New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	= 1046001	NA (NA)	14 (0.670)	11/166	0.6	82.3%	intergenic (+15/+418)	BW25113_RS05135/cspH	IS1‑like element IS1D family transposase/cold shock‑like protein CspH
	?	NZ_CP009273	= 1903046	3 (0.140)					intergenic (‑23/‑136)	mgrB/yobH	PhoP/PhoQ regulator MgrB/YobH family protein

TCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACAATACGTACGCTTGAGATCAGGATTGTCTACTTTGAGTATAACATCCTTGTGAAATCTCCCTTTCCTCATACCGCTTGCAC  >  NZ_CP009273/1045919‑1046085                                                                                   |                                                                                     tctcAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACAAta                                                                               <  1:276794/90‑1 (MQ=33) tctcAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACAAta                                                                               <  1:579796/90‑1 (MQ=33)    cAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACAAtacgt                                                                            <  2:520594/90‑1 (MQ=38)      aaaTCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACAAtacgtac                                                                          >  1:103446/1‑90 (MQ=40)                    gCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACAATACGTACGCTTGAGATCAGGa                                                            >  1:169518/1‑90 (MQ=255)                    gCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACAATACGTACGCTTGAGATCAGGa                                                            <  2:43882/90‑1 (MQ=255)                     cATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACAATACGTACGCTTGAGATCAGGAt                                                           <  2:169518/90‑1 (MQ=255)                      aTGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACAATACGTACGCTTGAGATCAGGAtt                                                          <  1:118836/90‑1 (MQ=255)                              gTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACAATACGTACGCTTGAGATCGGGATTGTCTACtt                                                  >  1:359533/1‑90 (MQ=255)                              gTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACAATACGTACGCTTGAGATCAGGATTGTCTACtt                                                  <  2:253683/90‑1 (MQ=255)                              gTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACAATACGTACGCTTGAGATCAGGATTGTCTACtt                                                  <  2:358036/90‑1 (MQ=255)                                cATCGGGCATTATCTGAACATAAAACTCTATCAATAAGTTGGAGTCATTACCGACAATACGTACGCTTGAGATCAGGATTGTCTACTTTg                                                <  2:331626/90‑1 (MQ=255)                                            tCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACAATACGTACGCTTGAGATCAGGATTGTCTACTTTGAGTATAACATcc                                    <  2:491197/90‑1 (MQ=255)                                               gAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACAATACGTACGCTTTAGATCAGGATTGTCTACTTTGAGtata                                          <  1:297997/81‑1 (MQ=255)                                               gAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACAATACGTACGCTTTAGATCAGGATTGTCTACTTTGAGtata                                          >  2:297997/1‑81 (MQ=255)                                                    tAAAACACTATCAATAAGTTGGAGTCATTACCGACAATACGTACGCTTGAGATCAGGATTGTCTACTTTGAGTATAACATCCTTGTGaaa                            <  2:458065/90‑1 (MQ=255)                                                      aaaCACTATCAATAAGTTGGAGTCATTACCGACAATACGTACGCTTGAGATCAGGATTGTCTACTTTGAGTATAACATCCTTGTGAAAtc                          >  2:251961/1‑90 (MQ=255)                                                                     gTTGGAGTCATTACCGACAATACGTACGCTTGAGATCAGGATTGTCTACTTTGAGTATAACATCCTtgt                                >  1:259011/1‑69 (MQ=255)                                                                     gTTGGAGTCATTACCGACAATACGTACGCTTGAGATCAGGATTGTCTACTTTGAGTATAACATCCTtgt                                <  2:259011/69‑1 (MQ=255)                                                                           gTCATTACCGACAATACGTACGCTTGAGATCGGGATTGTCTACTTTGAGTATAACATCCTTGTGAAATCTCCCTTTCCTCATACCGCTTg     <  2:359533/90‑1 (MQ=255)                                                                           gTCATTACCGACAATACGTACGCTTGAGATCAGGATTGTCTACTTTGAGTATAACATCCTTGTGAAATCTCCCTTTCCTCATACCGCTTg     <  1:98482/90‑1 (MQ=255)                                                                             cATTACCGACAATACGTACGCTTGAGATCAGGATTGTCTACTTTGAGTATAACATCCTTGTGAAATCTCCCTTTCCTCATACCGCTTGCa   >  1:32006/1‑90 (MQ=255)                                                                             cATTACCGACAATACGTACGCTTGAGATCAGGATTGTCTACTTTGAGTATAACATCCTTGTGAAATCTCCCTTTCCTCATACCGCTTGCa   <  2:103446/90‑1 (MQ=255)                                                                              aTTACCGACAATACGTACGCTTCAGATCAGGATTGTCTACTTTGAGTATAACATCCTTGTGAAATCTCCCTTTCCTCATACCGCTTGCAc  <  1:601752/90‑1 (MQ=255)                                                                                tACCGACAATACGTACGCTTGAGATCAGGATTGTCTACTTTGAGTATAACATCCTTGTGAAATCTCCCt                     >  1:177422/1‑69 (MQ=255)                                                                                tACCGACAATACGTACGCTTGAGATCAGGATTGTCTACTTTGAGTATAACATCCTTGTGAAATCTCCCt                     <  2:177422/69‑1 (MQ=255)                                                                                   |                                                                                     TCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACAATACGTACGCTTGAGATCAGGATTGTCTACTTTGAGTATAACATCCTTGTGAAATCTCCCTTTCCTCATACCGCTTGCAC  >  NZ_CP009273/1045919‑1046085

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ 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.