New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1414530 =	43 (0.750)	3 (0.050)	3/262	NT	5.5%	coding (264/810 nt)	recT	Rac prophage; recombinase, DNA renaturation
	?	NC_000913	= 1449280	60 (1.060)					coding (2070/2274 nt)	tynA	copper‑containing amine oxidase

TGGCGATTTGACCAGAACGGCGAGCCAGATCAATCATGCCGCGATAGCCAATGATTAGCTGAACGTTCTTTTTACCGCTCTTTTCGTTTTTATTACCAAAAGGCAGT‑AAATATGCATGACCGAGGGCGCTACCTGGCTCAAGTCCGAGCTGTGAACACTGTACGATCGCACTGACAAAACTCATAGTGTCACAGTTTCCTAACGCCGGAACTTTACGAATTTCTGTGGTGGCGATACGGATCATACGTTCAGCCGTCATATGGCGTGGAAGAGCTGCTGCCA  >  NC_000913/1414388‑1414669                                                                                                                                                |                                                                                                                                            tcgcgcTTTGACCAGAAGGGCGCGCCAGATCAATCATGCCGCGATAGCCGATGATTAGCTGAACGTTCTTTTTTCCGCTCTGTTCGTTTTTATTACCAAAAGGCAGT‑AAATATGCATGACCGAGGGCGCTACCTGGCTCAAGt                                                                                                                                             <  2:976654/141‑1 (MQ=255) tGGCGATTTGACCAGAACGGCGAGCCAGATCAATCATGCCGCGATAGCCAATGATTAGCTGCACGTTCTTTTTACCGCTCTTTTCGTTTTTATTACCAAAAGGCAGT‑AAATATGCATGACCGAGGGCGCTACCTCGCCCAAGt                                                                                                                                             >  2:269293/1‑143 (MQ=255)  cagagtatgtacccattcggtcggcataatcggccactcttcggcgcgggccacatgtgtggtgccggtggtcatccagacaacggcgtcggtgttgtccagcgactcgttatccttactgtattgtccaagaccggtgtcat                                                                                                                                             >  1:649806‑M1/143‑143 (MQ=255)  cagagtatgtacccattcggtcggcataatcggccactcttcggcgcgggccacatgtgtggtgccggtggtcatccagacaacggcgtcggtgttgtccagcgactcgttatccttactgtattgtccaagaccggtgtcat                                                                                                                                             <  1:779379‑M1/1‑1 (MQ=255)    gagtatgtacccattcggtcggcataatcggccactcttcggcgcgggccacatgtgtggtgccggtggtcatccagacaacggcgtcggtgttgtccagcgactcgttatccttactggattgtccaagaccggtgtcaTcc                                                                                                                                           <  2:1129298‑M1/3‑1 (MQ=255)      atctGACCAGAACGGCGAGCCAGATCAATCATGCCGCGATAGCCAATGATTAGCTGAACGTTCTTTTTACCGCTCTTTTCGTTTTTATTACCAAAAGGCAGT‑AAATATGCATGACCGAGGGCGCTACCTGGCTCAAGTCCGAg                                                                                                                                        <  1:399085/140‑1 (MQ=255)        ttGACCAGAACGGCGAGCCAGATCAATCATGCCGCGATAGCCAATGATTAGCTGAACGTTCTTTTTACCGCTCTTTTCGGTTTTCTTACCAACAGGCAGT‑AACTCTGCATGACCGCAGCCCCTACCTGAGTCGAGTCCGCGCt                                                                                                                                      >  2:440501/1‑143 (MQ=255)          gACCAGAACGGCGAGTCAGATCAATCATGCCGCGAGAGCCAATGATTAGCTGCACGTTCTGTTTACCGCTCTTTGCGTTTTGATTACCAAAAGGCAGT‑AAATATGCATGACCGAGGGCGCTACCTGGCTCAAGTCCGAGCtgt                                                                                                                                    <  1:87685/143‑1 (MQ=255)               gAACGGCGAGCCAGATCAATCATGCCGCGATAGCCAATGATTAGCTGAACGTTCTTTTTACCGCTCTTTTCGTTTTTATTACCAAAAGGCAGT‑AAATATGCATGACCGAGGGCGCTACCTGGCTCAACTCCGAGCTGTGAaca                                                                                                                               >  1:1113969/1‑143 (MQ=255)                    gCGAGCCAGATCAATCATGCCGCGATAGCCAATGATTAGCTGAACGTTCTTTTTACCGCTCTTTTCGTTTTTATTACCAAAAGGCAGT‑AAATATGCATGACCGAGGGCGCTACCTGGCTCAAGTCCGAGCTGTGAACACTGTa                                                                                                                          <  1:846150/143‑1 (MQ=255)                    gCGAGCCAGATCAAGCATGCCGCGATAGCCAATGATTAGCTGAACGTTCTTTTTACCGCTCTTTTCGTTTTTATTACCAAAAGGCAGT‑AAATATGCATGACCGAGGGCGCTACCTGGCTCAAGTCCGAGCTGTGAACACTGTa                                                                                                                          <  1:451669/143‑1 (MQ=255)                     cGAGCCAGATCAATCATGCCGCGATAGCCAATGATTAGCTGAACGTTCTTTTTACCGCTCTTTTCGTTTTTATTACCAAAAGGCAGT‑AAATATGCATGACCGAGGGCGCTACCTGGCTCAAGTCCGAGCTGTGAACACTGTAc                                                                                                                         >  1:907970/1‑143 (MQ=255)                             atcaatcaTGCCGCGATAGCCAATGATTAGCTGAACGTTCTTTTTACCGCTCTTTTCGTTTTTATTACCAAAAGGCAGT‑AAATATGCATGACCGAGGGCGCTACCTGGCTCAAGTCCGAGCTGTGAAAACAGTGCGAGTGCAc                                                                                                                 >  2:1393/1‑143 (MQ=255)                                aatcaTTCTGCAATAGCCAATAATTAGCTTAACGTTCTTTTTACCTTTCTTTTCGCTTTTAGGACCAAAAGGCAGT‑AAATATGCATGACCGGGGGCGCTACCTGGCTCAAGTCCGAGCTGTGAACACTGTACGATCGCACTGa                                                                                                              <  1:185764/143‑1 (MQ=255)                                aatcaTGCCGCGATAGCCAATGATTAGCTGAACGTTCTTTTTACCGCTCTTTTCGTTTTTATTACCAAAAGGCAGT‑AAATATGCATGACCGAGGGCGCTACCTGGCTCAAGTCCGAGCTGTGAACACTGTACGATCGCACTGa                                                                                                              <  1:745584/143‑1 (MQ=255)                                aatcaTGCCGCGATAGCCAATGATTAGCTGAACGTTCTTTTTACCGCTCTTTGCGTTTTTATTACCAAAAGGCAGT‑AAATATGCATGACCGAGGGCGCTACCTGGCTCAAGTCCGAGCTGTGAACACTGTACGATCGCACTGa                                                                                                              <  1:7369/143‑1 (MQ=255)                                 atcaTGCCGCGATAGTCAATGAGTAGCTGAACGTTCTTTTTACCGCTCTTTTCGTTTTTATTACCAAAAGGCAGT‑AAATATGCATGACCGAGGGCGCGACCGGGCTCAAGTCCGAGCTGTGAACACTGTACGATCGCACTGAc                                                                                                             <  2:287168/143‑1 (MQ=255)                                   caTGCAGCGATAGCCAATGATTAGCTGAACGTTCTTTTTACCGCTCTTTTCGTTTTTATTACCAAAAGGCAGT‑AAATATGCATGACCGAGGGCGCTACCTGGCTCAAGTCCGAGCTGTGAACACTGTACGATCGCACTGACac                                                                                                           >  2:940239/1‑142 (MQ=255)                                    cgtgctgcggtgcgtgccacctgtggggtgccggtggtcatccagacaacggcgtcggtggtgtccagcgactcgttatccgtactgtattgtccaagaccggtgtcaTCCGAGCTGTGAACACTGTACGATCGCACTGACaa                                                                                                           >  2:332123‑M1/109‑143 (MQ=255)                                                ccAATGATTAGCTGAACGTTCTTTTTACCGCTCTTTTCGTTTTTATTACCAAAAGGCAGT‑AAATATGCATGACCGAGGGCGCGACCTGGCTCAAGTCCGAGCTGTGAACACTGTACGATCGCACTAACAAAACTCATAGGGTc                                                                                              >  2:11368/1‑143 (MQ=255)                                                  aaTGATTAGCTGAACGTTCTTTTTACCGCTCTTTTCGTTTTTATTACCAAAAGGCAGT‑AAATATGCATGACCGAGGGCGCTACCTGGCTCAAGTCCGAGCTGTGAACACTGTACGATCGCACTGACAAAACTCATAGTGTcac                                                                                            >  1:1134990/1‑143 (MQ=255)                                                          gCTGAACGTTCTTTTTACCGCTCTTTTCGTTTTTATTACCAAAAGGCAGT‑AAATATGCATGACCGAGGGCGCTACCTGGCTCAAGTCCGAGCTGTGAACACTGTACGATCGCACTGACAAAACTCATAGTGTCACAGTTTCCt                                                                                    <  1:494411/143‑1 (MQ=255)                                                             gagcGTTCTTTTTACTGATCTTTTGGTTTTTATCACCAGATGG‑AGTGAAATATGCATGACTGAGGGCGCTACATGGCTGAAGTCCGAGCTGTGAACACTGTACGATCGAACTGACAAAACTCAGAGTGTGACAGATTACtcaa                                                                                 >  2:1051726/4‑140 (MQ=255)                                                                  ttCTTTTTACCGCTCTTTTCGTTTTTATTACCAAAAGGCAGT‑AAATATGCATGACCGAGGGCGCTACCTGGCTCAAGTCCGAGCTGTGAACACTGTACGATCGCACTGACAAAACTCATAGTGTCACAGTTTCCTAACGCCgg                                                                            <  1:7814/143‑1 (MQ=255)                                                                    cTTGTTGCCGCTGTTGTGGTGTTTGTTACCAAGAGGCAGT‑GAATACGGATGACCGAGGGCGCTGCCTGGCTCAAGTCCGTGCTGTGAACACTGTACGATCGCACTGACAAGACTCATAGTGTCGCAGTTTCCTAACGCCGGaa                                                                          <  2:94263/143‑1 (MQ=255)                                                                     tttttACCGCTCTTTTCGTTTTTATTACCAAAAGGCAGT‑AAATATGCATGACCGAGGGCGCTACCTGGCTCAAGTCCGAGCTGTGAACACTGTACGATCGCACTGACAAAACTCATAGTGTCACAGTTTCCTAACGCCGGAAc                                                                         >  1:880448/1‑143 (MQ=255)                                                                     tttttACCGCTCTTTTCGTTTTTATTACCAAAAGGCAGT‑AAATATGCATGACCGAGGGCGCTACCTGGAAAAACTCCGAGCTGTGAACGCAGTACGATCACACTGACAAAACTCATAGTGTCACAGTTTCCTAACGCCGGAAc                                                                         >  2:73887/1‑143 (MQ=255)                                                                           atccagacatcgtcgtcggtgttgtccagggacgcgttatccttactgtattgtccaagaccggtgtcaTCCGAGCTGTGAACACTGTACGATCGCACTGACAAAACTCATAGTGTCACAGTTTCCTAACGCCGGAACTTTAc                                                                    >  1:458665‑M1/70‑143 (MQ=255)                                                                            tccagacaacggcgtcggtgttgtccagcgactcgttatccttactgtattgtccaagaccggtgtcaTCCGAGCTGTGAACACTGTACGATCGCACTGACACACCTCATAGTGTCCCTGTTTCCTAACGCCGGatctttcct                                                                   <  1:86973‑M1/75‑4 (MQ=255)                                                                            cGCTCTTTTCGTTTTTATTACCAAAAGGCAGT‑AAATATGCATGACCGAGGGCGCTACCTGGCTCAAGTCCGAGCTGTGAACACTGTACGATCGCACTGACAAACCTCATAGTGTCACAGTTTCCTAACGCCGGAACTCTACGa                                                                  >  2:602604/1‑143 (MQ=255)                                                                             gCTCTTTTCGTTTTTATTACCCAAAGGCAGT‑AAATATGCATGACCGAGGGCGCTACCTGACTCAAGTCCGAGCTGTGAACACTGTACGATCGCACTGACAAAACTCATAGTGTCACAGTTTCCTAACGCCGGAACTTTACGaa                                                                 <  2:890877/143‑1 (MQ=255)                                                                             gCTCGTTTCGTTTTTATTACCAAAAGGCAGT‑AAATATGCATGACCGAGGGCGCTACCTGGCTCAAGTCCGAGCTGTGAACACTGTACGATCGCACTGACAAAACTCATAGTGTCACAGTTTCCTAACGCCGGAACTTTACGaa                                                                 <  2:758565/143‑1 (MQ=255)                                                                                ctTTTCGTTTTTATTACCAAAAGGCAGT‑AAATATGCATGACCGAGGGCGCTCCCTTGCTCAAGTCCGAGCTGTGAACACTGTACGATCGCACGGACAAAACTCCTGATGTCCCAGTGTCCTCACGCCGTCACTTTATGAtttg                                                              >  2:206115/1‑142 (MQ=255)                                                                                 ttttCGTTTTTATTACCAAAAGGCAGT‑AAATATGCATGACTGAGGGCGCTACCTGGCTCAAGTCCGAGCTGTGCACACTGTACGATCGCACTGACCAAACTCATAGTGTCCCAGTTTCCTAACGACGGAACTGTACGCAtttt                                                             >  2:317324/1‑142 (MQ=255)                                                                                        ttttATTACCAAAAGGCAGT‑AAATATGCATGACCGAGGGCGCTACCTGGCTCAAGTCCGAGCTGTGAACACTGTACGATCGCACTGACAAAACTCATAGTGTCACAGTTTCCTAACGCCGGAACTTTACGAATTTCTgtggtg                                                      <  1:489854/143‑1 (MQ=255)                                                                                              taCCAAAATGCAGT‑AAATATGCATGACCGAGGGCGCTATCTGGCTCAAGTCCGAGCTGTGAACACTGTACGATCGCACTGACAAAACTCATAGTGTCACAGTTTCCTAACGCCGGAACTTTACGAATTTCTGTGGTGGCGATa                                                <  1:905425/143‑1 (MQ=255)                                                                                                 cAAAAGGCAGT‑AAATATGCATGACCGAGGGCGCTACCTGGCTCAAGTCCGAGCTGTGAACACTGTACGATCGCACTGACAACCATCATAGTGTCACAGTTTCCTAACGCCGGAACTCTACCAATTTCTGTGGTGCCCATAccg                                             >  2:979078/1‑141 (MQ=255)                                                                                                 cAAAAGGCAGT‑AAATATGCATGACCGAGGGCGCTACCTGGCTCAAGTCCGAGCTGTGAACACTGTACGATCGCACTGACAAAACTCATAGTGTCACAGTTTCCTAACGCCGGCACTTTACGAATTTCTGTGGTGGCGATACgg                                             >  2:26870/1‑143 (MQ=255)                                                                                                 cAAAAGGCAGT‑AAATATGCATGACCGAGGGCGCTACCTGGCTCAAGTCCGAGCTGTGAACACTGTACGATCGCACTGACAAAACTCATAGTGTCACAGTTTCCTAACGCCGGAACTTTACGAATTTCTGTGGTGGCGATACgg                                             <  2:879501/143‑1 (MQ=255)                                                                                                   aaaGGCAGT‑AGTTTTGCTTGACCGATGGCGCTACCTGTCTCAAGTCCGAGCTGTGAACACTGTACGATCGCACTGACAAAACTCATTGTGTCACAGTTTCCTAACGCCGTAACTTTACGAATTTCTGTGGTGGCGATACGTAt                                           <  2:441156/143‑1 (MQ=255)                                                                                                   aaaGGCAGT‑AAATATGCATGACCGAGGGCGCTACCTGGCTCAAGTCCGCGCTGTGAACACTGTACGATCGCACTGACACAACTCATAGTGTCACAGTTTGCTAACGCCGGCACTTTACGAATTTCTGTGGTGGCGACACGCAt                                           >  1:419575/1‑143 (MQ=255)                                                                                                   aaaGGCAGT‑AAATATGCATGACCGAGGGCGCTACCTGGCTCAAGTCCGAGCTGTGAACACTGTACGATCGCACTGACAAAACTCATAGTGTCACAGTTTCCTAACGCCGGAACTTTACGACTTTCTGTGGTGGCGATACGGag                                           >  1:929814/1‑142 (MQ=255)                                                                                                   aaaGGCAGT‑AAATATGCATGACCGAGGGCGCTACCTGGCTCAAGTCCGAGCTGTGAACACTGTACGATCGCACTGACAAAACTCATAGTGTCACAGTTTCCTAACGCCGGAACTTTACGAATTTCTGTGGTGGCGATACGGAt                                           >  1:936360/1‑143 (MQ=255)                                                                                                     aGGCAGT‑AAATATGCATGCCCGCGGGCGCTACCTGGCTCAAGCCCGAGCTGTGAACACTGTACGATCGCACTGACAAAACTCATAGTGTCACAGTTTCCTAACGCCGGAACTTTACGAATTTCTGTGGTGGCGATACGGATCa                                         <  2:869911/143‑1 (MQ=255)                                                                                                         cgT‑ACATGTGCATGACCGCGGGCGCTACCTGGCTCAAGTCCGTGCTGTGAACCCTGTACGATCGCACTGACATCGCTCTGTGTGTCACAGTTTCCTAACGCCGGAACTTTTCGAATTTCTGTGGTGGCGATACGGATCATACg                                     <  2:657825/142‑1 (MQ=255)                                                                                                          gT‑AAATATGCATGACCGAGGGCGCTACCTGGCTCAAGTCCGAGCTGTGAACACTGTACGATCGCACTGACAAAACTCATAGTGTCACAGTTTCCTAACGCCGGAACTTTACGAATTTCTGTGGTGGCGCTACGGATCCTACGt                                    >  1:602292/1‑143 (MQ=255)                                                                                                               atatGCATGACCGAGGGCGATCCCTGGCTCAAGTCCGAGCTGTGAACACTGTACGATCGCACTGACAAAACTCATAGTGTCACAGTTTCCTAACGCCGGAACTTTACGAATTTCTGTGGTGGCGATACGGATCATACGTTCAg                                <  2:273814/143‑1 (MQ=255)                                                                                                                       gACCGAGGGCGCTACCTGGCTCAAGTCCGAGCTGTGAACACTGTACGGTCGCACTGACAAAACTCATAGTGTCACAGTTTCCTAACGCCGGAACTTTACGAATTTCTGTGGTCGCGATACGGATCATCCGTTCGGCCGTCata                        >  1:1082379/1‑143 (MQ=255)                                                                                                                         ccGAGGGCGCTACCTGGCTCAAGTCCGAGCTGTGAACACTGTACGATCGCACTGACAAAAGTCATAGTGTCACAGTTTCCTAACGGCGGAACTTTACGAATTTCTGTGGTGGCGATATGGATCATAAGGTGAGCAGTGATATg                      >  1:387052/1‑143 (MQ=255)                                                                                                                             gggCGCTACCTGGCTCAAGTCCGAGCTGTGAACACTGTACGATCGCACTGACAAAACTCATAGTGTCACAGTTTCCTAACGCCGGAACTTTACGAATTTCTGTGGTGGCGATACGGATCATACGTTCAGCCGTCATATGGCGt                  <  1:1393/143‑1 (MQ=255)                                                                                                                                 ctgaCCTGGCTCAAGAGCGAGCTGGGAACACTGTACGATCGCACCGACAAAGCTCATAGTGTCACAGCTTCCTAACGCCGGAACTTTACGAATTTCTGTGGTGGCGATACGGATCATACGTTCAGCCGTCATATGGCGTGGaa              <  2:538389/140‑1 (MQ=255)                                                                                                                                           tCAAGTCCGAGCTGTGAACACTGTACGATCGCACTGACAAAACTCATAGTGTCACAGTTTCCTAACGCCGGAACTTTACGAATTTCTGTGGTGGCGATACGGATCATACGTTCAGCCGTCATATGGCGTGGAAGAGCtgctgc    >  1:530074/1‑143 (MQ=255)                                                                                                                                             aaGTCCGAGCTGTGAACACTGTACGCTCGCACTGACAAAACTCATAGTGTCACAGTTTCCTAACGCCGGAACTTTACGAATTTCTGTGGTGGCGATACGGATCATACGTTCAGCCGTCATATGGCGTGGAAGAGCTGCTGCCa  <  2:144429/143‑1 (MQ=255)                                                                                                                                                |                                                                                                                                            TGGCGATTTGACCAGAACGGCGAGCCAGATCAATCATGCCGCGATAGCCAATGATTAGCTGAACGTTCTTTTTACCGCTCTTTTCGTTTTTATTACCAAAAGGCAGT‑AAATATGCATGACCGAGGGCGCTACCTGGCTCAAGTCCGAGCTGTGAACACTGTACGATCGCACTGACAAAACTCATAGTGTCACAGTTTCCTAACGCCGGAACTTTACGAATTTCTGTGGTGGCGATACGGATCATACGTTCAGCCGTCATATGGCGTGGAAGAGCTGCTGCCA  >  NC_000913/1414388‑1414669

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ 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.