New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	= 254374	0 (0.000)	44 (1.430)	21/166	0.3	100%	coding (59/402 nt)	crl	sigma factor‑binding protein Crl
	?	NZ_CP009273	269667 =	NA (NA)					intergenic (+3/+145)	ykfC/BW25113_RS01325	reverse transcriptase domain‑containing protein/IS5‑like element IS5 family transposase

CAGTCGTTATGGCGAGATGCGAGTGGTCTCAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGT  >  NZ_CP009273/269580‑269749                                                                                        |                                                                                   cAGTCGTTATGGCGAGATGCGAGTGGTCTCAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGaa                                                                                  >  2:566790/1‑90 (MQ=255) cAGTCGTTATGGCGAGATGCGAGTGGTCTCAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGaa                                                                                  <  1:118777/90‑1 (MQ=255)   gTCGTTATGGCGAGATGCGAGTGGTCTCAACGATCCCGCAGGAGAAGGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAgg                                                                                >  2:542870/1‑90 (MQ=255)   gTCGTTATGGCGAGATGCGAGTGGTCTCAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAgg                                                                                <  2:743044/90‑1 (MQ=255)   gTCGTTATGGCGAGATGCGAGTGGTCTCAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAgg                                                                                <  1:279163/90‑1 (MQ=255)              gagaTGCGAGTGGTCTCAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGc                                                                     <  2:896962/90‑1 (MQ=255)                gaTGCGAGTGGTCTCAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCgg                                                                   >  1:852671/1‑90 (MQ=255)                      aGTGGTCTCAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAAt                                                             <  2:550322/90‑1 (MQ=255)                              cAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCg                                                     >  2:318730/1‑90 (MQ=255)                                   aTCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGa                                                >  1:550085/1‑90 (MQ=255)                                      ccGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTc                                             <  1:75408/90‑1 (MQ=255)                                          aGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGtc                                         <  2:15835/90‑1 (MQ=255)                                            gagaAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGtcat                                       >  1:276756/1‑90 (MQ=255)                                                aaGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGtcatttca                                   <  1:610054/90‑1 (MQ=255)                                                aaGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGtcatttca                                   <  2:852671/90‑1 (MQ=255)                                                aaGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGtcatttca                                   <  1:705717/90‑1 (MQ=255)                                                     aGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGaa                                                                          <  1:818164/46‑1 (MQ=255)                                                     aGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGaa                                                                          >  2:818164/1‑46 (MQ=255)                                                       aaaCTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATttcttc                            <  2:866040/90‑1 (MQ=255)                                                            tCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGtcatttca                                   >  2:264486/1‑78 (MQ=255)                                                            tCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGtcatttca                                   >  2:460501/1‑78 (MQ=255)                                                            tCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGtcatttca                                   <  1:460501/78‑1 (MQ=255)                                                            tCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGtcatttca                                   <  1:264486/78‑1 (MQ=255)                                                                   aTCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCg                <  2:848407/90‑1 (MQ=255)                                                                         gACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGAttttt          <  1:632862/90‑1 (MQ=255)                                                                                 cagtATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGt  >  2:877801/4‑90 (MQ=18)                                                                                        |                                                                                   CAGTCGTTATGGCGAGATGCGAGTGGTCTCAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGT  >  NZ_CP009273/269580‑269749

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ 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.