New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1979486 =	2 (0.050)	55 (1.360)	41/284	0.0	96.5%	intergenic (‑271/‑267)	insA/uspC	IS1 repressor TnpA/universal stress protein
	?	NC_000913	2101749 =	NA (NA)					intergenic (‑5/+146)	wbbL/insH1	pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator

TTCACAGTACATAAAGTAACCTTGATCGAAGCCATTTACACGCACAAAATCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGAT‑TTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTA  >  NC_000913/2101609‑2101884                                                                                                                                             |                                                                                                                                         ttCACAGTACATAAAGTAACCTTGATCGAAGCCATTTACACGCACAAAATCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTaagga                                                                                                                                        >  1:31260/1‑143 (MQ=255) ttCACAGTACATAAAGTAACCTTGATCGAAGCCATTTACACGCACAAAATCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATAAACAACCACAACAAAATAGGTACTTCTATCAGAAATTTTTGTATTATTaagga                                                                                                                                        >  2:650808/1‑143 (MQ=255)  tCACAGTACATAAAGTAACCTTGATCGAAGCCATTTACACGCACAAAATATGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTaaggaa                                                                                                                                       <  2:285008/143‑1 (MQ=255)  tCACAGTACATAAAGTAACCTTGATCGAAGCCATTTACACGAACAAAATCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTaatgaa                                                                                                                                       >  2:721816/1‑143 (MQ=255)      aGTACATAAAGTAACCTTGATCGAAGCCATTTACACGCACAAAATCTGACAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACATACTTAAGGAATTTTTGAATTAATAAGGAAGGTg                                                                                                                                   >  2:319433/1‑143 (MQ=255)       gTACATAAAGTAACCTTGATCGAAGCCATTTACACGCACAAAATCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGc                                                                                                                                  >  1:387078/1‑143 (MQ=255)        tACATAAAGTAACCTTGATCGAAGCCATTTACACGCACAAAATCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCg                                                                                                                                 >  2:596636/1‑143 (MQ=255)           aTAAAGTAACCTTGATCGAAGCCATTTACACGCACAAAATCTGAAAAACGTACCAGCATAACTGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAAt                                                                                                                              >  1:692620/1‑143 (MQ=255)                   gccTTCATCAAATACATTTACATGCATAAAATCTGAACAACGCACCAGTATAAATGATCCTGCGCACCAATCAACGACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCgggg                                                                                                                      <  1:734283/142‑1 (MQ=255)                   aCCTTGATCGAAGCCATTTACACGCACAAAATCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCgggg                                                                                                                      >  1:447052/1‑143 (MQ=255)                             aaGTCATTTACACGCACAAAATCTGAAAAACTTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTAACAGAAAAGATAGTTTCTTTAGGAATTTTTGTTTTATTAGGGAAGGTGCGAATAAGCGGGGAAATtcttct                                                                                                            <  2:84406/143‑1 (MQ=39)                                  acgtagaggCACAACATCTGAAAAGCGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCACAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCt                                                                                                       <  1:567856/135‑1 (MQ=38)                                      aaactcacaAAATCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAGTCAACAACCTTATCAGAATAGTTACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACt                                                                                                   <  1:568924/138‑1 (MQ=255)                                       tactcacaAAGTATGAAAAACGTACAAGCATAAAAGAACATGCGCACCAAACAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTc                                                                                                  <  2:79314/139‑1 (MQ=37)                                        acGCACAAAATCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTCTTAAGGCAGGTGCGAATAACCGTGGCAACTCTTCTCGCCtctctcc                                                                                                 >  2:540290/1‑137 (MQ=255)                                        acGCACAAAATCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGAcaca                                                                                                 >  1:96388/1‑143 (MQ=255)                                              aaaaTCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCACttatt                                                                                           >  2:334850/1‑143 (MQ=255)                                                  tCTGAAAAACGTACCAGCATAAATTATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGtcatttcat                                                                                       <  2:453201/143‑1 (MQ=255)                                                    tGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATATACAACCGTATCAGAATAGATACTTTCTTTAGGGATTTTTGGCTGATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTcatttcattt                                                                                     <  2:268939/143‑1 (MQ=37)                                                                   cATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGATTGAGct                                                                      >  1:107365/1‑142 (MQ=255)                                                                   cATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCACGGCTGACTCAGTCATTTCATATCTTCATGTTTGAGcc                                                                      >  2:541267/1‑143 (MQ=255)                                                                      aaaTGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCAGCTGACACAGACAATTCATTTCTTCATGTTTGAGCCGAt                                                                   >  2:175778/1‑143 (MQ=255)                                                                      aaaTGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAACGTGCGAATAAGCGGCGAAATTCTTCTCGCCTGACTCAGTCTTTTCATTTCTTCATGttttcgcctat                                                                   >  1:248206/1‑135 (MQ=255)                                                                         tGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGCATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAATTTCTTCTTGGCTGACTCAGTCAATTCATTTCTTCATGTTTGAAACAAt‑ttt                                                               >  2:462908/1‑143 (MQ=25)                                                                           aTCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGAt‑ttttt                                                             <  1:292805/143‑1 (MQ=255)                                                                              ctacgcACCAATCAACAACCGTATCAGAAAAGATACTTTCTGTAGGAATTTTTGTTTTATGAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGAT‑TTTTtctc                                                          <  2:146814/140‑1 (MQ=255)                                                                                gcgcACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGAT‑TTTTTCTccc                                                        >  1:53170/1‑143 (MQ=255)                                                                                       aaTCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTATTCATGTTTGAGCCGAT‑TTTTTCTCACGTAACTg                                                 >  2:242972/1‑143 (MQ=255)                                                                                       aaTCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTAATTTCATTTCTTCATGTTTGAGCAGAT‑TTTTTCTCCCGTAAATg                                                 >  2:120514/1‑143 (MQ=255)                                                                                           agtatcgttgtCATAATACATACTTTCTTTAGGAATTTTTGTTTTATTAATTAAGGTTCGAATACGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGAT‑TTTTTCTCCCGTAAATGCCtt                                             <  1:231849/133‑1 (MQ=17)                                                                                           aacaacCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGAT‑TTTTTCTCCCGTAAATGCCtt                                             <  2:669456/143‑1 (MQ=255)                                                                                           aacaacCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGAT‑TTTTTCTCCCGTAAATGCCtt                                             <  2:387078/143‑1 (MQ=255)                                                                                              aacCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGAT‑TTTTTATCCCGTAAATGAATTGaa                                          >  2:300095/1‑143 (MQ=255)                                                                                                     tCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAACGAAGTTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCCTTTCTTCATGTTTG‑GTGTATCTCCTTCTCACGTAAATGCCTTGAATCactct                                   >  1:314561/1‑139 (MQ=18)                                                                                                            aGATACGTTCTTTAGGAATGTTTGTTGTATGAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTGATTTCATTTCTTCATGTTTGAGCCGAT‑TTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGa                            <  2:248206/143‑1 (MQ=14)                                                                                                             gATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGAT‑TTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGAc                           >  2:401776/1‑143 (MQ=255)                                                                                                             gATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGAT‑TTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGAc                           <  1:392038/143‑1 (MQ=255)                                                                                                               tACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATGTCTTCATGTTTGTGCCGCT‑TTTTTCTTCCTTGTAAACTTTTAATCATCCTAttaaaaaag                         >  2:349726/1‑136 (MQ=17)                                                                                                                    tctttAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGAT‑TTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTttct                    <  1:533367/143‑1 (MQ=255)                                                                                                                       ttAGGAATTTTTGTTTTATTAAGGAAGCTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGAT‑TTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCg                 <  1:34317/143‑1 (MQ=255)                                                                                                                         aGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGAT‑TTTTTCTCCCGTAACTGCCTTCAATCAGCCTATTTAGACCGTTTCTTCTcc               >  1:109351/1‑143 (MQ=255)                                                                                                                         aGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGAT‑TTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGcc               >  1:601352/1‑143 (MQ=255)                                                                                                                                    ttttATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGAT‑TTTTTCTCCCGTAAAAGAATTAAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAAGCGt    >  2:577219/1‑143 (MQ=11)                                                                                                                                     tttATTAATGAAGGTGCGAATAAGCGGGGAGATTCTTCTCGGCTGGTTCAGTCATTTCATTTCTTCATGTTTGAGCCGAT‑TTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGtt   <  1:544909/143‑1 (MQ=255)                                                                                                                                      ttattaAGGAAGGTGCGAATAAGCTGGGCAATTCTTCTCGGCTGACTCATTCATTTCATTTCTTCATATTAGAGCAGAT‑TTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCgatg  >  2:337855/1‑140 (MQ=11)                                                                                                                                             |                                                                                                                                         TTCACAGTACATAAAGTAACCTTGATCGAAGCCATTTACACGCACAAAATCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGAT‑TTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTA  >  NC_000913/2101609‑2101884

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ 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.