New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	1972748 =	8 (0.450)	4 (0.220)	4/268	NT	33.3%	intergenic (‑294/‑486)	flhD/uspC	flagellar class II regulon transcriptional activator, with FlhC/universal stress protein
	?	CP009273	= 2283592	NA (NA)					noncoding (1/1195 nt)	IS5	repeat region

CTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAA  >  CP009273/1972603‑1972877                                                                                                                                                  |                                                                                                                                  gacaagaaaatctcttttctggtctgacggcgcttactgctgaattcactgtcggcgaaggtaagttgatgactcatgatgaaccctgttctatggctccagatgacaaacatgatctcatatcagggacttgttcgcaccttccTTaa                                                                                                                                >  1:105936‑M1/146‑149 (MQ=255)     cAAATAGAAATGGGTCCTTACACTTAACTAAGATTTTTCCAAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaa                                                                                                                            >  1:111443‑M2/1‑145 (MQ=255)                  gTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCa                                                                                                               <  1:257981/149‑1 (MQ=255)                       tACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAggc                                                                                                                >  2:199884/1‑141 (MQ=255)                         cacTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTTCTTAACATAAATGTATAAGTCATACtttt                                                                                                        <  1:202552/149‑1 (MQ=255)                          acTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaataagcgg                                                                                                             <  2:202083‑M2/143‑20 (MQ=255)                                      ttgtccccaaaTCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTTgg                                                                                                 <  2:172532/135‑1 (MQ=255)                                            cTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaataagcggggaaattcttctcggctg                                                                                           <  2:233819‑M2/143‑38 (MQ=255)                                                      gCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaataagcggggaaattcttctcggctgactcagtcatttcatt                                                                           <  1:249487‑M2/149‑54 (MQ=255)                                                             tACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaataagcggggaaattcttctcggctgactcagtcatttcatttcttcat                                                                    >  1:167222‑M2/1‑89 (MQ=255)                                                                tCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACACAACACTCAATTACTTAAggaaggttcgaataagcggggaaattcttctcggctgactcaggaatttcatttctt                                                                       <  2:5893‑M2/143‑58 (MQ=255)                                                                  ttgatgactcatgatgaaccctgttctatggctccagatgacaaacatgatctcatatcagggacttgttcgcaccttccTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGttttt                                                                     >  2:245326‑M1/81‑143 (MQ=255)                                                                  gTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAAGGTATCAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGttttt                                                                     >  2:241/1‑143 (MQ=255)                                                                    gatgactcatgatgaaccctgttctacggctccagatgacaaacatgacctcatatcagggacttgttcgcaccttccTTAACATAATTGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgctacgc                                                             >  1:193145‑M1/79‑149 (MQ=255)                                                                     aCTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgctacgct                                                            >  1:2655/1‑149 (MQ=255)                                                                                 tACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCaaaaa                                                <  1:296959/149‑1 (MQ=255)                                                                                                           caaacatgatctcatatcagggacttgttcgcaccttccTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGaaa                            <  2:298248‑M1/104‑1 (MQ=255)                                                                                                                             tCACACAAAACACTCAATTACTTAAggaaggtgcgaataagcgggaaaattcttctcggctgactcagtcacttcatttcttcatgtttgagccgattttttctcccgtaaatgccttgaatcagcccatttagaccgtttcttcgcca    <  1:229906‑M2/149‑125 (MQ=255)                                                                                                                              cacacaAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATa   >  1:320732/1‑149 (MQ=255)                                                                                                                                     gttcgcaccttccTTAACATAAATGGATAAGTCATACTTTTGTTGTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATaa  >  2:246472‑M1/14‑143 (MQ=255)                                                                                                                                                  |                                                                                                                                  CTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAA  >  CP009273/1972603‑1972877

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ 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.