New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	= 1391495	NA (NA)	19 (0.380)	17/276	NT	65.5%	intergenic (+146/‑127)	insH1/ynaJ	IS5 transposase and trans‑activator/DUF2534 family putative inner membrane protein
	?	CP009273	= 1972751	10 (0.200)					intergenic (‑297/‑483)	flhD/uspC	flagellar class II regulon transcriptional activator, with FlhC/universal stress protein

GGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCT‑TATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATGG  >  CP009273/1391356‑1391631                                                                                                                                             |                                                                                                                                         gggATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCT‑TATTCGCACCTTCCCTAACTAAt                                                                                                                                 <  1:1749/149‑1 (MQ=32) gggATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCT‑TATTCGCACCTTCCCTAACTAAt                                                                                                                                 <  1:393324/149‑1 (MQ=32) gggATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCT‑GATTCGCACCTTCCCTAACTAAt                                                                                                                                 >  1:201229/1‑149 (MQ=17)                aTGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCT‑TATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGt                                                                                                                  <  1:518320/149‑1 (MQ=255)                  ggCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCT‑TATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTaa                                                                                                                <  1:663934/149‑1 (MQ=255)                     gaagaaACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAG‑ATTTCTGTGATGGATATCCACCTTCCCTCACTAATCAATGCGTTGATTGTAAATc                                                                                                             >  2:413779/1‑149 (MQ=14)                        gaaACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCT‑TATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAg                                                                                                          <  1:115168/149‑1 (MQ=255)                              gTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCT‑TATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAaga                                                                                                    >  2:307602/1‑149 (MQ=255)                               tCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCT‑TATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAagag                                                                                                   <  2:207718/149‑1 (MQ=255)                                                aaGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCT‑TATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCa                                                                                  <  2:841397/149‑1 (MQ=255)                                                  ggCATTTACGTGAGAAAAAATCGGCTCAAACATGACGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCT‑TATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGa                                                                                <  1:483968/149‑1 (MQ=255)                                                  ggCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCT‑TATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGa                                                                                <  2:140034/149‑1 (MQ=255)                                                       ttACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCT‑TATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACg                                                                           <  2:838916/149‑1 (MQ=255)                                                           gggAGAAAAAATCGGCTCCAACCTGCAGAAATGGAATGCCTGCGCCCGCCGAGAAGGCTCTCCCCGCT‑TATTCGCCGCTTCCCTGGCTAATCAGTTCGTTGATTGTGAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGa                                                                       <  1:637563/149‑1 (MQ=255)                                                                 aaaaaTCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCT‑TATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTc                                                                 <  1:307602/149‑1 (MQ=255)                                                                   aaaTCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCT‑TATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCAt                                                               <  1:56824/149‑1 (MQ=255)                                                                         gCTTAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCT‑TATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGCGGTGAGGTTTTCAGTGCAGACAACGGTGAAATGTCATGGTAtt                                                         <  2:389846/149‑1 (MQ=255)                                                                               aCATGAAGAAATGAAATGAATGAGTCAGCCGAGAAGAATTTCCCCGCT‑TATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACg                                                   >  2:630189/1‑149 (MQ=255)                                                                                    aagaaATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCT‑TATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAg                                              <  2:500608/149‑1 (MQ=255)                                                                                    aagaaATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCT‑TATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAg                                              <  2:736979/149‑1 (MQ=255)                                                                                    aagaaATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCT‑GATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAg                                              <  1:449368/149‑1 (MQ=255)                                                                                     agaaATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCT‑TATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTTAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAgg                                             <  2:598674/149‑1 (MQ=255)                                                                                     agaaATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCT‑TATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAgg                                             <  2:598531/149‑1 (MQ=255)                                                                                     agaaATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCT‑TATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCGAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAgg                                             <  1:826886/149‑1 (MQ=255)                                                                                        aatgaaatgaCTGAGTCAGCCGAGAAGAATTTCCCCGCT‑TATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGCGCAGCCAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTaa                                          >  2:377655/1‑149 (MQ=255)                                                                                          tgaaatgaCTGAGTCAGCCGAGAAGAATTTCCCCGCT‑TATTCGCACCTTCCTTAAGTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACa                                        >  2:108287/1‑149 (MQ=255)                                                                                                     aGTCAGCCGAGAAGAATTTCCCCGCT‑TATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTc                             >  2:719029/1‑149 (MQ=255)                                                                                                         aGCCGAGAAGAATTTCCCCGCT‑TATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGGGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTATGca                         >  2:286213/1‑149 (MQ=255)                                                                                                            cGAGAAGAATTTCCCCGCT‑TATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAGATCCACCTAAGAGGCAAGGTATTCAGAACAGACAAAGGTTAAATGTAATGGTATTATTAGGATTAGGTAAAAAGAAATTTAGCTGcacga                      >  1:284712/1‑147 (MQ=25)                                                                                                            cGAGAAGAATTTCCCCGCT‑TATTCGCACCTTCCCTAACTAATCAATGCGTTGATAGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTTAAATGTCATGGTATTGTTACGTTTAGGTAAGAAGAAGTTTGTCTGcacac                      >  1:744861/1‑148 (MQ=255)                                                                                                            cGAGAAGAATTTCCCCGCT‑TATTCGCACCGTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGATAAGAGGTGAGGTTTTCAGAGCAGATAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACaa                      >  2:550304/1‑149 (MQ=255)                                                                                                             gagaAGAATTTCCCCGCT‑TATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAg                     >  2:607481/1‑149 (MQ=255)                                                                                                                                 atgcGCACCTTCCCTAACTAAGCAAGGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATgg  <  1:295999/146‑1 (MQ=255)                                                                                                                                             |                                                                                                                                         GGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCT‑TATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATGG  >  CP009273/1391356‑1391631

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.