New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 1469240	NA (NA)	42 (0.930)	31/276	NT	100%	intergenic (‑91/‑1)	insC1/ydbA	IS2 repressor TnpA/pseudogene, autotransporter homolog; interrupted by IS2 and IS30
	?	NC_000913	= 1652258	0 (0.000)					pseudogene (708/1158 nt)	intQ	pseudogene, Qin prophage; phage integrase family;Phage or Prophage Related

CCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGATTCAATTGGTCAACGCAACAGTTATGTGAAAACATGGGGTTGCGGAGGTTTTTTGAATGAGACGAACATTTACAGCAGAGGAAAAA  >  NC_000913/1469101‑1469387                                                                                                                                            |                                                                                                                                                    ccTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGa                                                                                                                                            >  2:19006/1‑149 (MQ=34)     tgtgGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCCTCTGTTCTCCAATGACTATTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAactt                                                                                                                                        >  1:50259/1‑149 (MQ=255)     tgtgGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAactt                                                                                                                                        <  1:338606/149‑1 (MQ=38)       tgGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAacttac                                                                                                                                      <  2:561674/149‑1 (MQ=39)       gggTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAacttac                                                                                                                                      <  1:720893/148‑1 (MQ=39)          tACGCCGTCTGCGTTTCTGCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGGATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAACCCCCAGAacttgcgta                                                                                                                                   >  2:514977/1‑144 (MQ=255)          tACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAActtactta                                                                                                                                   >  2:162027/1‑149 (MQ=255)                   tGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTc                                                                                                                          >  2:571509/1‑149 (MQ=255)                            ccGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGaa                                                                                                                 >  2:557540/1‑149 (MQ=255)                            ccGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGaa                                                                                                                 >  2:538223/1‑149 (MQ=255)                            ccGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGaa                                                                                                                 >  1:402389/1‑149 (MQ=255)                                  cTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGCACTTACTTATGCTGATTCCGGTGCGACAATTGt                                                                                                           >  1:380584/1‑149 (MQ=255)                                  cTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAGTTGt                                                                                                           >  1:13137/1‑149 (MQ=255)                                         atcaatcaTCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATaaa                                                                                                    <  1:162027/149‑1 (MQ=255)                                          tccaccctcTGTCCTCCCATGACCAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAg                                                                                                   <  2:754578/142‑1 (MQ=21)                                                     ttCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGa                                                                                        <  2:519310/149‑1 (MQ=255)                                                           aaggaagaGTCTAAAAACGAGTATTAAGACTATCACTTATTTAAGTGATAGTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCTCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTAGTTGTAGATTCAAt                                                                                  <  2:489374/142‑1 (MQ=25)                                                                   gTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGATTCAATTGGTCAAc                                                                          <  2:179946/149‑1 (MQ=255)                                                                    tCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGATTCAATTGGTCAACg                                                                         >  1:37040/1‑149 (MQ=255)                                                                      tAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGATTCAATTGGTCAACGCa                                                                       >  1:474563/1‑149 (MQ=255)                                                                               gTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGATTCGATTGGTCAACGCAACAGTTAtg                                                              >  1:505715/1‑149 (MQ=255)                                                                                tATTAAGACTATCACTTATTTAAGTGAGGTTGGTTGTGTGGTGATTCAGGGGGCCAGTCTAAACCCCAGAACTTGCTTATGCTGAGTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGATACAATTGGTCGACGTAACAGTTCtgt                                                             >  2:137540/1‑149 (MQ=25)                                                                                    accaatATCACTTAAATAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGATTCAATTGGTCAACGCAACAGTTATGTGaaa                                                         >  1:435764/6‑149 (MQ=255)                                                                                        cTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGATTCAATTGGTCAACGCAACAGTTATGTGAAAACAt                                                     >  2:786530/1‑149 (MQ=255)                                                                                         tATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGACCAGACTAAACCACGGAACTTACTTATGCTGATTCCGGTGCCAAAATTGTTAATAAAGGTACTTGTAGATTGAATTGGTCAGCGCCACAGTTAAATGAAAACATg                                                    >  2:502226/1‑149 (MQ=37)                                                                                                tATTTAAGGTATATTGGTTGGCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGATTCAATTGGTCAACGCAACAGTTATGTGAAAACATGGGGTTGc                                             <  2:77672/149‑1 (MQ=255)                                                                                                   ttAAGTGATATTGGTTGGCGGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGATTCAATTGGTCAACGCAACAGTTATGTGAAAACATGGGGTTGCGGa                                          <  2:452056/149‑1 (MQ=255)                                                                                                    tAAGTGATATTGGTTGTCTGGAGATTCAGGGGCCCCGTCTACACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTTATAAAGGTACTTGTAGATTCAATTGGTCAACGCAACAGTTATGTGAAAACATGGGGTTGCGGAg                                         <  1:307492/149‑1 (MQ=255)                                                                                                         gATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGATTCAATTGGTCAACGCAACAGTTATGTGAAAACATGGGGTTGCGGAGGtttt                                    <  1:290974/149‑1 (MQ=255)                                                                                                             ttggttggCTGTAGCTTCAGGTGCCCAGTCTAAACCCCATAGCTTACTTATGCCGATTCCGGTGCCAAAATTGTGAATAAAGGGACGTGTAGATTCATTTGGTCAACGCAACAGGTATGTGAAAACATGGGGTTGCGGATGttttctta                                <  2:415944/149‑5 (MQ=21)                                                                                                               ggTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGATTCAATTGGTCAACGCAACAGTTATGTGAAAACATGGGGTTGCGGAGGTTTTTTGAAt                              <  1:19006/149‑1 (MQ=255)                                                                                                                 ttGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGATTCAATTGGTCAACGCAACAGTTATGTGAAAACATGGGGTTGCGGAGGTTTTTTGAATga                            <  1:202767/149‑1 (MQ=255)                                                                                                                   ggcTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGATTCAATTGGTCAACGCAACAGTTATGTGAAAACATGGGGTTGCGGAGGTTTTTTGAATgaga                          <  1:475801/147‑1 (MQ=255)                                                                                                                      tGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGATGCAATTGGTCAACGCAGCAGTTATGTGAAAACATGGGGGTGCGGAGGCTTTTTGAATGAGAGGa                       >  1:301438/1‑149 (MQ=37)                                                                                                                      tGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATGCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGATTCAATTGGTCAACGCAACAGTTATGTGAAAACATGGGGTTGCGGAGGTTTTTTGGATGACACGa                       >  2:153974/1‑149 (MQ=255)                                                                                                                             tCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGATTCAATTGGTCAACGCAACAGTTATGTGAAAACATGGGGTTGCGGAGGTTTTTTGAATGAGACGAACATTTa                <  2:756945/149‑1 (MQ=255)                                                                                                                             tCAGGGGGCCAGTCCAACCCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGATTCAATTGGTCAACGCAACAGTTATGTGAAAACATGGGGTTGCGGAGGTTTTTTGAATGAGACGAACATTTa                <  2:261048/149‑1 (MQ=255)                                                                                                                              cAGGGGGCCAGTCTAACCCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGATTCAATTGGTCAACGCAACAGTTATGTGAAAACATGGGGTTGCGGAGGTTTTTTGAATGAGACGAACATTTAc               <  2:86395/149‑1 (MQ=255)                                                                                                                                gggggCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGATTCAATTGGTCAACGCAACAGTTATGTGAAAACATGGGGTTGCGGAGGTTTTTTGAATGAGACGAACATTTAcag             <  2:31407/149‑1 (MQ=255)                                                                                                                                     ccAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGATTCAATTGGTCAACGCAACAGTTATGTGAAAACATGGGGTTGCGGAGGTTTTTTGAATGAGACGAACATTTACAGCagag        <  1:557540/149‑1 (MQ=255)                                                                                                                                         tCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGATTCAATTGGTCAACGCAACAGTTATGTGAAAACATGGGGTTGCGGAGGTTTTTTGAATGAGACGAACATTTACAGCAGAGGaaa    >  1:356923/1‑149 (MQ=255)                                                                                                                                           tAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGATTCAATTGGTCAACGTAACAGTTATGTGAAAACATGGGGTTGCGGAGGTTTTTTGAATGAGACGAACATTTACAGCAGAGGaaaaa  <  2:37040/149‑1 (MQ=255)                                                                                                                                            |                                                                                                                                                    CCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTTGTAGATTCAATTGGTCAACGCAACAGTTATGTGAAAACATGGGGTTGCGGAGGTTTTTTGAATGAGACGAACATTTACAGCAGAGGAAAAA  >  NC_000913/1469101‑1469387

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ 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.