New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 1207805	35 (0.850)	8 (0.220)	7/244	2.6	23.2%	coding (305/630 nt)	ycfK	e14 prophage; protein StfP
	?	NC_000913	= 1209602	22 (0.610)					pseudogene (54/537 nt)	stfE	e14 prophage; putative side tail fiber protein fragment

GCCAGCCTGGAGAAGGGGCGGCACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGG  >  NC_000913/1207666‑1207942                                                                                                                                            |                                                                                                                                          tacgttgtagatctgtgttctggtcatttgttgatacgcgtacatagccaataagcatgttaaatccccctggtaaaagcaggaatgatgccatttgcttgttatttcttcattttcataaacgTTGGTTTGGGAGAAgg                                                                                                                                           >  2:52763‑M1/125‑140 (MQ=255)  ccAGCCTGGAGAAGGGGCGGCACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGc                                                                                                                                          <  2:527230‑M1/140‑2 (MQ=255)      tgtagatctgtgttctggtcatttgttgatacgcgtacatagccaataagcatgttaaatccccctggtaaaagcaggaatgatgccatttgcttgttatttcttcattttcataaacgTTGGTTTGGGAGAAGGAGCaa                                                                                                                                      <  2:150710‑M1/21‑1 (MQ=255)        tGGAGAAGGGGCGGCACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGctctgca                                                                                                                                    <  2:523340‑M1/140‑8 (MQ=255)               ggggCGGCACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGctctgcattacctg                                                                                                                             >  1:380068‑M1/1‑126 (MQ=255)                gggCGGCACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGc                                                                                                                                          <  2:320281‑M1/126‑2 (MQ=255)                gggCGGCACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGc                                                                                                                                          >  1:320281‑M1/1‑125 (MQ=255)                gggCGGCACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATgc                                                                                                                            >  2:641528/1‑140 (MQ=255)                gggCGGCACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATgc                                                                                                                            >  1:504882/1‑140 (MQ=255)                   cggcACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATgcagc                                                                                                                         <  2:636067/140‑1 (MQ=255)                   cggcACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATgcagc                                                                                                                         <  2:377662/140‑1 (MQ=255)                    ggcACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATgcagca                                                                                                                        <  2:504882/140‑1 (MQ=255)                     gcACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCaa                                                                                                                       <  1:2177/140‑1 (MQ=255)                     gcACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCaa                                                                                                                       <  2:20079/140‑1 (MQ=255)                         gACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGc                                                                                                                   <  1:486379/140‑1 (MQ=255)                         catttgttgatacgcgtacatagccaataagcatgttaaatccccctggtaaaagcaggaatgatgccatttgcttgttatttcttcattttcataaacgTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGc                                                                                                                   >  1:150710‑M1/101‑140 (MQ=255)                                 acttacCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGctctgcattacctgttggtgtcccggttccgt                                                                                                           <  2:380068‑M1/140‑33 (MQ=255)                                   ttacCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGa                                                                                                         <  2:288789/140‑1 (MQ=255)                                     acCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACg                                                                                                       >  2:6316/1‑140 (MQ=255)                                      ccGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGc                                                                                                      >  2:409928/1‑140 (MQ=255)                                         cACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACgg                                                                                                                    >  1:466307/1‑123 (MQ=255)                                         cACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACgg                                                                                                                    <  2:466307/123‑1 (MQ=255)                                         cACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCAcc                                                                                                   >  1:493886/1‑140 (MQ=255)                                         cACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCAcc                                                                                                   >  2:1131/1‑140 (MQ=255)                                          aCTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCg                                                                                                  <  1:641528/140‑1 (MQ=255)                                              cgcgcgCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGttt                                                                                              <  2:625005/140‑1 (MQ=255)                                                    ctgctgTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGc                                                                                        >  1:317058/1‑140 (MQ=255)                                                        catgttaaatccccctggtaaaagcaggaatgatgccatttgcttgttatttcttcattttcataaacgTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCtata                                                                                    >  2:71820‑M1/70‑140 (MQ=255)                                                            ttaaatccccctggtaaaagcaggaatgatgccatttgcttgttatttcttcattttcataaacgTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGttt                                                                                              >  1:664777‑M1/66‑126 (MQ=255)                                                            ttaaatccccctggtaaaagcaggaatgatgccatttgcttgttatttcttcattttcataaacgTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGttt                                                                                              <  2:664777‑M1/61‑1 (MQ=255)                                                              gCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGtt                                                                              <  1:582571/140‑1 (MQ=255)                                                               ccGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTa                                                                             >  1:128342/1‑140 (MQ=255)                                                               ccGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTa                                                                             >  1:643367/1‑140 (MQ=255)                                                                  cAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGctctgcattacctgttggtgtcccggttccgtggccttcagccactccgccaacaggctggctga                                                                          >  2:585085‑M1/1‑75 (MQ=255)                                                                     gAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATtg                                                                       <  2:182255/140‑1 (MQ=255)                                                                     cctggtaaaagcaggaatgatgccatttgcttgttatttcttcattttcataaacgTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATtg                                                                       <  2:527565‑M1/84‑1 (MQ=255)                                                                             ttGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTAtt                                                               <  2:643367/140‑1 (MQ=255)                                                                                gCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAg                                                            <  1:1131/140‑1 (MQ=255)                                                                                gCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAg                                                            <  1:409928/140‑1 (MQ=255)                                                                                gCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAg                                                            <  2:493886/140‑1 (MQ=255)                                                                                 cGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGc                                                           >  1:243807/1‑140 (MQ=255)                                                                                      tCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGctctgcattacctgttggtgtcccggttccgtggccttcagccactccgccaacaggctggctgaaatgcaatggtgccgctttt                                                      >  2:348203‑M1/1‑55 (MQ=255)                                                                                         tgccatttgcttgttatttcttcattttcataaacgTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTa                                                   >  1:527565‑M1/37‑140 (MQ=255)                                                                                               aTGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTa                                                   <  2:13143/134‑1 (MQ=255)                                                                                               aTGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTa                                                   >  1:13143/1‑134 (MQ=255)                                                                                                        tgCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTggggg                                    >  2:699994/1‑140 (MQ=255)                                                                                                             aCGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGaa                               >  1:414477/1‑140 (MQ=255)                                                                                                              cGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAAt                              <  2:243807/140‑1 (MQ=255)                                                                                                                     cGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGTATGCCGCaa                       <  2:664118/140‑1 (MQ=255)                                                                                                                     cGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCaa                       <  1:699994/140‑1 (MQ=255)                                                                                                                       aaaaCCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCaaaa                     <  2:317058/140‑1 (MQ=255)                                                                                                                             ttGGTTTGGGAGAAGGctctgcattacctgttggtgtcccggttccgtggcttcagccactccgccaacaggctggctgaaatgcaatggtgccgctttttctgctgaagaatacccggaactggcaaaggcttatccga               <  1:141995‑M1/140‑125 (MQ=255)                                                                                                                             TTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCt               >  2:414477‑M1/1‑140 (MQ=255)                                                                                                                                     GGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTgg       <  2:277273‑M1/140‑1 (MQ=255)                                                                                                                                         aaGGctctgcattacctgttggtgtcccggttccgtggccttcagccactccgccaacaggctggctgaaatgcaatggtgccgctttttctgctgaagaatacccggaactggcaaaggcttatccgacaaataaattg   <  1:585085‑M1/140‑137 (MQ=255)                                                                                                                                          aGGctctgcattacctgttggtgtcccggttccgtggccttcagccactccgccaacaggctggctgaaatgcaatggtgccgctttttctgctgaagaatacccggaactggcaaaggcttatccgacaaataaattgc  <  2:346421‑M1/140‑138 (MQ=255)                                                                                                                                            |                                                                                                                                          GCCAGCCTGGAGAAGGGGCGGCACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAACTCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGG  >  NC_000913/1207666‑1207942

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ 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.