New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	= 3360109	NA (NA)	9 (0.590)	9/272	NT	56.2%	noncoding (1/1195 nt)	IS5	repeat region
	?	CP009273	3370794 =	7 (0.460)					intergenic (‑15/+380)	sspA/rpsI	stringent starvation protein A, phage P1 late gene activator, RNAP‑associated acid‑resistance protein, inactive glutathione S‑transferase homolog/30S ribosomal subunit protein S9

CCTTTTCCACGTGTTCGATCTCGAAACTTACACCTTTCTCAGCCAGCACAATGCGGACCTGATGGCTATAGATGTCAGTAGGACCGGAAAACAGCGTCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCTCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGTTCGAAAATCAAACAAAAAATGAGCAATACCCGACATTTGGGCAGAAAATTGGATGATAGTTTACC  >  CP009273/3370650‑3370939                                                                                                                                                 |                                                                                                                                                  acaagaaaatctcttttctggtctgacggcgcttactgctgaattcactgtcggcgaaggtaagttgatgactcatgatgaaccctgttctatggctccagatgacaaacatgatctcatatcagggacttgttcgcaccttccATAGt                                                                                                                                               <  2:60939‑M2/5‑1 (MQ=255)   acgaaaatcctctttctggtctgacggcgcttactgctgaattcactttcgccgaaggtaagttgatgcctcatgatgaaccctgttctatggctccagatgaccaacatgctctcatatcagggacttgttcgcaccttccAt                                                                                                                                                  <  1:101663‑M2/2‑1 (MQ=255)     gaaaatctcttttcgggtctgacggcgcttactgctgaattcactgtcggcgaaggtaagttgatgactcatgatgaaccctgttctatggttctagatgacaaacatgatctcatatcagggacttgtgcgcaccttccATAGTCAGa                                                                                                                                           <  2:93594‑M2/9‑1 (MQ=255)                    ctcGAAACTTACACCTTTCTCAGCCAGCACAATGCGGACCTGATGGCTATAGATGTCAGTAGGACCGGAAAACAGCGTCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCTCCAGGTATAGGCAGAATTTTTACTg                                                                                                                                 >  1:168924/1‑144 (MQ=255)                                                ctgtcggcgaaggtaagttgatgactcatgatgaaccctgttctatggctccagatgacaaacatgatctcatatcagggacttgttcgcaccttccATAGTCAGAATTTTTACTGCTACCGGCCAGCCGGTGGccagacagag                                                                                                     >  1:122842‑M2/98‑143 (MQ=255)                                                       ggACCTGATGGCTATAGATGTCAGTAGGACCGGAAAACAGCGTCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCTCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTgtgt                                                                                              <  1:93438/144‑1 (MQ=255)                                                            tGATGGCTATAGATGTCAGTAGGACGGGAAAACAGCGTCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCTCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATaa                                                                                    >  2:129522/1‑149 (MQ=255)                                                            gtaagttgatgactcatgatgaaccctgttctatggctccagatgacaaacatgatctcatatcagggacttgttcgcaccttccATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATaa                                                                                    <  2:40974‑M2/64‑1 (MQ=255)                                                                         tcaggatgaaccctcttctatggctccagatgacaaacatgatctcatatcagggacttgttcgcaccttccATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGAc                                                                            <  1:135404‑M2/72‑1 (MQ=255)                                                                            catgagtaCCGGAAAACAGCGTCATTACCGAACGGTTGTTGGCAGCGACAGACATGAAAACCTCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGActct                                                                         <  1:97455/137‑1 (MQ=255)                                                                             gatgaaccctgttctatggctccagatgacaaacatgatctcatatcagggacttgttcgcaccttccATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGt                                                                   >  2:252335‑M2/69‑149 (MQ=255)                                                                                               gctccatatgacaaacatgatctcatatcagggacttgttcgcaccttccATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGTTCGAAAATcaaac                                                      <  1:250408‑M2/94‑1 (MQ=255)                                                                                                                                   tgttcgcaccttccATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGTTCGAAAATCAAACTAAAAATGAGCAATAACCGACATTTGGGCAGAAAATTGgat             <  2:129696‑M2/135‑1 (MQ=255)                                                                                                                                      tcgcaccttccATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGTTCGAAAATCAAACAAAAAATGAGCAATACCCGACATTTGGGCAGAAAATTgg               <  1:123246‑M2/133‑1 (MQ=255)                                                                                                                                      aaCCTCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGTTCGAAAATCAAACAAAAAATGAGCAATACCCGACATTTGGGCAGAAAATTGgatgat          >  2:153163/1‑149 (MQ=255)                                                                                                                                      aaCCTCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGAGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGTTCGAAAATCAAACAAAAAATGAGCAATACCCGACATTTGGGCAGAAAATTGgatgat          >  2:19451/1‑149 (MQ=255)                                                                                                                                         cTCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGATGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGTTCGAAAATCAAACAAAAAATGAGCAATACCCGACATTTGGGCAGAAAATTGGATGATAGt       >  2:160734/1‑149 (MQ=255)                                                                                                                                           ccttccATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGTTCGAATATCAAATAAAAAATGAGCAATACCCGACATTTGGGCAGAAAATTGGATGATAGttt     <  2:136855‑M2/143‑1 (MQ=255)                                                                                                                                              tccATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCAAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGTTCGAAAATCAAACAAAAAATGAGCAATACCCGACATTTGGGCAGAAAATTGGATGATAGTTTAcc  <  2:103634‑M2/146‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                  CCTTTTCCACGTGTTCGATCTCGAAACTTACACCTTTCTCAGCCAGCACAATGCGGACCTGATGGCTATAGATGTCAGTAGGACCGGAAAACAGCGTCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCTCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGTTCGAAAATCAAACAAAAAATGAGCAATACCCGACATTTGGGCAGAAAATTGGATGATAGTTTACC  >  CP009273/3370650‑3370939

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