New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_pgi	= 4556738	53 (0.960)	5 (0.100)	5/260	6.9	8.9%	coding (812/912 nt)	hypT	hypochlorite‑responsive transcription factor
	?	NC_000913_3_pae_pgi	= 4556749	54 (1.060)					coding (801/912 nt)	hypT	hypochlorite‑responsive transcription factor
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

ATCTGGTCTGGGATAATGGCGGTTGGCGCAGTGCGACGCTGGAGAATGTCAGCTAAGCACAATCTCCAGCTCGCGCAGTTCACGCCAGAAGCGTTCGGCAACGGGATTCATGCGGGTATTCATCCGGTATGCATAGGCCTGAATCGGGATCACCAGTTCGTCCCGATTCAGTACAACGAGCTTCCCGCTGCGAATTTCTTGTTGGATGGCGTACTCCGGCAGCCAGGCAATCCCACAGCCGTCGAGGGCAACCTGCTTTAAAAGCTCGCTCATCGAAGAGACAAAAAAGGTG  >  NC_000913_3_pae_pgi/4556590‑4556881                                                                                                                                                     |                                                                                                                                                aTCTGGTCTGGGATAATGGCGGTTGGCGCAGTGCGACGCTGGAGAATGTCAGCTAAGCACAATCTCCAGCTCGCGCAGTTCACGCCAGAAGCGTTCGGCAACGGGCTTCATGCGGGTATTCATCCGGTATGCATAGGCCTGAATCGGGa                                                                                                                                                 >  1:869775/1‑149 (MQ=255)  tctggtctggGATAATGGCGGTTGGCGCAGTGCGACGCTGGAGAATGTCAGCTAAGCACAATCTCCAGCTCGCGCAGTTCACGCCAGAAGCGTTCGGCAACGGGATTCATGCGGGTATTCATCCGGTATGCATAGGCCTGAATCGGGAt                                                                                                                                                >  1:147539/1‑149 (MQ=255)    tggtctggGATAATGGCGGTTGGCGCAGTGCGACGCTGGAGAATGTCCGCTCGCCACAGGGTCCAGCGAGCGCAGTTCACGCCAGAACCGTTCGGCAACGGGATTCATGCGGGTCTTCCTCCGGGATGCACAGGGCTGAGTCGGGATcg                                                                                                                                              >  2:160314/1‑148 (MQ=255)       tctggGATAATGGCGGTTGGCGCAGTGCGACGCTGGAGAATGTCAGCTAAGCACAATCTCCAGCTCGCGCAGTTCACGCCAGAAGCGTTCGGCAACGGGATTCATGCGGGTATTCATCCGGTATGCATAGGCCTGAATCGGGATCACCa                                                                                                                                           <  2:441781/149‑1 (MQ=255)       tctggGATAATGGCGGTTGGCGCAGTGCGACGCTGGAGAATGTCAGCTAAGCACAATCTCCAGCTCGCGCAGTTCACGCCAGAAGCGTTCGGCAACGGGATTCATGCGGGTATTCATCCGGTATGCATAGGCCTGAATCGGGATCACCa                                                                                                                                           >  1:441781/1‑149 (MQ=255)           ggATAATGGCGGTTGGCGCAGTGCGACGCTGGAGAATGTCAGCTAAGCACAATCTCCAGCTCGCGCAGTTCACGCCAGAAGCGTTCGGCAACGGGATTCATGCGGGTATTCATCCGGTATGCATAGGCCTGAATCGGGATCACCAGTTc                                                                                                                                       >  1:912642/1‑149 (MQ=255)                 tGGCGGTTGGCGCAGTGCGACGCTGGAGAATGTCAGCTAAGCACAATGTCCAGCTCGCGCAGTTCACGCCAGAAGCGTTCGGCAACGGGATTCATGCGGGTATTCATCCGGTATGCATAGGCCTGATTCGGGATCACCAGTTCGTCCCg                                                                                                                                 >  2:49353/1‑149 (MQ=255)                         ggCGCAGTGCGACGCTGGAGAATGTCAGCTAAGCACAATCTCCAGCTCGCGCAGTTCACGCCAGAAGCGTTCGGCAACGGGATTCATGCGGGTATTCATCCGGTATGCATAGGCCTGAATCGGGATCACCAGTTCGTCCCGATTCAGTa                                                                                                                         <  1:929401/149‑1 (MQ=255)                                                gTCAGCTAAGCACAATCTCCAGCTCGCGCAGTTCACGCCAGAAGCGTTCGGCAACGGGATTCATGCGGGTATTCATCCGGTATGCATAGGCCTGAATCGGGATCACCAGTTCGTCCCGATTCAGTACAACGAGCTTc                                                                                                              >  1:402849/1‑137 (MQ=255)                                                gTCAGCTAAGCACAATCTCCAGCTCGCGCAGTTCACGCCAGAAGCGTTCGGCAACGGGATTCATGCGGGTATTCATCCGGTATGCATAGGCCTGAATCGGGATCACCAGTTCGTCCCGATTCAGTACAACGAGCTTc                                                                                                              <  2:402849/137‑1 (MQ=255)                                                    gCTAAGCACAATCTCCAGCTCGCGCAGTTCACGCCAGGAGCGCTCGGCCACGGGATTCCTGCGGGTATTTAATCCGTATGCATACGCCTGACTCGGGATCAGCTGTTCGTCCCGGTTCAGTTCACCGACCTCTCCCCTGCGAATTTCtg                                                                                              >  2:696754/1‑148 (MQ=255)                                                    gCTAAGCACAATCTCCAGCTCGCGCAGTTCACGCCAGAAGCGTTCGGCAACGGGATTCATGCGGGTATTCATCCGGTATGCATAGGCCTGAATCGGGATCACCAGTTCGTCCCGATTCAGTACAACGAGCTTCCCGCTGCGAATTTCtt                                                                                              >  1:534875/1‑149 (MQ=255)                                                       aaGCACGATCTCCAGCTCGCGAAGTTCACGCCAGAAGCGTTCGGCAACGGGATTCATGCGGGTATTCATCCGGTATGCATAGGCCTGAATCGGGATCACCAGTTCGTCCCGATTCAGTACAACGAGCTTCACGCTGTGAATTTCttgtt                                                                                           <  2:604858/149‑1 (MQ=255)                                                       aaGCACAATCTCCAGCTCGCGCAGTTCACGCCAGAAGCGTTCGGCAACGGGATTCATGCGGGTATTCATCCGGTATGCATAGGCCTGAATCGGGATCACCAGTTCGTCCCGATTCAGTACAACGAGCTTCCCGCTGCGAATTTCttgtt                                                                                           >  2:623635/1‑149 (MQ=255)                                                        aGCACAATCTTCAGCTCGCGCAGTTCACGCCAGAAGCGTTCGGCAACGGGATTCATGCGGGTATTCATCCGGTATGCATAGGCCTGAATCGGGATCACCAGTTCGTCCCGATTCAGTACAACGAGCTTCCCGCTGCGAATTTCttgttg                                                                                          <  2:354060/149‑1 (MQ=255)                                                        aGCACAATCTCCAGCTCGAGCAGTGCACGCCAAAAGCGTTCGGCAACGGGATTCATGCGGGTATTCATCCGGTATGCATAGGCCTGAATCGGGATCACCAGTTCGTCCCGATTCAGTACAACGAGCTTCCCGCTGCGAATTTCttgttg                                                                                          <  1:203066/149‑1 (MQ=255)                                                            caATCTCCAGCTCGCGCAGTTCACGCCAGAAGCGTTCGGCAACGGGATTCATGCGGGTCTTCATCCGGTATGCATAGGCCTGAATCGGGATCACCAGTTCGTCCCGATTCAGTACAACGAGCTTCCCGCTGCGAATTTCTTGTTGGATg                                                                                      >  1:279139/1‑149 (MQ=255)                                                              aTCTCCAGCTCGCGCAGTTCACGCCAGAAGCGTTCGGCAACGGGATTCATGCGGGTATTCATCCGGTATGCATAGGCCTGAATCGGGATCACCAGTTCGTCCCGATTCAGTACAACGAGCTTCCCGCTGCGAATTTCTTGTTGGATGGc                                                                                    <  2:869775/149‑1 (MQ=255)                                                                 tcCAGCTCGCGCAGTTCACGCCAGAAGCGTTCGGCAACGGGATTCATGCGGGTATTCATCCGGTATGCATAGGCCTGAATCGGGATCACCAGTTCGTCCCGATTCAGTACAACGAGCTTCCCGCTGCGAATTTCTTGTTGGATGGCGTa                                                                                 >  1:541522/1‑149 (MQ=255)                                                                 tcCAGCTCGCGCAGTTCACGCCAGAAGCGTTCGGCAACGGGATTCATGCGGGTATTCATCCGGTATGCATAGGCCTGAATCGGGATCACCAGTTCGTCCCGATTCAGTACAACGAGCTTCCCGCTGCGAATTTCATGTTGGATGGCGTa                                                                                 >  1:867718/1‑149 (MQ=255)                                                                 tcCAGCTCGCGCAGTTCACGCCAGAAGCGTTCGGCAACGGCACTCATGCGGGTATTGATCCGGTATGCATAGGCCTGGATCGGGATCCCCAGTTCGTCCCGATTTAGTACAACGGCCTTCCCGCTGCGAATTTCGTGTTGGTGGGCGTa                                                                                 >  2:438987/1‑149 (MQ=255)                                                                    aGCTCGCGCAGTTCCGGCCAGAAGGGTTCGGCAACGGTATTCATGCGGGTATTCATCCGGTATGCATAGGCCTGAATCGGGATCACCAGTTCGTCCCGATTCAGTACAACGAGCTTCCCGCTGCGAATTTCTTGTTGGATGGCGTACTc                                                                              <  2:36113/149‑1 (MQ=255)                                                                    aGCTCGCGCAGTTCACGCCAGAAGCGTTCGGCAACGGGATTCATGCGGGTATTCATCCGGTATGCATAGGCCTGAATCGGGATCACCAGTTCGTCCCGAGTCAGTACAACGAGCTTCCCGCTGCGAATTTCTTGTTGGATGGCGTACTc                                                                              <  1:136495/149‑1 (MQ=255)                                                                         gcgcAGTTCACGCCAGAAGCGTTCGGCAACGGGATTCATGCGGGTATTCATCCGGTATGCATAGGCCTGAATCGGGATCACCAGTTCGTCCCGATTCAGTACAACGAGCTTCCCGCTGCGAATTTCTTGTTGGATGGCGTACTCCGGCa                                                                         >  1:889942/1‑149 (MQ=255)                                                                          cgcAGTTCACGCCAGAAGCGTTCGGCAACGGGATTCATGCGGGTATTCATCCGGTATGCATAGGCCTGAATCGGGATCACCAGTTCGTCCCGATTCAGTACAACGAGCTTCCCGCTGCGAATTTCTTGTTGGATGGCGTACTCCGGCAg                                                                        >  1:363643/1‑149 (MQ=255)                                                                              gTTCCCGCCAGAAGCGTTCGGCAACGGGATTCATGCGGGTATCAATCCGGGATGCATAGGCCTGAATCGGGATCACCAGTTCGTCCCTATTCAGTACAACGAGCTTCCCGCTGCGAATTTCTTGTTGGATGGCGTACTCCGGCAGCCAg                                                                    <  1:329001/149‑1 (MQ=255)                                                                               ttCACGCCAGAAGCGTTCGGCAACGGGATTCATGCGGGTATTCATCCGGTATGCATAGGCCTGAATCGGGATCACCAGTTCGTCCCGATTCAGTACAACGAGCTTCCCGCTGCGAATTTCTTGTTGGATGGCGTACTCCGGCAGCCAgg                                                                   <  1:6041/149‑1 (MQ=255)                                                                                  aCGCCAGAAGCGTTCGGCAACGGGATTCATGCGGGTATTCATCCGGTATGCATAGGCCTGAATCGGGATCACCAGTTCGTCCCGATTCAGTACAACGAGCTTCCCGCTGCGAATTTCTTGTTGGATGGCGTACTCCGGCAGCCAGGCaa                                                                <  1:680584/149‑1 (MQ=255)                                                                                        gAAGCGTTCGGCAACGGGATTCATGCGGGTATTCATCCGGTATGCATAGGCCTGAATCGGGATCACCAGTTCGTCCCGATTCAGTACAACGAGCTTCCCGCTGCGAATTTCTTGTTGGATGGCGTACTCCGGCAGCCAGGCAATCCaac                                                          >  1:821506/1‑149 (MQ=255)                                                                                         aaGCGTTCCGCAACGCGATCCATGCGGGTATTCATCCGGTATGCATAGGCCTGAATCGGGATCACCAGTTCGTCCCGCTTCAGTCCAACGAGCTTCCCGCTGCGAATTTCTTGTTGGATGGCGTACTCCGGCAGCCAGGCAATCCcaca                                                         <  1:842777/149‑1 (MQ=255)                                                                                                   cAACGGGATTCATGCGGGTATTCATCCGGTATGCATAGGCCTGAATCGGGATCACCAGTTCGTCCCGATTCAGTACAACGAGCTTCCCGCTGCGAATTTCTTGTTGGATGGCGTACTCCGGCAGCCAGGCAATCCCACAGCCGTCGAgg                                               <  2:363643/149‑1 (MQ=255)                                                                                                       gggATTCATGCGGGTATTCATCCGGTATGCATAGGCCTGAATCGGGATCACCAGTTCGTCCCGATTCAGTACAACGAGCTTCCCGCTGCGAATTTCTTGTTGGATGGCGTACTCCGGCAGCCAGGCAATCCCACAGCCGTCGAGGGCaa                                           >  1:726698/1‑149 (MQ=255)                                                                                                          aTTCATGCGGGTATTCATCCGGTATGCATAGGCCTGAATCGGGATCACCAGTTCGTCCCGATTCAGTACAACGAGCTTCCCGCTGCGAATTTCTTGTTGGATGGCGTACTCCGGCAGCCAGGCAATCCCACAGCCGTCGAGGGCAACCt                                        >  1:720214/1‑149 (MQ=255)                                                                                                              aTGCGGGTATTCATCCGGTATGCATAGGCCTGAATCGGGATCACCAGTTCGTCCCGATTCAGTACAACGAGCTTCCCGCTGCGAATTTCTTGTTGGATGGCGTACTCCGGCAGCCAGGCAATCCCACAGCCGTCGAGGGCAACCTGCtt                                    >  2:946107/1‑149 (MQ=255)                                                                                                                 cGGGTATTCATCCGGTATGCATAGGCCTGAATCGGGATCACCAGTTCGTCCCGATTCAGTACAACGAGCTTCCCGCTGCGAATTTCttg                                                                                             <  2:181158/89‑1 (MQ=255)                                                                                                                 cGGGTATTCATCCGGTATGCATAGGCCTGAATCGGGATCACCAGTTCGTCCCGATTCAGTACAACGAGCTTCCCGCTGCGAATTTCttg                                                                                             >  1:181158/1‑89 (MQ=255)                                                                                                                   ggTATTCATCCGGTATGCATAGGCCTGAATCGGGATCACCAGTTCGTCCCGATTCAGTACAACGAGCTTCCCGCTGCGAATTTCTTGTTGGATGGCGTACTCCGGCAGCCAGGCAATCCCACAGCCGTCGAGGGCAACCTGCTTTaaaa                               <  2:154844/149‑1 (MQ=255)                                                                                                                      attctgccGGTATGCATAGGCCTGAATCGGGATCACCAGTTCGTCCCGATTCAGTACAACGAGCTTCCCGCTGAGAATTTCTTGTTGGATGGCGTACTCCGGCAGCCAGGCAATCCCACAGCCGTCGAGGGCAACCTGCTTTAAAAgct                            <  2:147539/143‑1 (MQ=255)                                                                                                                       ttCATCCACTATTCATAGGCCTGAATCTGTATCACCAGTTCGTCCCCATTCAGTACAACAAACTTCCCACTGCGAATTTCTTGTTGGATGGCTTACTCCTTCAGCCACTCAATCCCAAAGACGTCGATGGCAACCGGCTTTAAAAtctc                           <  2:253899/149‑1 (MQ=255)                                                                                                                         cATCCGGTATGCATAGGCCTGAATCGGGATCACCAGTTCGTCCCGATTCAGTACAACGAGCTTCCCGCTGCGAATTTCTTGTTGGATGGCGTACTCCGGCAGCCAGGCAATCCCACAGCCGTCGAGGGCAACCTGCTTTAAAAgctcgc                         >  2:324151/1‑149 (MQ=255)                                                                                                                               gTATGCATAGGCCTGAATCGGGATCACCAGTTCGTCCCGATTCAGTACAACGAGCTTCCCGCTGCGAATTTCTTGTTGGATGGCGTACTCCGGCAGCCAGGCAATCCCACAGCCGTCGAGGGCCACCTGCTTTAAAAGCTCGCTCATCg                   >  2:75590/1‑149 (MQ=255)                                                                                                                                tATGCATAGGCCTGAATCGGGGTCACAAGTACGTCCCGATTAAGTACAACGAGCGTACCGCGGCTATTTTCTTGTTGGATGGCTTACTTCGGTAGCCAGGCAAACCCACAGCCGACGAGGGCGACCTCATTGAAAAGCGAGCTCATcac                  >  2:197421/1‑147 (MQ=255)                                                                                                                                 aTGCATAGGCCTGAATCGGGATCACCAGTTCGTCCCGATTCAGTACAACGAGCTTCCCGCTGCGAATTTCTTGTTGGATGGCGTACTCCGGCAGCCAGGCAATCCCACAGCCGTCGAGGGCAACCTGCTTTAAAAGCTCGCTCATCGaa                 <  2:534875/149‑1 (MQ=255)                                                                                                                                 aTGCAGAGGCCTGAATCGGGATCACCAGTTCGTCCCGATTCAGTACAACGAGCTTCCCGCTGCGAATTTCTTGTTGGATGGCGTACTCCGGCAGCCAGGCAATCCCACAGCCGTCGAGGGCAACCTGCTTTAAAAGCTCGCTCATCGaa                 <  2:593630/149‑1 (MQ=255)                                                                                                                                   gCATTGGCCTGCAGCGGGCACACCCGTTCGTCCCGATCCAGCACCGCGCGCTGCCCACAGCGAATTTCTTCTTGGTTCGCGTACTCCGGCAGCCCGGCAATACCACAGCCGCCGAGGGCAACCTGCTTTAAACGCTCGCTCCTCGAaga               >  2:470121/1‑149 (MQ=255)                                                                                                                                   gCATAGGCCTGAATCGGGATCACCAGTTCGTCCCGATTCAGTACAACGAGCTTCCCGCTGCGAATTTCTTGTTGGATGGCGTACTCCGGCAGCCAGGCAATCCCACAGCCGTCGAGGGCAACCTGCTTTAAAAGCTCGCTCATCGAaga               <  1:243655/149‑1 (MQ=255)                                                                                                                                   gCATAGGCCTGAATCGGGATCACCAGTTCGCCCCGATTCAGTACAACGAGCTTCCCGCTGCGAATTTCTTGTTGGATGGCGTACTCCGGCAGCCAGGCAATCCCACAGCCGTCGAGGGCAACCTGCTTTAAAAGCTCGCTCATCGAaga               <  1:590611/149‑1 (MQ=255)                                                                                                                                     aTAGGCCTGAATCGGGATCACCAGTTCGTCCCGATTCAGTACAACGAGCTTCCCGCTGCGAATTTCTTGTTGGATGGCGTACTCCGGCAGCCAGGCAATCCCACAGCCGTCGAGGGCAACCTGCTTTAAAAGCTCGCTCATCGAAgaga             >  1:761508/1‑149 (MQ=255)                                                                                                                                      tAGGCCTGAATCGGGATCACCAGTTCGTCCCGATTCAGTACAACGAGCTTCCCGCTGCGAATTTCTTGTTGGATGGCGTACTCCGGCAGCCAGGCAATCCCACAGCCGTCGAGGGCAACCTGCTTTAAAAGCTCGCTCATCGACGAGAc            >  1:290225/1‑149 (MQ=255)                                                                                                                                         gCCTGAATCGGGATCACCAGTTCGTCCCGATTCAGTACAACGAGCTTCCCGCTGCGAATTTCTTGTTGGAt                                                                                       <  1:917200/71‑1 (MQ=255)                                                                                                                                         gCCTGAATCGGGATCACCAGTTCGTCCCGATTCAGTACAACGAGCTTCCCGCTGCGAATTTCTTGTTGGAt                                                                                       >  2:917200/1‑71 (MQ=255)                                                                                                                                            tGAATCGGGATCACCAGTTCGTCCCGATTCAGTACAACGAGCTTCCCGCTGCGAATTTCTTGTTGGATGGCGTACTCCGGCAGCCAGGCAATCCCACAGCCGTCGAGGGCAACCTGCTTTAAAAGCTCGCTCATCGAAGAGACaaaaaa      <  1:324151/149‑1 (MQ=255)                                                                                                                                              aactggtaTCACCAGTTCGTCCCGATTCAGTACAACGAGCTTCCAGCTGCGAATTTCTTGTTGGATGGCGTACTCCGGCAGCCAGGCAATCCCACAGCCGTCGAGGGCAACCTGCTTTAAAAGCTCGCTCATCGAAGAGACAAAAAAgg    <  2:137865/142‑1 (MQ=255)                                                                                                                                                tCGGGATCACCAGTTCGTCCCGATTCAGTACAACGAGCTTCCCGCTGCGAATTTCTTGTTGGATGGCGTACTCCGGCAGCCAGGCAATCCCACAGCCGTCGAGGGCAACCTGCTTTAAAAGCTCGCTCATCGAAGAGACAAACAAGGTg  >  2:861860/1‑149 (MQ=255)                                                                                                                                                     |                                                                                                                                                ATCTGGTCTGGGATAATGGCGGTTGGCGCAGTGCGACGCTGGAGAATGTCAGCTAAGCACAATCTCCAGCTCGCGCAGTTCACGCCAGAAGCGTTCGGCAACGGGATTCATGCGGGTATTCATCCGGTATGCATAGGCCTGAATCGGGATCACCAGTTCGTCCCGATTCAGTACAACGAGCTTCCCGCTGCGAATTTCTTGTTGGATGGCGTACTCCGGCAGCCAGGCAATCCCACAGCCGTCGAGGGCAACCTGCTTTAAAAGCTCGCTCATCGAAGAGACAAAAAAGGTG  >  NC_000913_3_pae_pgi/4556590‑4556881

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