New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 1397238	NA (NA)	22 (0.760)	20/484	0.4	100%	noncoding (1195/1195 nt)	IS5	repeat region
	?	NC_000913	= 1978494	0 (0.000)					intergenic (‑297/+24)	flhD/insB5	DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB

ATAACCAACTGGCGATGTTATTCACGCTGGCCAACCTGTTTCGGGCGGACCAAATGATACGTCAGTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATGGCGAAACTGAAGTCAGCGAAAGGGAAGAAATTTCTCTTTGGTTTGTTGGCGGTTTTCATTATTGCGGCGTCGGTTGTGACTCGCGCGACCATCGGCGGCG  >  NC_000913/1397010‑1397473                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                            aTAACCAACTGGCGATGTTATTCACGCTGGCCAACCTGTTTCGGGCGGACCAAATGATACGTCAGTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGAtt                                                                                                                                                                                                                       <  2:41886/251‑1 (MQ=37)      cAACTGGCGATGTTATTCACGCTGGCCCACCTGTTTCGGGCGGACAACATGAAACGTCAAAGGGAGAGATCTCCCTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCCACGCATTTACGGGAGAAAAAATCGGCTCAAACACGCAGAAATGACATGACTGAGACAGCCGAGACGAATTTCCCCGCTTATTCGAACCTTCCCTAAATAATCAATGCGTTGATTGTaa                                                                                                                                                                                                                   >  1:19357/1‑250 (MQ=11)      cAACTGGCGATGTTATTCACGCTGGCCAACCTGTTTCGGGCGGACCAAATGATACGTCAGTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTaaa                                                                                                                                                                                                                  <  1:206711/251‑1 (MQ=39)             cGATGTTATTCACGCTGGCCAACCTGTTTCGGGCGGACCAAATGATACGTCAGTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCCCCTTCCCTAAATAATCAATGCGTTGATTGTAAATCCAGCt                                                                                                                                                                                                           >  1:246743/1‑251 (MQ=255)             cGATGTTATTCACGCTGGCCAACCTGTTTCGGGCGGACCAAATGATACGTCAGTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCt                                                                                                                                                                                                           >  1:201068/1‑251 (MQ=255)                 gTTATTCACGCTGGCCAACCTGTTTCGGGCGGACCAAATGATACGTCAGTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTACCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTa                                                                                                                                                                                                          >  1:242453/1‑248 (MQ=255)                             ggCCAACCTGTTTCGGGCGGACCAAAGTATACGTCAGTAGGATAGATCTCCCTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGttt                                                                                                                                                                                             <  2:207390/249‑1 (MQ=255)                                 aatcgctttagggCGGACCAAATTATACGTCAGCGGTAGAGATCTCAATAAAAACTGGGGATAAAGTCTTAAATGGCGAATAAACGGTCTAAATAGGCTTATTCAAGGCATTTACGGGATAAAAAATCGGCTCAAACATGAAGAAATGAAATGACGGAGTCATCCGCTAAGAATTTCCCCGCTTATTCGCTCCTTCCCGAACTATTCAATGCGGTGATTGTAAAGCCAGCTAAGAGGTGAGGTTTTCa                                                                                                                                                                                          <  2:61331/238‑1 (MQ=14)                                   ccTGTTTCGGGCGGACCAAATGATACGTCAGTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGAGAGGTTTTCagcgc                                                                                                                                                                                      >  1:193045/1‑247 (MQ=255)                                    cTGTTTCGAGCGGACCAAATGATACGTCAGTGGGCGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAAAGGTCTAAATAGGCTGATTCAAGGCATTTCCGGGAGGAAAAATCGGATCAAACATGAAGCAATGACATGACTGGGACAGCCGAGAAAACTTTCACCCATTATTCGCACCTTCCATAACTTATCAATGCGGTGATTGTCAATCCAGATACGAGGTGAAGTTTTCagaac                                                                                                                                                                                      >  2:211541/1‑247 (MQ=14)                                     tGTTTCGGGCGGACCAAATGATACGTCAGTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGGCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGGAAATCCAGCTAAGAGGTGAGGTTTTCAGAGc                                                                                                                                                                                      >  2:66505/1‑248 (MQ=255)                                         tCGGGCGGACCAAATGATACGTCAGTGGGAGAGATAACTCTAAAAACTGGGGATAACTCCGTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTTAGTGTAAATCCACCTAAGAGGTGAGTTTTTCAGAGCAGACaa                                                                                                                                                                                <  1:249448/250‑1 (MQ=17)                                                      aTGATACGTCAGTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAACCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCAt                                                                                                                                                                  <  1:54139/251‑1 (MQ=255)                                                               cAGTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGTCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGtt                                                                                                                                                         <  1:207961/251‑1 (MQ=255)                                                                       gagaTCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGAGAGGTTTTCAGAGCAGACAACGGTGAAATGACATGGTATTGTTACGttt                                                                                                                                                   >  2:181614/1‑249 (MQ=255)                                                                              cACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTaa                                                                                                                                             <  1:181614/248‑1 (MQ=255)                                                                              cACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTa                                                                                                                                              <  1:191027/247‑1 (MQ=255)                                                                                    aaaCTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATGCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAAtt                                                                                                                                    <  1:142852/251‑1 (MQ=255)                                                                                            gATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGca                                                                                                                            <  1:339864/251‑1 (MQ=255)                                                                                                      tAAATGGCGAAGAAACGGTCTAAAAAGGCTGATTCAAGGCATTGACGGGAGAAAAAATCGGCTCAAACAGTAAGAAATGAAATGACTGAGTCAGCCGATAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGAtt                                                                                                                    <  2:190012/249‑1 (MQ=255)                                                                                                                agaaACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTa                                                                                                        <  1:66505/251‑1 (MQ=255)                                                                                                                    aCGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATGGc                                                                                                    >  1:132899/1‑251 (MQ=255)                                                                                                                      ggTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAAGTGGCTCAAACATGAAAAAATGAAATGACTGAATCACCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAAGCTATGCGTTGATTGTAAATCCAGCTAAGCGGTGAGGttt                                                                                                                                                                                             <  1:216947/160‑1 (MQ=17)                                                                                                                        tCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGt                                                                                                                                                                            <  1:1085/175‑1 (MQ=255)                                                                                                                        tCTAAATAGGCTGATTCAAAGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGCTTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGCGCAGACAACGGt                                                                                                                                                                            >  2:1085/1‑175 (MQ=255)                                                                                                                             aTAGTCTGATGCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAATAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAATTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATGGCGAAACtaaa                                                                                           <  1:246235/251‑4 (MQ=255)                                                                                                                              tAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATGGCGAAACTGa                                                                                            >  1:123565/1‑249 (MQ=255)                                                                                                                                           ggCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCAGCTTATTCGCACGTTCCCTAACTAATCAATGAGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAAAGGTGAAATGTCATGGTATTGATACGTTTAGATAACAAGAAATTTGTCTGCACAAGGATTACATAATGATTATGGCGAAACTGAAGTCAGCGAAAggt                                                                              >  1:338288/1‑249 (MQ=37)                                                                                                                                                   cGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATTATTATGGCGAAACTGAAGTCAGCGAAAGGGAAGAAAttt                                                                     <  1:131350/251‑1 (MQ=255)                                                                                                                                                              aTCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTAGGGCGAAACTGAAGTCAGCGAAAGGGAAGAAATTTCTCTTTGGttt                                                          <  1:293224/251‑1 (MQ=255)                                                                                                                                                                   cTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATGGCGAAACTGAAGTCAGCGAAAGGGAAGAAATTTCTCTTTGGTTTGTTgg                                                     >  2:83496/1‑251 (MQ=255)                                                                                                                                                                     cAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATGGCGAAACTGAAGTCAGCGAAAGGGAAGAAATTTCTCTTTGGTTTGTTgg                                                     <  1:61277/249‑1 (MQ=255)                                                                                                                                                                              aaaaatgaaatgACTGAGACAGACGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTGTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTTCACAAGGATTACATCATGATTATGGCGAAACTGAAGTCATCGAAAGGGAAGAAATTTCTCTTTGGTTTGTTGGCGGTTGTCatt                                          <  2:95529/249‑1 (MQ=255)                                                                                                                                                                                             gAGTCAGCCGAGAAGAATTTCCCCGCGTATTCGCACCTTCCTTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATGGCGAAACTGAAGTCAGCGAAAGGGAAGAAATTTCTCTTTGGTTTGTTGGCGGTTTTCATTATTGCGGCGTCgg                             <  2:123565/249‑1 (MQ=255)                                                                                                                                                                                                                tCCCCGCTTAATCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGGTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATGGCGAAACTGAAGTCAGCGAAAGGGAAGAAATTTCTCTTTGGTTTGTTGGCGGTTTTCATTATTGCGGCGTCGGTTGTGACTCGCGCGACCATc         <  2:132899/250‑1 (MQ=255)                                                                                                                                                                                                                      cTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATGGCGAAACTGAAGTCAGCGAAAGGGAAGAAATTTCTCTTTGGTTTGTTGGCGGTTTTCATTATTGCGGCGTCGGTTGTGATTCGCGCGCCCATCGgcggcg  >  2:75190/1‑251 (MQ=255)                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                            ATAACCAACTGGCGATGTTATTCACGCTGGCCAACCTGTTTCGGGCGGACCAAATGATACGTCAGTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATGGCGAAACTGAAGTCAGCGAAAGGGAAGAAATTTCTCTTTGGTTTGTTGGCGGTTTTCATTATTGCGGCGTCGGTTGTGACTCGCGCGACCATCGGCGGCG  >  NC_000913/1397010‑1397473

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ 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.