New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	= 1046001	NA (NA)	27 (0.850)	21/166	0.3	93.1%	intergenic (+15/+418)	BW25113_RS05135/cspH	IS1‑like element IS1D family transposase/cold shock‑like protein CspH
	?	NZ_CP009273	= 1903046	2 (0.060)					intergenic (‑23/‑136)	mgrB/yobH	PhoP/PhoQ regulator MgrB/YobH family protein

TCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACAATACGTACGCTTGAGATCAGGATTGTCTACTTTGAGTATAACATCCTTGTGAAATCTCCCTTTCCTCATACCGCTTGCAC  >  NZ_CP009273/1045919‑1046085                                                                                   |                                                                                     tctcAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACAAta                                                                               >  2:784880/1‑90 (MQ=33) tctcAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACAAta                                                                               <  2:131470/90‑1 (MQ=33)    cAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACAAtacgt                                                                            <  2:927666/90‑1 (MQ=38)      aaaTCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACAAtacgtac                                                                          <  1:876364/90‑1 (MQ=40)           ggTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACAATACGTACGCTTg                                                                     <  2:927671/90‑1 (MQ=255)           ggTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACAATACGTACGCTTg                                                                     <  2:602194/90‑1 (MQ=255)                    gCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACAATACGTACGCTTGAGATCAGGa                                                            <  1:178043/90‑1 (MQ=255)                      aTGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACAAtacgt                                                                            <  2:940041/72‑1 (MQ=39)                      aTGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACAAtacgt                                                                            >  1:940041/1‑72 (MQ=39)                      aTGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACAATACGTACGCTTGAGATCAGGAtt                                                          >  1:10369/1‑90 (MQ=255)                            aaGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACAATACGTACGCTTGAGATCAGGATTGTCTAc                                                    >  1:552748/1‑90 (MQ=255)                              gTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACAATACGTACGCTTGAGATCAGGATTGTCTACtt                                                  <  1:463067/90‑1 (MQ=255)                              gTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACAATACGTACGCTTGAGATCAGGATTGTCTACtt                                                  <  2:393890/90‑1 (MQ=255)                              gTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACAATACGTACGCTTGAGATCAGGATTGTCTACtt                                                  >  1:905556/1‑90 (MQ=255)                                 aTCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACAATACGTACGCTTGAGATCAGGATTGTCTACTTTGa                                               >  2:256078/1‑90 (MQ=255)                                                       aaCACTATCAATAAGTTGGAGTCATTACCGACAATACGTACGCTTGAGATCAGGATTGTCTACTTTGAGTATAACATCCTTGTGAAAtct                         <  1:784880/90‑1 (MQ=255)                                                           cTATCAATAAGTTGGAGTCATTACCGACAATACGTACGCTTGAGATCAGGATTGTCTACTTTGAGTATAACATCCTtgt                                >  2:482754/1‑79 (MQ=255)                                                           cTATCAATAAGTTGGAGTCATTACCGACAATACGTACGCTTGAGATCAGGATTGTCTACTTTGAGTATAACATCCTtgt                                <  1:482754/79‑1 (MQ=255)                                                           cTATCAATAAGTTGGAGTCATTACCGACAATACGTACGCTTGAGATCAGGATTGTCTACTTTGAGTATAACATCCTTGTGAAATCTCCCt                     <  1:902009/90‑1 (MQ=255)                                                                    aGTTGGAGTCATTACCGACAATACGTACGCTTGAGATCAGGATTGTCTACTTTGAGTATAACATCCTTGTGAAATCTCCCTTTCCTCATa            <  1:189412/90‑1 (MQ=255)                                                                       tGGAGTCATTACCGACAATACGTACGCTTGAGATCAGGATTGTCTACTTTGAGTATAACATCCTTGTGAAATCTCCCTTTCCTCATACCg         >  2:821956/1‑90 (MQ=255)                                                                         gAGTCATTACCGACAATACGTACGCTTGAGATCAGGATTGTCTACTTTGAGTATAACATCCTTGTGAAATCTCCCTTTCCTCATACCGCt       <  2:67548/90‑1 (MQ=255)                                                                         gAGTCATTACCGACAATACGTACGCTTGAGATCAGGATTGTCTACTTTGAGTATAACATCCTTGTGAAATCTCCCTTTCCTCATACCGCt       <  1:683213/90‑1 (MQ=255)                                                                         gAGTCATTACCGACAATACGTACGCTTGAGATCAGGATTGTCTACTTTGAGTATAACATCCTTGTGAAATCTCCCTTTCCTCATACCGCt       <  1:373507/90‑1 (MQ=255)                                                                         gAGTCATTACCGACAATACGTACGCTTGAGATCAGGATTGTCTACTTTGAGTATAACATCCTTGTGAAATCTCCCTTTCCTCATACCGCt       <  1:795674/90‑1 (MQ=255)                                                                           gTCATTACCGACAATACGTACGCTTGAGATCAGGATTGTCTACTTTGAGTATAACATCCTTGTGAAATCTCCCTTTCCTCATACCGCTTg     <  2:10369/90‑1 (MQ=255)                                                                           gTCATTACCGACAATACGTACGCTTGAGATCAGGATTGTCTACTTTGAGTATAACATCCTTGTGAAATCTCCCTTTCCTCATACCGCTTg     <  1:493326/90‑1 (MQ=255)                                                                           gTCATTACCGACAATACGTACGCTTGAGATCAGGATTGTCTACTTTGAGTATAACATCCTTGTGAAATCTCCCTTTCCTCATACCGCTTg     <  2:135422/90‑1 (MQ=255)                                                                              aTTACCGACAATACGTACGCTTGAGATCAGGATTGTCTACTTTGAGTATAACATCCTTGTGAAATCTCCCTTTCCTCATACCGCTTGCAc  <  2:131435/90‑1 (MQ=255)                                                                                   |                                                                                     TCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACAATACGTACGCTTGAGATCAGGATTGTCTACTTTGAGTATAACATCCTTGTGAAATCTCCCTTTCCTCATACCGCTTGCAC  >  NZ_CP009273/1045919‑1046085

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ 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.