New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	= 2071714	34 (0.850)	6 (0.160)	5/292	NT	15.0%	intergenic (+126/+316)	yeeW/yoeD	CP4‑44 prophage; uncharacterized protein;Phage or Prophage Related/pseudogene, CP4‑44 putative prophage remnant;Phage or Prophage Related
	?	CP009273	= 2072110	36 (0.950)					pseudogene (49/129 nt)	yoeD	pseudogene, CP4‑44 putative prophage remnant;Phage or Prophage Related

GCACATTGTCGTTGACATTGATGGTGTTAATATCACTGAACTGATTAATAAGGCCGCTGAAAACGGTTATTCACTCCGCGTGGTGGATGACCGTGACTCTACCGAAACACCGGCAACTTATGCCAGCCCTCACCAGTTGCTGTAAGACAATGCAGTGATACAGGGTATAGTGCCATTAACCACAGAAACAGCACTGTTGTCCTGTATTAAGCAGGCAAGAGAAGATGTCCTTACCCTGCGCCATCTGCAGCTTCTGCACCAGAACCGGTGAATCTCACTCAACAGGCTTCATTTCTCCTGACGCCAGCCTGAATACAGCTGGCGTTTTCATTTATAAACAGAAAGGAAAACCGATAATAATGGAATGGACGCCCCGACCATGAAGCAACGGTAGGATATTACTGATAAACCTTCCAGTGGAGGTGCGTTATGGCCGTTTTAACGATTAGCATTGACCTGACAAAAAATGAATTCCAAATCCACGGTCTG  >  CP009273/2071471‑2071959                                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                                      gCACATTGTCGTTGACATTGATGGTGTTAATATCACTGAACTGATTAATAAGGCCGCTGAAAACGGTTATTCACTCCGCGTGGTGGATGACCGTGACTCTACCGAAACACCGGCAACTTATGCCAGCCCTCACCAGTTTCTGTAAGACAATGCAGTGATACAGGGTATAGTGCCATTAACCACAGAAACAGCACTGTTGTCCTGTATTAAGCAGGCAAGAGAAGATGTCCTTACCCTGCGCCATattctgagcatactaccggaatagccctcc                                                                                                                                                                                                                         >  1:267933‑M1/1‑244 (MQ=255)   acaTTGTCGTTGACATTGATGGTGTTAATATCACTGAACTGATTAATAAGGCCGCTGAAAACGGTTATTCACTCCGCGTGGTGGATGACCGTGACTCTACCGAAACACCGGCAACTTATGCCAGCCCTCACCAGTTGCTGTAAGACAATGCAGTGATACAGGGTATAGTGCCATTAACCACAGAAACAGCACTGTTGTCCTGTATTAAGCAGGCAAGAGAAGATGTCCTTACCCTGCGCCATCTGCAGCTTCTGCACCAGAACCGGTGAATctca                                                                                                                                                                                                                      <  1:397949/275‑1 (MQ=255)              gACATTGATGGTGTTAATATCACTGAACTGATTAATAAGGCCGCTGAAAACGGTTATTCACTCCGCGTGGTGGATGACCGTGACTCTACCGAAACACCGGCAACTTATGCCAGCCCTCACCAGTTGCTGTAAGACAATGCAGTGATACAGGGTATAGTGCCATTAACCACAGAAACAGCACTGTTGTCCTGTCTTAAGCAGGCAAGAGAAGATGTCCTTACCCTGCGCCATCTTCCGCTTCTGCACCAGAACCGTTGAATCTCACTCAACCGGc                                                                                                                                                                                                            >  1:444175/1‑274 (MQ=255)                                       atgtgattaNAAAGGCCGCTGAAAACTGTTATTCACTCAGCGTGGTGGATGACCGTGACGCTACCGAAACACCGGCAACATACGACAGCCCTCAACAGTTGCTGTAAGACAATGCAGTGATACAGGGTATAGTGCCATTAACCACAGAAACAGCACTGTTGTCCTGTATTAAGCAGGCAAGAGAAGATGTCCTTACCCTGCGCCATattctgagcatactgccggaatggccctccaaccgtgttgacgaactcctgccatggaacgtagttctc                                                                                                                                                                                  <  2:267929‑M1/272‑70 (MQ=255)                                       aactgaTTAATAAGGCCGCTGAAAACGGTTATTCACTCCGCGTGGTGGATGACCGTGACTCTACCGAAACACCGGCAACTTATGCCAGCCCTCACCAGTTGCTGTAAGACAATGCAGTGATACAGGGTATAGTGCCATTAACCACAGAAACAGCACTGTTGTCCTGTATTAAGCAGGCAAGAGAAGATGTCCTTACCCTGCGCCATCTGCAGCTTCt                                                                                                                                                                                                                                            >  2:93824/1‑217 (MQ=255)                                           gaTTAATAAGGCCGCTGAAAACGGTTATTCACTCCGCGTGGTGGATGACCGTGACTCTACCGAAACACCGGCAACTTATGCCAGCCCTCACCAGTTGCTGTAAGACAATGCAGTGATACAGGGTATAGTGCCATTAACCACAGAAACAGCACTGTTGTCCTGTATTAAGCAGGCAAGAGAAGATGTCCTTACCCTGCGCCATCTGCAGCTTCTGCAc                                                                                                                                                                                                                                        <  1:93825/217‑1 (MQ=255)                                                      ccGCTGAAAACGGTTATTCACTCCGCGTGGTGGATGACCGTGACTCTACCGAAACACCGGCAACTTATGCCAGCCCTCACCAGTTGCTGTAAGACAATGCAGTGATACAGGGTATAGTGCCATTAACCACAGAAACAGCACTGTTGTCCTGTATTAAGCAGGCAAGAGAAGATGTCCTTACCCTGCGCCATCTGCTGCTTCTGCACCAGAACCGGTGAATCTCACTCAACAGGCTTCATTTCTCCTGACGCAAGCCTGCATACAGcctgtctcta                                                                                                                                                                   >  1:739602/1‑266 (MQ=255)                                                                            ccGCGTTGTTGATGACCGTGACTCTTCCGAAATACCGGCACCTTATGCCAGCCCTCACCAGTTTCTGTAAGACAATTCAGTGATACAGGGTATAGTGCCATTAACCACAGAAACAGCACTGTCTTCCTCTATTAAGCAGGCAAGAGAAGATGTCCTTACCCTGCGCCATCTGCAGCTTCTGCACCAGAACCGGTGAATCTCACTCAACAGGCTTCATTTCTCCTGACGCCAGCCTGAATACAGCTGGCGTTTTCATTTATAAACAGAAAGGaaaa                                                                                                                                             <  1:637576/275‑1 (MQ=255)                                                                                                   ctACCGAAACACCGGCAACTTATGCCAGCCCTCACCAGTTGCTGTAAGACAATGCAGTGATACAGGGTATAGTGCCATTAACCACAGAAACAGCACTGTTGTCCTGTATTAAGCAGGCAAGAGAAGATGTCCTTACCCTGCGCCATCTGCAGCTTCTGCACCAGAACCGGTGAATCTCACTCAACAGGCTTCATTTCTCCTGACGCCAGCCTGAATACAGCTGGCGTTTTCATTTATAAACa                                                                                                                                                       >  1:70620/1‑242 (MQ=255)                                                                                                   ctACCGAAACACCGGCAACTTATGCCAGCCCTCACCAGTTGCTGTAAGACAATGCAGTGATACAGGGTATAGTGCCATTAACCACAGAAACAGCACTGTTGTCCTGTATTAAGCAGGCAAGAGAAGATGTCCTTACCCTGCGCCATCTGCAGCTTCTGCACCAGAACCGGTGAATCTCACTCAACAGGCTTCATTTCTCCTGACGCCAGCCTGAATACAGCTGGCGTTTTCATTTATAAACa                                                                                                                                                       <  2:70619/242‑1 (MQ=255)                                                                                                                     cTTATGCCAGCCCTCACCAGTTGCTGTAAGACAATGCAGTGATACAGGGTATAGTGCCATTAACCACAGAAACAGCACTGTTGTCCTGTATTAAGCAGGCAAGAGAAGATGTCCTTACCCTGCGCCATCTGCAGCTTCTGCACCAGAACCGGTGAATCTCACTCAACAGGCTTCATTTCTCCTGACGCCAGCCTGAATACAGCTGGCGTTTTCATTTATAAACAGAAAGGAAAACCGATAATAATGGCATGGACGCCCCGACCATGAAGCAACgg                                                                                                    <  1:431472/275‑1 (MQ=255)                                                                                                                         tGCCAGCCCTCACCAGTTGCTGTAAGACAATGCAGTGATACAGGGTATAGTGCCATTAACCACAGAAACAGCACTGTTGTCCTGTATTAAGCAGGCAAGAGAAGATGTCCTTACCCTGCGCCATCTGCAGCTTCTGCACCAGAACCGGTGAATCTCACTCAACAGGCTTCGTTTCTCCTGACGNCAGCCTGANTACAGCTGGCGTTTTCATTTATAAACAGAAAGGAAAACCGATAATaatgg                                                                                                                                >  1:480788/1‑243 (MQ=255)                                                                                                                                                       tGCAGTGATACAGGGTATAGTGCCATTAACCACAGAAACAGCACTGTTGTCCTGTATTAAGCAGGCAAGAGAAGATGTCCTTACCCTGCGCCATCTGCAGCTTCTGCACCAGAACCGGTGAATCTCACTCAACAGGCTTCATTTCTACTGACGCCAGCCTGAATACAGCTGGCGTTTTCATTTATAAACAGAAAGGAAAACCGATAATAATGGAATGGACGCCCCGACCATGAAGCAACGGTAGGATATTACTGATAAACCTTCCAGTGGAGGTg                                                                  >  1:640701/1‑275 (MQ=255)                                                                                                                                                                      tataGTGCCATTAACCACAGAAACAGCACTGTTGTCCTGTATTAAGCAGGCAAGAGAAGATGTCCTTACCCTGCGCCATattctgagcatactgccggaatggccctccaaccgtgttgacgaactcctgccatggaacgtag                                                                                                                                                                                       >  2:604153‑M1/1‑79 (MQ=255)                                                                                                                                                                          gTGCCATTAACCACAGAAACAGCACTGTTGTCCTGTATTAAGCAGGCAAGAGAAGATGTCCTTACCCTGCGCCATattctgagcatactgccggaatggccctccaaccgtgttgacgaactcatgccatggaacgtagttct                                                                                                                                                                                   <  1:604166‑M1/143‑69 (MQ=255)                                                                                                                                                                           tGCCATTAACCACAGAAACAGCACTTTTGCTCGGTAATAAGCAGGCAAGTGAAGATTTCCTTACCCTGCGCCATCTGAAGCTTCTGCACCAGTACCGGTGAATCTCGCTCAACATGCTTCATTTCTCCTGACGACACCCTGAATACAGCTGGCGTTTTCATTTCTAACCAGAACGAAAAACCGATAATAATGGAATGGACGCCCCGACAATGACGCAAAGGTAGGATATTACTGATAAACGTACAAGTTAAGGTGCGTTANGTCGGTATTacctc                                              >  2:545664/1‑271 (MQ=255)                                                                                                                                                                            gCCATTAACCACAGAAACAGCACTGTTGTCCTGTATTAAGCAGGCAAGGGAAGATGTCCTTACCGTGCGCCATCTGCAGCTTCTGCACCAGAACCGGTGAATCTCACTCAACAGGCTTCATTTCTCCTGACGCCAGCCTGAATACAGCTGGCGTTTTCATTTATAAACAGAAAGGAAAACCGATAAGAATGGAATGGACGCCCCGACCATGAAg                                                                                                          <  1:593809/214‑1 (MQ=255)                                                                                                                                                                              cATTAACCACAGAAACAGCACTGTTGTCCTGTATTAAGCAGGCAAGAGAAGATGTCCTTACCCTGCGCCATattctgagcatactgccggaatggccctccaaccgtgttgacgaactcctgccatggaacgtag                                                                                                                                                                                       >  1:125795‑M1/1‑71 (MQ=255)                                                                                                                                                                                  aaCCACAGAAACAGCACTGTTGTCCTGTATTAAGCAGGCAAGAGAAGATGTCCTTACCCTGCGCCATattctgagcatactgccggaatggccctccaaccgtgttgacgaactcctgccatggaacgtagttct                                                                                                                                                                                   <  2:125794‑M1/135‑69 (MQ=255)                                                                                                                                                                                       caGAAACAGCACTGTTGTCCTGTATTAAGCAGGCAAGAGAAGATGTCCTTACCCTGCGCCATCTGCAGCTTCTGCACCAGAACCGGTGAATCTCACTCAACAGGCTTCATTTCTCCTGACGCCAGCCTGAATACAGCTGGCGTTTTCATTTATAAACAGAAAGGAAAACCGataa                                                                                                                                      >  1:307849/1‑175 (MQ=255)                                                                                                                                                                                           aaCAGCACTGTTGTCCTGTATTAAGCAGGCAAGAGAAGATGTCCTTACCCTGCGCCATCTGCAGCTTCTGCACCAGAACCGGTGAATCTCACTCAACAGGCTTCATTTCTCCTGACGCCAGCCTGAATACAGCTGGCGTTTTCATTTATAAACAGAAAGGAAAACCGATaataat                                                                                                                                  <  2:307844/175‑1 (MQ=255)                                                                                                                                                                                               gCACTGTTGTCCTGTATTAAGCAGGCAAGAGAAGATGTCCTTACCCTGCGCCATCTGCAGCTTCTGCACCAGAACCGGTGAATCTCACTCAACAGGCTTCATTTCTCCTGACGCCAGCCTGAATACAGCTGGCGTTTTCATTTATAAACAGAAAGGAAAACCGATAATAATGGAATGGACGCCCCGACCAt                                                                                                              >  2:47560/1‑191 (MQ=255)                                                                                                                                                                                                   tgttgtCCTGTATTAAGCAGGCAAGAGAAGATGTCCTTACCCTGCGCCATCTGCAGCTTCTGCACCAGAACCGGTGAATCTCACTCAACAGGCTTCATTTCTCCTGACGCCAGCCTGAATACAGCTGGCGTTTTCATTTATAAACAGAAAGGAAAACCGATAATAATGGAATGGACGCCCCGACCATGAAg                                                                                                          <  1:47561/191‑1 (MQ=255)                                                                                                                                                                                                          cTGTATTAAGCAGGCAAGAGAAGATGTCCTTACCCTGCGCCATCTGCAGCTTCTGCACCAGAACCGGTGAATCTCACTCAACAGGCTTCATTTCTCCTGACGCCAGCCTGAATACAGCTGGCGTTTTCATTTATAAACAGAAAGGAAAACCGATAATAATGGAATGGACGCCCCGACCATGaa                                                                                                           >  2:546796/1‑183 (MQ=255)                                                                                                                                                                                                          cTGTATTAAGCAGGCAAGAGAAGATGTCCTTACCCTGCGCCATCTGCAGCTTCTGCACCAGAACCGGTGAATCTCACTCAACAGGCTTCATTTCTCCTGACGCCAGCCTGAATACAGCTGGCGTTTTCATTTATAAACAGAAAGGAAAACCGATAATAATGGAATGGACGCCCCGACCATGAAGCAACGGTAGGATATTACTGATAAACCTTCAAGAGGGGGTGCGGAAGGGCGGGTTTAACGATTAGAATTTCACTGACAAAAAATGAATTCCa               >  2:293824/1‑275 (MQ=255)                                                                                                                                                                                                             tATTAAGCAGGCAAGAGAAGATGTCCTTACCCTGCGCCATCTGCAGCTTCTGCACCAGAACCGGTGAATCTCACTCAACAGGCTTCATTTCTCCTGACGCCAGCCTGAATACAGCTGGCGTTTTCATTTATAAACAGAAAGGAAAACCGATAATAATGGAATGGACGCCCCGACCATGAAGCAACGGTAGGATATTACTGATAAACCTTCCAGTGGAGGTGCGTTATGGCCGTTTTAACGATTAGCATTGACCTGACAAAAAATGAATTCCAAAt            >  1:437227/1‑275 (MQ=255)                                                                                                                                                                                                              aTTAAGCAGGCAAGAGAAGATGTCCTTACCCTGCGCCATCTGCAGCTTCTGCACCAGAACCGGTGAATCTCACTCAACAGGCTTCATTTCTCCTGACGCCAGCCTGAATACAGCTGGCGTTTTCATTTATAAACAGAAAGGAAAACCGATAATAATGGAATGGACGCCCCGACCATGAAGCaa                                                                                                       <  1:546807/183‑1 (MQ=255)                                                                                                                                                                                                                       gCAAGAGAAGATGTCCTTACCCTGCGCCATCTGCAGCTTCTGCAcc                                                                                                                                                                                                                                       >  2:174923/1‑46 (MQ=255)                                                                                                                                                                                                                       gCAAGAGAAGATGTCCTTACCCTGCGCCATCTGCAGCTTCTGCACCAGAAc                                                                                                                                                                                                                                  >  1:471963/1‑51 (MQ=255)                                                                                                                                                                                                                       gCAAGAGAAGATGTCCTTACCCTGCGCCATCTGCAGCTTCTGCACCAGAACCGGTGAATCTCACTCAACAGGCTTCATTTCTCCTGACGc                                                                                                                                                                                           >  2:589965/1‑90 (MQ=255)                                                                                                                                                                                                                       gCAAGAGAAGATGTCCTTACCCTGCGCCATCTGCAGCTTCTGCACCAGAACCGGTGAATCTCACTCAACAGGCTTCATTTCTCCTGACGc                                                                                                                                                                                           >  2:705681/1‑90 (MQ=255)                                                                                                                                                                                                                       gCAAGAGAAGATGTCCTTACCCTGCGCCATCTGCAGCTTCTGCACCAGAACCGGTGAATCTCACTCAACAGGCTTCATTTCTCCTGACGCCAGCCTGAATACAGCTGGCGTTTTCAtt                                                                                                                                                               >  1:302857/1‑118 (MQ=255)                                                                                                                                                                                                                       gCAAGAGAAGATGTCCTTACCCTGCGCCATCTGCAGCTTCTGCACCAGAACCGGTGAATCTCACTCAACAGGCTTCATTTCTCCTGACGCCAGCCTGAATACAGCTGGCGTTTTCATTTATAAACAGAAAGGAAAACCGATAATAATGGAATGGACGCCCCGACCATGAAGCAACGGTAGGATATTACTGATAAACCTTCCAGTGGAGGTGCGTTATGGCCGATTTAACGCTTATCATTGACGTGACAACCAAGGAAGTCTACATCCagcggcgt  >  2:405807/1‑268 (MQ=255)                                                                                                                                                                                                                           gagaAGATGTCCTTACCCTGCGCCATCTGCAGCTTCTGCACCAGaa                                                                                                                                                                                                                                   <  1:174925/46‑1 (MQ=255)                                                                                                                                                                                                                           gagaAGATGTCCTTACCCTGCGCCATCTGCAGCTTCTGCACCAGAACCGGt                                                                                                                                                                                                                              <  2:471955/51‑1 (MQ=255)                                                                                                                                                                                                                           gagaAGATGTCCTTACCCTGCGCCATCTGCAGCTTCTGCACCAGAACCGGTGAATCTCACTCAACAGGCTTCATTTCTCCTGACGCCAGc                                                                                                                                                                                       <  1:705695/90‑1 (MQ=255)                                                                                                                                                                                                                           gagaAGATGTCCTTACCCTGCGCCATCTGCAGCTTCTGCACCAGAACCGGTGAATCTCACTCAACAGGCTTCATTTCTCCTGACGCCAGc                                                                                                                                                                                       <  1:589978/90‑1 (MQ=255)                                                                                                                                                                                                                           gagaAGATGTCCTTACCCTGCGCCATCTGCAGCTTCTGCACCAGAACCGGTGAATCTCACTCAACAGGCTTCATTTCTCCTGACGCCAGCCTGAATACAGCTGGCGTTTTCATTtata                                                                                                                                                           <  2:302852/118‑1 (MQ=255)                                                                                                                                                                                                                                 aTGTCCTTACCCTGCGCCATCTGCAGCTTCTGCACCAGAACCGGTGAATCTCACTCAACAGGCTTCATTTCTCCTGACGCCAGCCTGAATACAGCTGGCGTTTTCATTTATAAACAGAAAGGAAAACCGATAATAATGGAATGGACGCCCCGACCATGAAGCa                                                                                                        >  1:86532/1‑163 (MQ=255)                                                                                                                                                                                                                                     ccTTACCCTGCGCCATCTGCAGCTTCTGCACCAGAACCGGTGAATCTCACTCAACAGGCTTCATTTCTCCTGACGCCAGCCTGAATACAGCTGGCGTTTTCATTTATAAACAGAAAGGAAAACCGATAATAATGGAATGGACGCCCCGACCATGAAGCAACgg                                                                                                    <  2:86531/163‑1 (MQ=255)                                                                                                                                                                                                                                                    tattctgagcatactgccggaatggccctccaaccgtgttgacgaactcctgccatggaacgtagttctcaccaataaataagcgtcaatacggtgctccgttgacgcttactttaatccgttttctgagcttagatttttctgttcctacccagaccgtggatttggaattcattttttgtcaggtcaa                                                          >  1:371556‑M1/1‑1 (MQ=255)                                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                                      GCACATTGTCGTTGACATTGATGGTGTTAATATCACTGAACTGATTAATAAGGCCGCTGAAAACGGTTATTCACTCCGCGTGGTGGATGACCGTGACTCTACCGAAACACCGGCAACTTATGCCAGCCCTCACCAGTTGCTGTAAGACAATGCAGTGATACAGGGTATAGTGCCATTAACCACAGAAACAGCACTGTTGTCCTGTATTAAGCAGGCAAGAGAAGATGTCCTTACCCTGCGCCATCTGCAGCTTCTGCACCAGAACCGGTGAATCTCACTCAACAGGCTTCATTTCTCCTGACGCCAGCCTGAATACAGCTGGCGTTTTCATTTATAAACAGAAAGGAAAACCGATAATAATGGAATGGACGCCCCGACCATGAAGCAACGGTAGGATATTACTGATAAACCTTCCAGTGGAGGTGCGTTATGGCCGTTTTAACGATTAGCATTGACCTGACAAAAAATGAATTCCAAATCCACGGTCTG  >  CP009273/2071471‑2071959

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ 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.