New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 4407748	40 (0.790)	4 (0.080)	4/246	NT	8.2%	coding (96/1299 nt)	PP_3889	putative Phage integrase
	?	NC_002947	= 4407806	52 (1.080)					coding (38/1299 nt)	PP_3889	putative Phage integrase

GGCGCTGACGCAGCGCGGGCAGCTCGGCCAGCACCGCCGCCACGCTCAACTCAGGCCAGCGGGCGATCGGTACCCATTTCTTGCCGCGCACCAGGTGCCAGGTACCACGCTCACGGCTGCTCCAAAAGCGCAGGTACAGGCCGGGGTGACGC‑GGGTCACGCAGGTCGCGCACCGACTTGTCGGTCGCCTGACGCCGCACCTCGGCCTCGCTCAACTTCACTTCGCGGGTCGCGCTCATGCGGCCACCGTGGCGGGCAGGAGGAGGTAGGCACGGATGGCCTCGACGGCGT  >  NC_002947/4407606‑4407895                                                                                                                                               |                                                                                                                                                     ggCGCTGACGCAGCGCGGGCAGCTCGGCCAGCACCGCCGCCACGCTCAACTCAGGCCAGCGGGCGATCGGTACCCATTTCTTGCCGCGCACCAGGTGCCAGGTACCACGCTCACGGCTGCTCCAAAAGCGCAGGTACAGGCCGGGGTGa                                                                                                                                                >  4:25464/1‑149 (MQ=255)    gcTGACGCAGCGCGGGCAGCTC‑GCCAGCACCGCCGCCACGCTCAACTCAGGCCAGCGGGCGATCGGTACCCATTTCTTGCCGCGCACCAGGTGCCAGGTACCACGCTCACGGCTGCTCCAAAAGCGCAGGTACAGGCCGaggtgcggcg                                                                                                                                            >  6:143832‑M1/1‑139 (MQ=255)          gCAGCGCGGGCAGCTCGGCCAGCACCGCCGCCACGCTCAACTCAGGCCAGCGGGCGATCGGTACCCATTTCTTGCCGCGCACCAGGTGCCAGGTACCACGCTCACGGCTGCTCCAAAAGCGCAGGTACAGGCCGGGGTGACGC‑GGGTCa                                                                                                                                      >  7:268583/1‑149 (MQ=255)            aGCGCGGGCAGCTCGGCCAGCACCGCCGCCACGCTCAACTCAGGCCAGCGGGCGATCGGTACCCATTTCTTGCCGCGCACCAGGTGCCAGGTACCACGCTCACGGCTGCTCCAAAAGCGCAGGTACAGGCCGGGGTGAcgc‑g                                                                                                                                           <  5:135551/142‑1 (MQ=255)            aGCGCGGGCAGCTCGGCCAGCACCGCCGCCACGCTCAACTCAGGCCAGCGGGCGATCGGTACCCATTTCTTGCCGCGCACCAGGTGCCAGGTACCACGCTCACGGCTGCTCCAAAAGCGCAGGTACAGGCCGGGGTGAcgc‑g                                                                                                                                           >  6:135551/1‑142 (MQ=255)                        tCGGCCAGCACCGCCGCCACGCTCAACTCAGGCCAGCGGGCGATCGGTACCCATTTCTTGTCGCGCACCAGGTGCCAGGTACCACGCTCACGGCTGCTCCAAAAGCGCAGGTACAGGCCGGGGTGACGC‑GGGTCACGCAGGTCGCGCAc                                                                                                                        >  4:270620/1‑149 (MQ=255)                           gCCAGCACCGCCGCCACGCTCAACTCAGGCCAGCGGGCGATCGGTACCCATTTCTTGCCGCGCACCAGGTGCCAGGTACCACGCTCACGGCTGCTCCAAAAGCGCAGGTACAGGCCGGGGTGACGC‑GGGTCACGCAGGTCGcg‑accgac                                                                                                                    <  8:268583/149‑1 (MQ=255)                                   cgccgcCACGCTCAACTCAGGCCAGCGGGCGATCGGTACCCATTTCTTGCCGCGCACCAGGTGCCAGGTACCACGCTCACGGCTGCTCCAAAAGCGCAGGTACAGGCCGGGGTGACGC‑GGGTCACGCAGGTCGCGCACCGACtt                                                                                                                  >  1:314274/1‑144 (MQ=255)                                   cgccgcCACGCTCAACTCAGGCCAGCGGGCGATCGGTACCCATTTCTTGCCGCGCACCAGGTGCCAGGTACCACGCTCACGGCTGCTCCAAAAGCGCAGGTACAGGCCGGGGTGACGC‑GGGTCACGCAGGTCGCGCACCGACtt                                                                                                                  <  2:314274/144‑1 (MQ=255)                                    gccgccACGCTCAACTCAGGCCAGCGGGCGATCGGTACCCATTTCTTGCCGCGCACCAGGTGCCAGGTACCACGCTCACGGCTGCTCCAAAAGCGCAGGTACAGGCCGaggtgcggcgtcaggcgaccgacaagtcggtgcgcgacctg                                                                                                             >  2:173148‑M1/1‑108 (MQ=255)                                         cACGCTCAACTCAGGCCAGCGGGCGATCGGTACCCATTTCTTGTCGCGCACCAGGTGCCAGGTACCACGCTCACGGCTGCTCCAAAAGCGCAGGTACAGGCCGGGGTGACGC‑GGGTCACGCAGGTCGCGCACCGACTTGTCGGTCGCCt                                                                                                       <  3:270620/149‑1 (MQ=255)                                         cACGCTCAACTCAGGCCAGCGGGCGATCGGTACCCATTTCTTGCCGCGCACCAGGTGCCAGGTACCACGCTCACGGCTGCTCCAAAAGCGCAGGTACAGGCCGGGGTGACGC‑GGGTCACGCAGGTCGCGCACCGACTTGTCGGTCGCCt                                                                                                       >  5:266459/1‑149 (MQ=255)                                            gCTCAACTCAGGCCAGCGGGCGATCGGTACCCATTTCTTGCCGCGCACCAGGTGCCAGGTACCACGCTCACGGCTGCTCCAAAAGCGCAGGTACAGGCCGGGGTGACGC‑GGGTCACGCAGGTCGCGCACCGACTTgtcggtcg                                                                                                          <  1:50629/143‑1 (MQ=255)                                            gCTCAACTCAGGCCAGCGGGCGATCGGTACCCATTTCTTGCCGCGCACCAGGTGCCAGGTACCACGCTCACGGCTGCTCCAAAAGCGCAGGTACAGGCCGGGGTGACGC‑GGGTCACGCAGGTCGCGCACCGACTTgtcggtcg                                                                                                          >  2:50629/1‑143 (MQ=255)                                             cTCAACTCAGGCCAGCGGGCGATCGGTACCCATTTCTTGCCGCGCACCAGGTGCCAGGTACCACGCTCACGGCTGCTCCAAAAGCGCAGGTACAGGCCGGGGTGACGC‑GGGTCACGCAGGTCGCGCACCGACTTGTCGGTCGCCTGAcg                                                                                                   >  5:140056/1‑149 (MQ=255)                                                aaCTCAGGCCAGCGGGCGATCGGTACCCATTTCTTGCCGCGCACCAGGTGCCAGGTACCACGCTCACGGCTGCTCCAAAAGCGCAGGTACAGGCCGGGGTGACGC‑GGGTCACGCAGGTAGCGCACCGACTTGTCGGTCGCCTGAcgccg                                                                                                >  8:2041/1‑149 (MQ=255)                                                 aCTCAGGCCAGCGGGCGATCGGTACCCATTTCTTGCCGCGCACCAGGTGCCAGGTACCACGCTCACGGCTGCTCCAAAAGCGCAGGTACAGGCCGGGGTGACGC‑GGGTCACGCAGGTCGCGCACCGACTTGTCGGTCGCCTGAcgccgc                                                                                               <  6:140056/149‑1 (MQ=255)                                                   tCAGGCCAGCGGGCGATCGGTACCCATTTCTTGCCGCGCACCAGGTGCCAGGTACCACGCTCACGGCTGCTCCAAAAGCGCAGGTACAGGCCGGGGTGACGC‑GGGTCACGCAGGTCGCGCACCGACTTGTCGGTCGCCTGACGCCGCAc                                                                                             >  6:49248/1‑149 (MQ=255)                                                     aGGCCAGCGGGCGATCGGTACCCATTTCTTGCCGCGCACCAGGTGCCAGGTACCACGCTCACGGCTGCTCCAAAAGCGCAGGTACAGGCCGGGGTGACGC‑GGGTCACGCAGGTCGCGCACCGACTTgtcggtc                                                                                                           <  7:139131/133‑1 (MQ=255)                                                     aGGCCAGCGGGCGATCGGTACCCATTTCTTGCCGCGCACCAGGTGCCAGGTACCACGCTCACGGCTGCTCCAAAAGCGCAGGTACAGGCCGGGGTGACGC‑GGGTCACGCAGGTCGCGCACCGACTTgtcggtc                                                                                                           >  8:139131/1‑133 (MQ=255)                                                     aGGCCAGCGGGCGATCGGTACCCATTTCTTGCCGAGCACCAGGTGCCAGGTACCACGCTCACCGCTGCTCCAAAAGCGCAGGTACACGCCGCGGTGAAGC‑GGGTCACGAAGGACGCGCACCGACTTGTCGTTCGCCTGACGCCGCACCt                                                                                           >  7:57769/1‑149 (MQ=255)                                                       gCCAGCGGGCGATCGGTAGCCATTTCTTGCCGCGCACCAGGTGCCAGGTACCACGCTCACGGCTGCTCCAAAAGCGCAGGTACAGGCCGaggtgcggcgtcaggcgaccgacaagtcggtgcgcgacctgcgtgacccgcgtcaccccg                                                                                          <  1:173148‑M1/149‑61 (MQ=255)                                                        ccAGCGGGCGATCGGTACCCATTTCTTGCCGCGCACCAGGTGCCAGGTACCACGCTCACGGCTGCTCCAAAAGCGCAGGTACAGGCCGGGGTGCCGC‑GGGTCACGCAGGTCGCGCACCGACTTGTCGGTCGCCTGACGCCGCCCCTcgg                                                                                        <  8:285839‑M2/149‑4 (MQ=255)                                                         cAGCGGGCGATCGGTACCCATTTCTTGCCGCGCACCAGGTGCCAGGTACCACGCTCACGGCTGCTCCAAAAGCGCAGGTACAGGCCGaggtgcggcgtcaggcgaccgacaagtcggtgcgcgacctgcgtgacccgcgtcaccccggc                                                                                        <  5:143832‑M1/149‑63 (MQ=255)                                                             gggCGATCGGTACCCATTTCTTGCCGCGCACCAGGTGCCAGGTACCACGCTCACGGCTGCTCCAAAAGCGCAGGTACAGGCCGGGGTGACGC‑GGGTCACGCAGGTCGCGCACCGACTTGTCGGTCGCCTGACGCCGCACCTCGGCCTCg                                                                                   <  6:49616/149‑1 (MQ=255)                                                                          ccATTTCTTGCCGCGCACCAGGTGCCAGGTACCACGCTCACGGCTGCTCCAAAAGCGCAGGTACAGGCCGGGGTGACGC‑GGGTCACGCAGGTCGCGCACCGACTTGTCGGTCGCCTGACGCCGCACCTCGGCCTCGc                                                                                  >  5:209227/1‑137 (MQ=255)                                                                          ccATTTCTTGCCGCGCACCAGGTGCCAGGTACCACGCTCACGGCTGCTCCAAAAGCGCAGGTACAGGCCGGGGTGACGC‑GGGTCACGCAGGTCGCGCACCGACTTGTCGGTCGCCTGACGCCGCACCTCGGCCTCGc                                                                                  <  6:209227/137‑1 (MQ=255)                                                                                   gCCGCGCACCAGGTGCCAGGTACCACGCTCACGGCTGCTCCAAAAGCGCAGGTACAGGCCGGGGTGACGC‑GGGTCACGCAGGTCGCGCACCGACTTGTCGGTCGCCTGACGCCGCACCTCGGCCTCGCTCAACTTCACTTCGCGGGTcg                                                             >  1:149374/1‑149 (MQ=255)                                                                                   gCCGCGCACCAGGTGCCAGGTACCACGCTCACGGCTGCTCCAAAAGCGCAGGTACAGGCCGGGGTGACGC‑GGGTCACGCAGGTAGCGCACCGACTTGTCGGTCGCCTGACGCCGCACCTCGGCCTCGCTCAACTTCACTTCGCggg                                                                <  7:2041/146‑1 (MQ=255)                                                                                      gcgcACCAGGTGCCAGGTACCACGCTCACGGCTGCTCCAAAAGCGCAGGTACAGGCCGGGGTGACGC‑GGGTCACGCAGGTCGCGCACCGACTTGTCGGTCGCCTGACGCCGCACCTCGGCCTCGCTCAACTTCACTTCGCGGGTCgcgc                                                          <  3:25464/149‑1 (MQ=255)                                                                                                      gTACCACGCTCACGGCTGCTCCAAAAGCGCAGGTACAGGCCGGGGTGACGC‑GGGTCACGCAGGTCGCGCACCGACTTGTCGGTCGCCTGACGCCTCACCTCGGCCTCGCTCAACTTCACTTCGCGGGTCGCGCt                                                         <  5:16779/134‑1 (MQ=255)                                                                                                      gTACCACGCTCACGGCTGCTCCAAAAGCGCAGGTACAGGCCGGGGTGACGC‑GGGTCACGCAGGTCGCGCACCGACTTGTCGGTCGCCTGACGCCGCACCTCGGCCTCGCTCAACTTCACTTCGCGGGTCGCGCt                                                         >  6:16779/1‑134 (MQ=255)                                                                                                          cACGCTCACGGCTGCTCCAAAAGCGCAGGTACAGGCCGGGGTGACGC‑GGGTCACGCAGGTCGCGCACCGACTTGTCGGTCGCCTGACGCCGCACCTCGGCCTCGCTCAACTTCACTTCGCGGGTCGCGCTCATGCGGCCACCGTGGCgg                                      >  2:256490/1‑149 (MQ=255)                                                                                                               tCACGGCTGATCCAAAAGCGCAGGTACAGGCCGGGGTGACGC‑GGGTCACGCAGGTCGCGCACCGACTTGTCGGTCGCCTGACGCCGCACCTCGGCCTCGCTCAACTTCACTTCGCGGGTCGCGCTCATGCGGCCACCGTGGCGGGCag                                  >  5:324227/1‑148 (MQ=255)                                                                                                                     ctgctCCAAAAGCGCAGGTACAGGCCGGGGTGACGC‑GGGTCACGCAGGTCGCGCACCGACTTGTCGGTCGCCTGACGCCGCACCTCGGCCTCGCTCAACTTCACTTCGCGGGTCGCGCTCATGCGGCCACCGTGGCGGGCaggaggagg                           <  6:266459/149‑1 (MQ=255)                                                                                                                        ctCCAAAAGCGCAGGTACAGGCCGGGGTGACGC‑GGGTCACGCAGGTCGCGCACCGACTTGTCGGTCGCCTGACGCCGCACCTCGGCCTCGCTCAACTTCACTTCGCGGGTCGCGCTCATGCGGCCACCGTGGCGGGCAGGAGGAGGTAg                        >  1:266167/1‑149 (MQ=255)                                                                                                                        ctCCAAAAGCGCAGGTACAGGCCGGGGTGACGC‑GGGTCACGCAGGTCGCGCACCGACTTGTCGGTCGCCTGACGCCGCACCTCGGCCTCGCTCAACTTCACTTCGCGGGGCGCGCTCATGCGGCCACCGTGGCGGGCAGGAGGAGGt                          <  3:82546/147‑1 (MQ=255)                                                                                                                            aaaaGCGCAGGTACAGGCCGGGGTGACGCTGGGTCACGCAGGTCGCGCACCGACTTGTCGGTCGCCTGACGCCGCACCTCGGCCTCGCTCAACTTCACTTCGCGGGTCGCGCTCATGCGGCCACCGTGGCgg                                      >  1:24043/1‑132 (MQ=255)                                                                                                                            aaaaGCGCAGGTACAGGCCGGGGTGACGC‑GGGTCACGCAGGTCGCGCACCGACTTGTCGGTCGCCTGACGCCGCACCTCGGCCTCGCTCAACTTCACTTCGCGGGTCGCGCTCATGCGGCCACCGTGGCgg                                      <  2:24043/131‑1 (MQ=255)                                                                                                                            aaaaGCGCAGGTACAGGCCGGGGTGACGC‑GGGTCACGCAGGTCGCGCACCGACTTGTCGGTCGCCTGACGCCGCACCTCGGCCTCGCTCAACTTCACTTCGCGGGTCGCGCTCATGCGGCCACCGTGGCGGGCAGGAGGAGGTAGGCAc                    <  5:49248/149‑1 (MQ=255)                                                                                                                            aaaaGCGCAGGTACAGGCCGGGGTGACGC‑GGGTCACGCAGGTCGCGCACCGACTTGTCGGTCGCCTGACGCCGCACCTCGGCCTCGCTCAACTTCACTTCGCGGGTCGCGCTCATGCGGCCACCGTGGCGGGCAGGAGGAGGTAGGCAc                    >  4:153436/1‑149 (MQ=255)                                                                                                                               aGCGCAGGTACAGGCCGGGGTGACGC‑GGGTCACGCAGGTCGCGCACCGACTTGTCGGTCGCCTGACGCCGCACCTCGGCCTCGCTCAACTTCACTTCGCGGGTCGCGCTCATGCGGCCACCGTGGCGGGCAGGAGGAGGTAGGCACGGa                 >  8:278035/1‑149 (MQ=255)                                                                                                                                    aGGTACAGGCCGGGGTGACGC‑GGGTCACGCAGGTCGCGCACCGACTTGTCGGTCGCCTGACGCCGCACCTCGGCCTCGCTCAACTTCACTTCGCGGGTCGCTCTCATGCGGCCACCTTGGCGGGCAGGAGGAGGTAGGCACGGATg               <  1:61045/146‑1 (MQ=255)                                                                                                                                    aGGTACAGGCCGGGGTGACGA‑GGGTCACGCAGGTCGCGCACCGACTTGTCGGTCGCCTGACGCCGCACCTCGGCCTCGCTCAACTTCACTTCGCGGGTCGCGCTCATGCGGCCACCGTGGCGGGCAGGACGAGGTAGGCACGCATg               >  2:61045/1‑146 (MQ=255)                                                                                                                                        aCAGGCCGGGGTGACGC‑GGGTCACGCAGGTCGCGCACCGACTTGTCGGTCGCCTGACGCCGCACCTCGGCCTCGCTCAACTTCACTTCGCGGGTCGCGCTCATGCGGCCACCGTGGCGGGCAGGAGGAGGTAGGCACGGAAGGccgcca        >  7:45829/1‑145 (MQ=255)                                                                                                                                            gCCGGGGTGACGC‑GGGTCACGCAGGTCGCGCACCGACTTGTCGGTCGCCTGACGCCGCACCTcggcctgtacctgcgcttttggagcagccgtgagcgtggtacctggcacctggtgcgcggcaagaaatgggtaccgatcgcccgctg    <  5:143832‑M2/149‑88 (MQ=255)                                                                                                                                            gCCGGGGTGACGC‑GGGTCACGCAGGTCGCGCACCGACTTGTCGGTCGCCTGACGCCGCACCTCGGCCTCGCTCAACTTCACTTCGCGGGTCGCGCTCATGCGGCCACCGTGGCGGGCAGGAGGAGGTAGGCACGGATGGCCTCGACGGc    >  3:176307/1‑149 (MQ=255)                                                                                                                                             ccGaggggcggcgtcaggcgaccgacaagtcggtgcgcgacctgcgtgacccgcggcaccccggcctgtacctgcgcttttggagcagccgtgagcgtggtacctggcacctggtgcgcggcaagaaatgggtaccgatcgcccgctgg    <  8:285839‑M1/149‑147 (MQ=255)                                                                                                                                              cGGGGTGACGC‑GGGTCACGCAGGTCGCGCACCGACTTGTCGGTCGCCTGACGCCGCACCTcggcctgtacctgcgcttttggagcagccgtgagcgtggtacctggcacctggtgcgcggcaagaaatggctaccgatcgcccgctggc  <  1:173148‑M2/149‑90 (MQ=255)                                                                                                                                               |                                                                                                                                                     GGCGCTGACGCAGCGCGGGCAGCTCGGCCAGCACCGCCGCCACGCTCAACTCAGGCCAGCGGGCGATCGGTACCCATTTCTTGCCGCGCACCAGGTGCCAGGTACCACGCTCACGGCTGCTCCAAAAGCGCAGGTACAGGCCGGGGTGACGC‑GGGTCACGCAGGTCGCGCACCGACTTGTCGGTCGCCTGACGCCGCACCTCGGCCTCGCTCAACTTCACTTCGCGGGTCGCGCTCATGCGGCCACCGTGGCGGGCAGGAGGAGGTAGGCACGGATGGCCTCGACGGCGT  >  NC_002947/4407606‑4407895

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.