New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	275525 =	25 (0.650)	5 (0.130)	5/308	NT	23.5%	noncoding (117/768 nt)	IS1	repeat region
	?	CP009273	= 3576990	8 (0.210)					coding (148/276 nt)	insA	IS1 repressor TnpA

ATGCGCGAGGTTACCGACTGCGGCCTGAGTTTTTTAAATGGCGGAAAATCGTGTTGAGGCCAACGCCCATAATGCGGGCGGTTGCCCGGCATCCAACGCCATTCATGGCCATATCAATGATTTTCTGGTGCGTACCGGGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGT‑TTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAGAACACAAATGGGCTAATTCGGCAGTACTTTCCTAAAAAGACATGTCTTGCCCAATATACTCAACATGAACTAGATCTGGTTGCTGCTCAGCTAAACAACAGACCGAGAAAGACACTGAAGTTCAAAACACCGAAAGAGATAATTGA  >  CP009273/275301‑275790                                                                                                                                                                                                                                  |                                                                                                                                                                                                                                                                          aatatttacttatgacattaaaggtgatgctgccaacttactgatttactgtatgatggtgtttttgaggtgctccagtggcttctgtttctatcagctgtccctcctgttcagctactgacggggtggtgcgtaacggcaaaagcaccgccggacatcagcgctatctctgctctcactgccgtaaaacatggcaactgcagttcacttacaccgcttctcaacc                                                                                                                                                                                                                                                                           >  1:386401‑M1/226‑226 (MQ=255)                                                                             ggcggTTGCCCGGCATCCAACGCCATTCATGGCCATATCAATGATTTTCTGGTGCGTACCGGGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGT‑TTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGATCAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCCTACACTAAATCAGTAAGATCACAGCATCACCGAAAAcaca                                                                                                                                              >  1:360956/1‑274 (MQ=9)                                                                                      ccGCCATCCAACGCCATTCATGGCCTTATTAATGCTTTTCTGGTGCGTTCCGGGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGT‑TTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAGAACACAAATGGGCTaa                                                                                                                                    <  2:195045/275‑1 (MQ=255)                                                                                                     tccctcctgttcagctactgacggggtggtgcgtaacggcaaaagcaccgccggacatcagcgctatctctgctctcactgccgtaaaacatggcaactgcagttcacttacaccgcttctcaacCCg                                                                                                                                                                                                                                                                         <  2:595822‑M1/3‑1 (MQ=255)                                                                                                           ggCCATATCAATGATTTTCTGGTGCGTACCGGGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGT‑TTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGAAAGTTGGCAGCAACAACGAAAACACAAAGGTTATAATTCTGCAGTACTTTTCTaaa                                                                                                                >  2:582244/1‑274 (MQ=11)                                                                                                               ncagatactgtttnNGGGTGAGTGCCGGGGTGAGGAAGGGGGTGAGTGATCTGAAGTTTCC‑TGTGTTTATGGCAGGGAGGTCCGATAGAGCAGTGATGTCGCGCAGTGCTGTGTCCGTTAAGCACCACACCGTCAGTAGCTGAACAGGACGGATAGCTGACAGAAACAGAAGACACTGGAGCACCTCAAAAACACCATCATCCGCTAAATCAGTAAGTTGGCAGCATCACCGAGAACACAAATGGGCTAATTCGGCAGTACTTTCCTAAAAAGAc                                                                                                           <  2:512914/265‑1 (MQ=9)                                                                                                                            tCTGGGGCGTACCGTGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGT‑TTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAGAACACAAATGGGCTAATTCGGCAGTACTTTCCTAGAAAGACATGTCTTGCCCaa                                                                                              <  1:582253/275‑1 (MQ=255)                                                                                                                                  gCGTACCGGGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGT‑TTTACGGCCGTGAGAGCAGAGATAGCGCTGATGTCCGGCAGTGCTTTTGCCGCTACGCACCACCCCGTCAGTAGCTCCACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCCCCTCAAAAACACCATCATANACTAAATCAGTAAGTTGGCAGCATCACCGAGAACACAAATGGGCTAATTCGTCAGTACTTTCCTAAAAAGACAAGTCTTGCCCAATATAcc                                                                                        >  1:550724/1‑274 (MQ=255)                                                                                                                                           gTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGT‑TTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCNGTAAGTTGGCAGAATCACCAAGAACACAAATGGGCTAATTCGGCAGTACTTTCCTAAAAAGACATGTCTTGCCCAAAATACTCAACATg                                                                                 >  1:528507/1‑273 (MQ=255)                                                                                                                                                    cGGTGTAAGTGAACTGCAGTTGCCATGT‑TTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAGAACACAAATGGGCTAATTCGGCAGTACTTTCCTAAAAAGACATGTCTTGCCCAAAATACACAAAAAAAACTAGATCTg                                                                      >  1:140394/1‑275 (MQ=255)                                                                                                                                                         ggacatcagcgctatctctgctctcactgccgtaaaacatggcaactgcagttcacttacaccgcttctcaacc                                                                                                                                                                                                                                                                           >  1:366241‑M1/74‑74 (MQ=255)                                                                                                                                                            catcagcgctatctctgctctcactgccgtaaaacatggcaactgcagttcacttacaccgcttctcaacCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGa                                                                                                                                                                                                                          <  1:704808‑M1/50‑1 (MQ=255)                                                                                                                                                               aaCTGCAGTTGCCATGT‑TTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAGAACACAAATGGGCTAATTCGGCAGTACTTTCCTAAAAAGACATGTCTTGCCCAATATACTCAACATGAACTAGATCTGGTtgctgata                                                            >  1:217068/1‑271 (MQ=255)                                                                                                                                                                agcgctatctctgctctcactgccgtaaaacatggcaactgcagttcacttacaccgcttctcaacCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACa                                                                                                                                                                                                                      >  2:704798‑M1/67‑120 (MQ=255)                                                                                                                                                                 gcgctatctctgctctcactgccgtaaaacatggcaactgcagttcacttacaccgcttctcaacCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGCCAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATa                                                                                                                                                                                    <  2:632626‑M1/88‑1 (MQ=255)                                                                                                                                                                     tatctctgctctcactgccgtaaaacatggcaactgcagttcacttacaccgcttctcaacCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACt                                                                                                                                                                                >  1:632635‑M1/62‑153 (MQ=255)                                                                                                                                                                      gTTGCCATGT‑TTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCAACTCAAACACACCATCATACACTAAACCCGTAAGTTGGCAGCATCACCTAAAACACAAATGGGCTAATTCGGCAGTACTTTACTAAAAAGACATGCATAGNCCAAAAAACTCAACATGAACAATAACTCATTACTTCTCAACTaaaa                                                    >  2:453061/1‑274 (MQ=17)                                                                                                                                                                        tatctctgctctcactgccgtaaaacatggcaactgcagttcacttacaccgcttttgCCGTGCCGCACCACCCCGTCAGTAGCTGAACAGGAGGGAc                                                                                                                                                                                                                                    >  1:438499‑M1/59‑98 (MQ=255)                                                                                                                                                                         gCCATGT‑TTTACGGCGGTGAGAGGAGAGAAAGCGCTGATGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAGAACACAANTGGGCTAATTCGGCAGTACTTTCCTAAAAAGACATGTCTTGCCCAATATACTCAACATGAACTAGATCTGGTTGCTGCTCAGCTAaacaac                                                 >  1:502768/1‑275 (MQ=255)                                                                                                                                                                                      ggtaGTGAGAGCAGAGATAGCGCTGATGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGGTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAGAACACAAATGGGCGAATTCGGCAGTACt                                                                                                                        <  1:420119/189‑1 (MQ=255)                                                                                                                                                                                      ggaaGTGAGGGCCGGGCTAGCGCTGATGACCGGCAGTGCTTTTGCCGTTAAGAACCACCCCGTCAGGAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAGAACACAAATGGGCTAATTCGGCAGTACTTTCCTAAAAAGACATGTCTTGCCCAATATACTCAACATGAACTAGATCTGGTTGCTGCTCAGCTAAACAACAGACCGAGaa                                       <  2:502761/270‑1 (MQ=255)                                                                                                                                                                                        cAGTGAGAGCAGAGATAGCGCTGATGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAGAACACAAATGGGCTAATTCGGCAGTACTTTCCTAAAAAGACATGTCTTGCCCAATATACt                                                                                        >  2:211781/1‑222 (MQ=255)                                                                                                                                                                                          gTGAGAGCAGAGATAGCGCTGATGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAGAACACAAATGGGCTAATTCGGCAGTACTTTCCTAAAAAGACATGTc                                                                                                      >  1:143281/1‑206 (MQ=255)                                                                                                                                                                                            gagaGCAGAGATAGCGCTGATGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAGAACACAAATGGGCTAATTCGGCAGTACTTTCCTAAAAAGACATGTCTTGCCCAATATACTCAAc                                                                                    <  1:211785/222‑1 (MQ=255)                                                                                                                                                                                              gagCAGAGATAGCGCTGTTGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAGAACACAAATGGGCTAATTCGGCAGTACTTTCCTAAAAAGACATGTCTTGc                                                                                                  <  2:143280/206‑1 (MQ=255)                                                                                                                                                                                                      aTAGCGCTGATGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAGAACACAAATGGGCTAATTCGGCAGTACTTACCTAAAAAGACATGTCTTGCCCAATATACTCAACATGAACTAGATCTGGTTGCTGCTCAGCTAAACAACAGACCGAGAAAGACACTGAAGTTCaaaa                     >  1:365001/1‑275 (MQ=255)                                                                                                                                                                                                         gcgcTGATGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAGAACACAAATGGGCTAATTCGGCAGTACTTTcc                                                                                                                    >  2:403927/1‑177 (MQ=255)                                                                                                                                                                                                          cgcTGATGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAGAACACAAATGGGCTAATTCGGCAGTACTTTCCTAAAAAGACATGTCTTg                                                                                                   >  2:686245/1‑193 (MQ=255)                                                                                                                                                                                                             tGATGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAGAACACAAATGGGCTAATTCGGCAGTACTTTCCTaaa                                                                                                                <  1:403934/177‑1 (MQ=255)                                                                                                                                                                                                              gATGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAGAACACAAATGGGCTAATTCGGCAGTACTTTCCTAAAAAGACATGTCTTGCCCa                                                                                               <  1:686254/193‑1 (MQ=255)                                                                                                                                                                                                                tGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAGAACACAAATGGGCTAATTCGGCAg                                                                                                                            >  2:644296/1‑162 (MQ=255)                                                                                                                                                                                                                    cGGCAGTGCATTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAGAACACAAATGGGCTAATTCGGCAGTACt                                                                                                                        <  1:644305/162‑1 (MQ=255)                                                                                                                                                                                                                         tccccgttGCCATTACACACCACCCCGTCCGTCACTGAACAGGAGGGACAGCTGATAGAAACAGTAGCCCCTCGCGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAGAACACAAATGGGCTAATTCGGCAGTACTTTCCTAAAAAGACATGTCTTGCCCAATATACTCAACATGAACTAGATCTGGTTGCTGCTCAGCTAAACAACAGACCGAGAAAGACACTGAAGTTCAAAACACCGAAAGAGATAATTGa  <  2:217064/269‑1 (MQ=21)                                                                                                                                                                                                                            cTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAGAACACAAATGGGCTAATTCGGCAGTACTTTCCTAAAAAGACATGTCTTGCCCAATATACTc                                                                                       >  1:139648/1‑187 (MQ=255)                                                                                                                                                                                                                              tttGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAGAACACAAATGGGCTAATTCGGCAGTACTTTCCTAAAAAGACATGTCTTGCCCAATATACTCAACATGAACTAGATCTGGTtgc                                                                 >  2:631668/1‑207 (MQ=255)                                                                                                                                                                                                                                tGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAGAACACAAATGGGCTAATTCGGCAGTACTTTCCTAAAAAGACATGTCTTGCCCAATATACTCAACa                                                                                   <  2:139647/187‑1 (MQ=255)                                                                                                                                                                                                                                 gCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAGAACACAAATGGGCTAATTCGGCAGTACTTTCCTAAAAAGACATGTCTTGCCCAATATACTc                                                                                       >  1:120916/1‑182 (MQ=255)                                                                                                                                                                                                                                  CCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAGAACACAAATGGGCTAATTCGGCAGTACTTTCCTAAAAAGACATGTCTTGCCCAATATACTCAACATGAACTAGATCTGGTTgctgct                                                             >  1:631677‑M1/1‑207 (MQ=255)                                                                                                                                                                                                                                  |                                                                                                                                                                                                                                                                          ATGCGCGAGGTTACCGACTGCGGCCTGAGTTTTTTAAATGGCGGAAAATCGTGTTGAGGCCAACGCCCATAATGCGGGCGGTTGCCCGGCATCCAACGCCATTCATGGCCATATCAATGATTTTCTGGTGCGTACCGGGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGT‑TTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAGAACACAAATGGGCTAATTCGGCAGTACTTTCCTAAAAAGACATGTCTTGCCCAATATACTCAACATGAACTAGATCTGGTTGCTGCTCAGCTAAACAACAGACCGAGAAAGACACTGAAGTTCAAAACACCGAAAGAGATAATTGA  >  CP009273/275301‑275790

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 21 ≤ 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.