGCGTCGACAGGCTCAGGGCGGCGATGACGCGGGACTCGTGGTTCCACACCg           >  4:586492/1‑149 (MQ=255)                                                                                                                                      aGGCCGGGctcgcgctctcgcgcgcgctgggctacccggcctgagccgttagaccggctcgtaggtgaagtagtcgaagtccgcgtagcagccgtcgccgctgatgtcctcgcagtgcaggcccacaaacgcgccggtgaagaagccgc         >  1:531755‑M1/1‑8 (MQ=255)                                                                                                                                      aGGCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGcccggcctgagccgttagaccggctcgtaggtgaagtagtcgaagtccgcgtagcagccgtcgccgctgatgtcctcgcagtgcaggcccacaaacgcgccggtgaagaagccgc         <  1:180638‑M2/149‑116 (MQ=255)                                                                                                                                       ggCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGcccggcctgagccgttagaccggctcgtaggtgaagtagtcgaagtccgcgtagcagccgtcgccgctgatgtcctcgcagtgcaggcccacaaacgcgccggtgaagaagccgcg        <  4:525004‑M2/149‑117 (MQ=255)                                                                                                                                       ggCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGcccggcctgagccgttagaccggctcgtaggtgaagtagtcgaagtccgcgtagcagccgtcgccgctgatgtcctcgcagtgcaggcccacaaacgcgccggtga                  <  4:414346‑M2/139‑107 (MQ=255)                                                                                                                                       ggCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGcccggcctgagccgttagaccggctcgtaggtgaagtagtcgaagtccgcgtagcagccgtcgccgctgatgtcctcgcagtgcaggcccacaaacgcgccggtga                  >  3:414346‑M2/1‑33 (MQ=255)                                                                                                                                           gggctcgcgctctcgcgcgcgctgggctacccggcctgagccgttagaccggctcgtaggtgaagtagtcgaagtccgcgtagcagccgtcgccgctgatgtcctcgcagtgcaggcccacaaacgcgccggtgaagaagccgcgcccg    >  1:418256‑M1/1‑3 (MQ=255)                                                                                                                                             gctcgcgctctcgcgcgcgctgggctacccggcctgagccgttagaccggctcgtaggtgaagtagtcgaagtccgcgtagcagccgtcgccgctgatgtcctcgcagtgcaggcccacaaacgcgccggtgaagaagccgcgcccgcc  >  4:18743‑M1/1‑1 (MQ=255)                                                                                                                                             |                                                                                                                                                     GCTGTCGGACGACTACATCGGCGGGCGCGGCTTCTTCACCGGCGCGTTTGTGGGCCTGCACTGCGAGGACATCAGCGGCGACGGCTGCTACGCGGACTTCGACTACTTCACCTACGAGCCGGTCTAACGGCTCAGGCCGGGTAGCCCAGCGCGCGCGAGAGCGCGAGCCCGGCCTGCTGAAGCTGCTCGCGGAAATTAGCCAGCTCCGCGTCGTCCACGCGGGAGGTCAGCGTCGACAGGCTCAGGGCGGCGATGACGCGGGACTCGTGGTTCCACACCGGCACCGCCA  >  NC_000913/288273‑288561

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ 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.