New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_KO_pgi	= 2756000	52 (0.900)	17 (0.300)	14/252	4.1	23.9%	intergenic (+622/‑159)	smpB/intA	tmRNA‑binding trans‑translation protein/CP4‑57 prophage; integrase
	?	NC_000913_3_KO_pgi	= 2756030	57 (1.000)					intergenic (+652/‑129)	smpB/intA	tmRNA‑binding trans‑translation protein/CP4‑57 prophage; integrase
Rejected: Coverage evenness skew score above cutoff.

AGACTGACTAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCC  >  NC_000913_3_KO_pgi/2755884‑2756178                                                                                                                                                   |                                                                                                                                                     aGACTGACTAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCttttt                                                                                                                                                   <  1:546088/150‑1 (MQ=255)  gactgactAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCtttttt                                                                                                                                                  >  4:51418/1‑150 (MQ=255)       actAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACTAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGcc                                                                                                                                             <  4:406705/150‑1 (MQ=255)         tAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCt                                                                                                                                           >  1:575484/1‑150 (MQ=255)         tAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCt                                                                                                                                           >  4:225127/1‑150 (MQ=255)              aTGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAAtt                                                                                                                                      <  4:409400/150‑1 (MQ=255)               tGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAAttt                                                                                                                                     <  2:449297/150‑1 (MQ=255)                    taCCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTccc                                                                                                                                >  2:609409/1‑150 (MQ=255)                         aGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGcc                                                                                                                                             >  1:54134/1‑132 (MQ=255)                         aGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGcc                                                                                                                                             <  2:54134/132‑1 (MQ=255)                         aGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGaa                                                                                                                           <  2:575484/150‑1 (MQ=255)                                      ttCGGACGCGGGTTCAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAAc                                                                                                              <  1:609409/150‑1 (MQ=255)                                        cGGACGCGGGTTCAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTa                                                                                                            >  1:226301/1‑150 (MQ=255)                                           aCGCGGGTTCAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAAtt                                                                                                         >  1:434868/1‑150 (MQ=255)                                             gcgGGTTCAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTaa                                                                                                       >  3:151595/1‑150 (MQ=255)                                             gcgGGTTCAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGGGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTaa                                                                                                       >  3:238887/1‑150 (MQ=255)                                                  ttCAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCg                                                                                                  <  2:123459/150‑1 (MQ=255)                                                    cAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGaa                                                                                                <  1:631581/150‑1 (MQ=255)                                                        tCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCtt                                                                                            >  4:32495/1‑150 (MQ=255)                                                        tCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCtt                                                                                            >  4:32583/1‑150 (MQ=255)                                                          ccGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCg                                                                                                                      <  1:1726/122‑1 (MQ=255)                                                          ccGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCg                                                                                                                      >  2:1726/1‑122 (MQ=255)                                                             ccAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAAATAAATCCGAACCTTTTAgg                                                                                       >  2:684144/1‑150 (MQ=255)                                                               aGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGcc                                                                                     >  1:693151/1‑150 (MQ=255)                                                                gCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGccc                                                                                    <  3:51418/150‑1 (MQ=255)                                                                   ccaccaAAAGTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCAtt                                                                                 <  2:15106/150‑1 (MQ=255)                                                                    caccaAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTg                                                                                <  3:32583/150‑1 (MQ=255)                                                                    caccaAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTg                                                                                <  3:32495/150‑1 (MQ=255)                                                                        aaaaTTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAg                                                                            <  2:88387/150‑1 (MQ=255)                                                                              ctcCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCaa                                                                      <  1:244215/150‑1 (MQ=255)                                                                               tcCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAAc                                                                     <  4:151595/150‑1 (MQ=255)                                                                                  aTCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGaa                                                                  >  1:275318/1‑150 (MQ=255)                                                                                              cAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCcg                                                                                                                               >  2:131401/1‑77 (MQ=255)                                                                                              cAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCcg                                                                                                                               <  1:131401/77‑1 (MQ=255)                                                                                              cAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCcg                                                                                                                               <  1:479524/77‑1 (MQ=255)                                                                                              cAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCcg                                                                                                                               >  2:479524/1‑77 (MQ=255)                                                                                              cAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAAtt                                                                                                         >  3:222425/1‑99 (MQ=255)                                                                                              cAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAAtt                                                                                                         <  4:222425/99‑1 (MQ=255)                                                                                               agagTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGtt                                                     >  1:560682/1‑150 (MQ=255)                                                                                                     aTCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGtt                                               >  2:687784/1‑150 (MQ=255)                                                                                                           tGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCt                                         <  4:238887/150‑1 (MQ=255)                                                                                                                tCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTa                                                   <  2:348217/135‑1 (MQ=255)                                                                                                                tCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTa                                                   >  1:348217/1‑135 (MQ=255)                                                                                                                  cTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGctct                                                           >  4:331494/1‑125 (MQ=255)                                                                                                                  cTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGctct                                                           <  3:331494/125‑1 (MQ=255)                                                                                                                   tAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAg                                 <  3:225127/150‑1 (MQ=255)                                                                                                                    aaGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAgg                                <  2:434868/150‑1 (MQ=255)                                                                                                                         cccGCACGGCGCAAGCCCTGCGGGCTTTTTTTTTTCTTCTATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGAc                           >  2:48495/1‑150 (MQ=255)                                                                                                                         cccGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGAc                           >  4:385326/1‑150 (MQ=255)                                                                                                                            gCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCa                                                                       <  2:464624/103‑1 (MQ=255)                                                                                                                            gCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCa                                                                       >  1:464624/1‑103 (MQ=255)                                                                                                                                ggCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTaaa                                      <  2:62528/132‑1 (MQ=255)                                                                                                                                ggCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTaaa                                      >  1:62528/1‑132 (MQ=255)                                                                                                                                    cAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCa                >  1:312650/1‑150 (MQ=255)                                                                                                                                          cTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTg                                              >  1:174984/1‑114 (MQ=255)                                                                                                                                          cTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTg                                              <  2:174984/114‑1 (MQ=255)                                                                                                                                                  ttttttGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGcc  <  1:538538/150‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                                     AGACTGACTAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGCCAGCTCCACCAAAATTCTCCATCGGTGATTACCAGAGTCATCCGATGAAGTCCTAAGAGCCCGCACGGCGCAAGCCCTGCGGGCTTTTTTGTGCCCTCAATTTGTCCCGCGAAGTCCGAAGAGAACTAATTAAATCCGAACCTTTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCC  >  NC_000913_3_KO_pgi/2755884‑2756178

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ 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.