New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	2065000 =	28 (0.700)	3 (0.080)	3/304	NT	8.3%	intergenic (+1/‑20)	isrC/flu	novel sRNA, CP4‑44; putative prophage remnant/CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter
	?	CP009273	2065385 =	39 (0.990)					coding (366/3120 nt)	flu	CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter

GTGCAATAGCTCAATAATAGAATAAAACGATCAATATCTATTTTATCGATCGTTTATATCGATCGATAAGCTAATAATAACCTTTGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGTGTGGCGGTTGCACTGTCTCTTGCCGCAGTCACGTCACTCCCGGTGCTGGCTGCTGACATCGTTGTGCACCCGGGAGAAACCGTGAACGGCGGAACACTGGCAAATCAT  >  CP009273/2064770‑2065232                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                         gTGCAATAGCTCAATAATAGAATAAAACGATCAATATCTATTTTATCGATCGTTTATATCGATCGATAAGCTAATAATAACCTTTGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCACAATCTAAGGAAAAGCTGATTAAACGCCATCTTaaaaacttct                                                                                                                                                                                              >  2:588568/1‑267 (MQ=255)   gCAATAGCTCAATAATAGAATAAAACGATCAATATCTATTTTATCGATCGTTTATATCGATCGATAAGCTAATAATAACCTTTGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACATGCCGGTATCCACGTTTGTGGGTACCGGCTTTTGTATTAACCCTCAATCTAAGGAAAAGCTGCTGACACGACATCTGACGACTTGCt                                                                                                                                                                                              >  2:87562/1‑273 (MQ=255)                       tAAAACGATCAATATCTATTTTATCGATCGTTTATATAGATCGATAGGCTAATAATAACCTTTGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTCCCGGTATCCACGTTTGTGGGTACCAGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGAAGAAACGAAATCAGAATACCTTCTACAGTCGCGTAAGTAATcacaa                                                                                                                                                                        >  2:519070/1‑274 (MQ=255)                                        aTTTTATCGATCGTTTATATCGATCGATAAGCTAATAATAACCTTTGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGa                                                                                                                                                                                                                              >  1:486799/1‑204 (MQ=255)                                            tATCGATCGTTTATATCGATCGATAAGCTAATAATAACCTTTGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAg                                                                                                                                                                                                                          <  2:486790/204‑1 (MQ=255)                                                gatcgTTTATATCGATCGATAAGCTAATAATAACCTTTGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTTCCGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCCATCTAAGGAAAAGCTGATGACACGACATCTGAATACCTGCTCCATGCTGGTATGGTATCACATGACGGGCGCTTTCGTTGTTGCCTc                                                                                                                                                >  1:317186/1‑274 (MQ=255)                                                              atcgatAAGCTAATAATAACCTTTGTCAGTAACATGCACAGATACGTCCAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTACGGAAAAGCTGATGAAACGACATCTGAATCCCTGCTACAGGCTGGAATGTAATCACAAAACGGTCGATATCTTGGTGACATCCGAAATGAccagagc                                                                                                                                 >  1:315886/1‑270 (MQ=255)                                                               tcgatAGGCTTATAATAACCCTTGTCAGTAACATGCACAGTTACGTACAGAAAGACATTCAGGGAACAACAGAACCACAAGTCAGAAACTCNCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCTGAACTGGCCCGCGCa                                                                                                                                <  1:519079/275‑1 (MQ=255)                                                               tcgatAAGCTAATAATAACCTTTGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAATGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATTACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCa                                                                                                                                >  1:86495/1‑275 (MQ=255)                                                                  atAAGCTAATAATAACCTTTGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTACGAACTGGCCCGCGCACgg                                                                                                                             <  1:588581/275‑1 (MQ=255)                                                                      cctgccagcccttatcattaatgacggttcctgtggctatcgccccctcatgcatccactgttcgccaccattcagcgtggtgttcacagcccgtccctgaaggctctgtccgcctccggcactgataaccgtgtctgagacacttccaccggggttcactCCCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGGCCGCGCAAGGGGTa                                                                                                                         <  1:382474‑M1/114‑1 (MQ=255)                                                                           taataaCCTTTGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTAAGGAATCACATGACGGGCGCTTTCGGGGGGGACTCCGAACTGGCCCGCGCACGGGGTaaaagg                                                                                                                    >  2:329777/1‑272 (MQ=255)                                                                                   attGTCAGTAACATGCACAGATACGTACAGAAAGACATTCACGGACCCACAGAACCACAATTCAGACACTCCCACATCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACgtggcggtgt                                                                                                            <  2:296078/274‑1 (MQ=255)                                                                                     tGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCGAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGGGCACGGGGAAAAActgggggggtgg                                                                                                          >  1:296083/1‑275 (MQ=255)                                                                                                                gAAAGACAGTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCTGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGTGTGGCGGTTGCACTGTCTCTTGCCGCAgtc                                                                                <  1:87563/274‑1 (MQ=255)                                                                                                                 aaaGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCt                                                                                                                                                                                                 >  2:651629/1‑160 (MQ=255)                                                                                                                     aCATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTa                                                                                                                                                                                             <  1:651643/160‑1 (MQ=255)                                                                                                                                   acaGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATNAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGTGTGGCGGTTGCACTGTCTCTTGCCGCAGTCACGTCACTCCCGGTgctggc                                                            <  1:622655/275‑1 (MQ=255)                                                                                                                                                  cgtggtgttcacagcccgtccctgaaggctctgtccgcctccggcactgataaccgtgtctgagacacttccaccggggttcactCTCAATCTAAGGAAAAGCTGATGAAACGACAt                                                                                                                                                                                                           <  2:65318‑M1/32‑1 (MQ=255)                                                                                                                                                      gtgttcacagcccgtccctgaaggctctgtccgcctccggcactgataaccgtgtctgagacacttccaccggggttcactCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGa                                                                                                                                                                                                       >  1:65319‑M1/82‑117 (MQ=255)                                                                                                                                                        tCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGTGTGGCGGTTGCACTGTCTCTTGCCGCAGTCACGTCACTCCCGGTGCTGGCTGCTGACATCGTTGTGCAccc                                       <  1:364306/275‑1 (MQ=255)                                                                                                                                                                        ccGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGc                                                                                                                                                                                               >  1:362608/1‑107 (MQ=255)                                                                                                                                                                            cACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACa                                                                                                                                                                                           <  2:362601/107‑1 (MQ=255)                                                                                                                                                                                gTAACCCTTTACCTGACGGTATCAACGTGTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGTGTGNCGGTTGCACTGTCTCTTGCCGCAGTCACGTCACTCCCGGTGCTGGCTGCTGACATCGTTGTGCACCCGGGAGAAACCGTGAACGGCGGAac               >  1:502619/1‑275 (MQ=255)                                                                                                                                                                                             tgtcGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGTGTGGCGGTTGCACTGTCTCTTGCCGCAGTCACGTCACTCCCGGTGCTGGCTGCTGACATCGTTGTGCACCCGGGAGAAACCGTGAACGGCGGAACACTGGCAAATCAt  <  1:329783/272‑1 (MQ=255)                                                                                                                                                                                               ccGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCt                                                                                                                                                                                       >  2:276376/1‑92 (MQ=255)                                                                                                                                                                                                   tATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTa                                                                                                                                                                                   <  1:276380/92‑1 (MQ=255)                                                                                                                                                                                                         cGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGa                                                                                                                                                                               >  1:438991/1‑90 (MQ=255)                                                                                                                                                                                                             tgtgGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATca                                                                                                                                                                           <  2:438984/90‑1 (MQ=255)                                                                                                                                                                                                               tgGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTAc                                                                                                                                                                                            >  2:444776/1‑71 (MQ=255)                                                                                                                                                                                                                   tACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGc                                                                                                                                                                                        <  1:444783/71‑1 (MQ=255)                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                         GTGCAATAGCTCAATAATAGAATAAAACGATCAATATCTATTTTATCGATCGTTTATATCGATCGATAAGCTAATAATAACCTTTGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGTGTGGCGGTTGCACTGTCTCTTGCCGCAGTCACGTCACTCCCGGTGCTGGCTGCTGACATCGTTGTGCACCCGGGAGAAACCGTGAACGGCGGAACACTGGCAAATCAT  >  CP009273/2064770‑2065232

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 34 ≤ 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.