New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	1973115 =	6 (0.170)	30 (0.870)	22/270	NT	83.3%	intergenic (‑661/‑119)	flhD/uspC	flagellar class II regulon transcriptional activator, with FlhC/universal stress protein
	?	CP009273	= 3577555	NA (NA)					intergenic (+15/‑1)	insB1/yrhA	IS1 transposase B/pseudogene, interrupted by IS1E

TTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCAAAAGGAAACAAAAATCATTGTAAA  >  CP009273/3577410‑3577699                                                                                                                                                  |                                                                                                                                                 ttGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGACATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGAc                                                                                                                                               >  2:447492/1‑149 (MQ=17)                cgAACCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGt                                                                                                                                      <  1:211793/142‑1 (MQ=25)                         ggCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACtttttt                                                                                                                             <  1:253049/143‑1 (MQ=255)                            agcaCCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTaga                                                                                                                    >  2:204941/1‑149 (MQ=255)                             gcaCCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGaaa                                                                                                                         <  1:108475/143‑1 (MQ=255)                              cccagggCACGGCTGGGCCGGAAGTCGCTGCCGTTCTCAAACTCGGTGGGGCGGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGGTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAgaga                                                                                                                  <  2:47474/144‑1 (MQ=17)                                   ggCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTagag                                                                                                                   <  1:32171/143‑1 (MQ=255)                                    gCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAgaga                                                                                                                  >  1:43854/1‑143 (MQ=255)                                         gCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTGAAGctaata                                                                                                             >  1:15457/1‑143 (MQ=255)                                                cGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGaaaa                                                                                                <  2:233433/149‑1 (MQ=255)                                                     gTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAatatat                                                                                           >  2:344362/1‑149 (MQ=255)                                                        gCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAACACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATCAGAGATAATATTGGCACAGAAAATATATTCa                                                                                        >  2:428071/1‑149 (MQ=255)                                                             cGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTc                                                                                         <  1:18084/143‑1 (MQ=255)                                                              gTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCgg                                                                                  >  2:139169/1‑148 (MQ=255)                                                                            tGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAGCACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAACATATATTCAGTTCGTTTAGTGAt                                                                          <  1:389415/143‑1 (MQ=255)                                                                                                 tCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGAACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATg                                               >  2:18486/1‑149 (MQ=255)                                                                                                 tCGGGCATTATCTGAACATAAAACACTATCAATAAGTTCAAGTCATTACCCACAATAAAAGTAACTATTTTGAAATTAGAGTTAATATTGGCACAGAAAATATATTCAGTTCATTTAGTGATTTCTCTTCATTCCTACACGac                                                     >  1:212544/1‑142 (MQ=37)                                                                                                        ttATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAgtt                                        >  2:446749/1‑149 (MQ=255)                                                                                                           tCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACa                                           <  1:492557/143‑1 (MQ=255)                                                                                                           tCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAgttgtt                                     <  2:224558/149‑1 (MQ=255)                                                                                                                  aTAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTc                                    <  1:520449/143‑1 (MQ=255)                                                                                                                    aaaaCACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCat                                  <  1:419788/143‑1 (MQ=255)                                                                                                                           tATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGCAATCATGGACAGTTGTTCATAATAATCAAAAgg                     >  2:260935/1‑149 (MQ=255)                                                                                                                               aaTAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCaaaa                       <  1:304100/143‑1 (MQ=255)                                                                                                                                  taattagAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCAAAAGGa                    <  1:58872/137‑1 (MQ=255)                                                                                                                                        gAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAAGATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCAAAAGGAAACAAAAATCAt        >  2:335703/1‑149 (MQ=255)                                                                                                                                        gAGTCATTACCGACATTAAAAGTAACTTTGTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCAAAAGGAAACAAAAATCAt        <  2:31754/149‑1 (MQ=255)                                                                                                                                         aGTCATTACCGACATTAAAAGTAACTTTTTTGCAATTAGAGATCATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATAAAAAGGAAACaaaa             >  1:494700/1‑143 (MQ=255)                                                                                                                                           tCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCAAAAGGAAACAAAAATCATTGt     >  2:6832/1‑149 (MQ=255)                                                                                                                                             aTTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATGATAATCAAAAGGAAACAAAAATCa         >  1:83772/1‑143 (MQ=255)                                                                                                                                              ttACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCAAAAGGAAACAAAAATCATTGTaaa  <  2:558470/149‑1 (MQ=255)                                                                                                                                              ttACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCAAAAGGAAACAAAAATCATTGTaaa  <  2:601891/149‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                 TTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCAAAAGGAAACAAAAATCATTGTAAA  >  CP009273/3577410‑3577699

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ 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.