New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	2564404 =	23 (0.840)	3 (0.110)	3/584	3.4	11.4%	intergenic (+32/‑119)	yffR/yffS	CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein
	?	NC_000913	2564423 =	24 (0.900)					intergenic (+51/‑100)	yffR/yffS	CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below cutoff threshold.

CCGCAAAAATAATGGGTCGCGACTACGCATGGAAACATGTAAAAGAAGACAGGTTGCCATGTCTGTTTGCCGCCGGGGTTGTTGCTGATAACATCCTGGTAAAATACCATTTCAGCAATGAAACTGAGTTCAAACTTAAAGCGGCAGCGGTCAGAGAATGCGCCAACGTAGCAGAAAACAACGGCTTTGTTTTGGTAGGTAGAGTATTTGAAAAACGTAATTGATTGCGAATAGCAACAACTAAACAACCAATACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGACAATATAAGGGCGCTCAACGTGGGGCCAAATGCGAGGAGATCGCAAACGAGTTAACTCGCCGGGGAGTTAAAAACAACAAGGGAGAGGTTATTACTAAGGGCGGCGTTAGCCATTGGCTGGAAGGTAGACGGGAGCCAAATTTCGAC  >  NC_000913/2564149‑2564723                                                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                                                                                             ccGCAAAAATAATGGGTCGCGACTACGCATGGAAACATGTAAAAGAAGACAGGTTGCCATGTCTGTTTGCCGCCGGGGTTGTTGCTGATAACATCCTGGTAAAATACCATTTCAGCAATGAAACTGAGTTCAAACTTAAAGCGGCAGCGGTCAGAGAATGCGCCAACGTAGCAGAAAACAACGGCTTTGTTTTGGTAGGTAGAGTATTTGAAAAACGTAATTGATTGCGAATAGCAACAACTAAACAACCAATACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCTTCATTATTcc                                                                                                                                                                                                                                                                                      >  1:6809/1‑299 (MQ=255)     tcagacgtgtgctcttccgatctcATGGAAACATGTAAAAGAAGACAGGTTGCCATGTCTGTTTGCCGCCGGGGTTGTTGCTGATAACATCCTGGTAAAATACCATTTCAGCAATGAAACTGAGTTCAAACTTAAAGCGGCAGCGGTCAGAGAATGCGCCAACGTAGCAGAAAACAACGGCTTTGTTTTGGTAGGTAGAGTATTTGAAAAACGTAATTGATTGCGAATAGCAACAACTAAACAACCAATACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCg                                                                                                                                                                                                                                                                                <  2:250226/278‑1 (MQ=255)       aaaTAATGGGTCGCGACTACGCATGGAAACATGTAAAAGAAGACAGGTTGCCATGTCTGTTTGCCGCCGGGGTTGTTGCTGATAACATCCTGGTAAAATACCATTTCAGCAATGAAACTGAGTTCAAACTTAAAGCGGCAGCGGTCAGAGAATGCGCCAACGTAGCAGAAAACAACGGCTTTGTTTTGGTAGGTAGAGTATTTGAAAAACGTAATTGATTGCGAATAGCAACAACTAAACAACCAATACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGtt                                                                                                                                                                                                                                                                              <  2:245495/301‑1 (MQ=255)                 tCGCGAATACGCATGGAAACATGTAAAAGAAGACAGGTTGCCATGTCTGTTTGCCGCCGGGGTTGTTGCTGATAACATCCTGGTAAAATACCATTTCAGCAATGAAACTGAGTTCAAACTTAAAGCGGCAGCGGTCAGAGAATGCGCCAACGTAGCAGAAAACAACGGCTTTGTTTTGGTAGGTAGAGTATTTGAAAAACGTAATTGATTGCGAATAGCAACAACTAAACAACCAATACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTAccc                                                                                                                                                                                                                                                                    <  2:6809/301‑1 (MQ=255)                    cgACTACGCATGGAAACAGGTAAAAGAAGACAGGTTGCCATGTCTGTTTGCCGCCGGGGTTGTTGCTGATAACATCCTGGTAAAATACCATTTCAGCAATGAAACTGAGTTCAAACTTAAAGCGGCAGCGGTAAGAGAATGCGCCAACGTAGCAGAAAACAACGGCTTTGTTTTGGTAGGTAGAGTATTTGAAAAACGTAATTGATTGCGAATAGCAACAACTAAACAACCAATACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTc                                                                                                                                                                                                                                                                  <  1:31692/300‑1 (MQ=255)                            cATGGAAACATGTAAAAGAAGACAGGTTGCCATGTCTGTTTGCCGCCGGGGTTGTTGCTGATAACATCCTGGTAAAATACCATTTCAGCAATGAAACTGAGTTCAAACTTAAAGCGGCAGCGGTCAGAGAATGCGCCAACGTAGCAGAAAACAACGGCTTTGTTTTGGTAGGTAGAGTATTTGAAAAACGTAATTGATTGCGAATAGCAACAACTAAACAACCAATACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCgagatcggaagagcgtcgtgtagg                                                                                                                                                                                                                                                         >  1:249915/1‑278 (MQ=255)                                       cacgacgctcttccgatctcATGTCTGTTTGCCGCCGGGGTTGTTGCTGATAACATCCTGGTAAAATACCATTTCAGCAATGAAACTGAGTTCAAACTTAAAGCGGCAGCGGTCAGAGAATGCGCCAACGTAGCAGAAAACAACGGCTTTGTTTTGGTAGGTAGAGTATTTGAAAAACGTAATTGATTGCGAATAGCAACAACTAAACAACCAATACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAAcc                                                                                                                                                                                                                                              <  1:245318/282‑1 (MQ=255)                                                          cATGTCTGTTTGCCGCCGGGGTTGTTGCTGATAACATCCTGGTAAAATACCATTTCAGCAATGAAACTGAGTTCAAACTTAAAGCGGCAGCGGTCAGAGAATGCGCCAACGTAGCAGAAAACAACGGCTTTGTTTTGGTAGGTAGAGTATTTGAAAAACGTAATTGATTGCGAATAGCAACAACTAAACAACCAATACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAAccagatcggaagagcacacgt                                                                                                                                                                                                                           >  2:245611/1‑282 (MQ=255)                                                                ttcagacgtgtgctcttccgatctaTAACATCCTGGTAAAATACCATTTCAGCAATGAAACTGAGTTCAAACTTAAAGCGGCAGCGGTCAGAGAATGCGCCAACGTAGCAGAAAACAACGGCTTTGTTTTGGTAGGTAGAGTATTTGAAAAACGTAATTGATTGCGAATAGCAACAACTAAACAACCAATACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCTATGAGATgg                                                                                                                                                                                                                       <  2:16922/275‑1 (MQ=255)                                                                    tGCCGCCGGGGTTGTTGCTGATAACATCCTGGTAAAATACCATTTCAGCAATGAAACTGAGTTCAAACTTAAAGCGGCAGCGGTCAGAGAATGCGCCAACGTAGCAGAAAACAACGGCTTTGTTTTGGTAGGTAGAGTATTTGAAAAACGTAATTGATTGCGAATAGCAACAACTAAACAACCAATACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCTATGATATGGGAGATa                                                                                                                                                                                                                 >  1:177421/1‑301 (MQ=255)                                                                                 gttgCTGATAACATCCTGGTAAAATACCATTTCAGCAATGAAACTGAGTTCAAACTTAAAGCGGCAGCGGTCAGAGAATGCGCCAACGTAGCAGAAAACAACGGCTTTGTTTTGGTAGGTAGAGTATTTGAAAAACGTAATTGATTGCGAATAGCAACAACTAAACAACCAATACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGtt                                                                                                                                                                                                    >  2:15607/1‑301 (MQ=255)                                                                                      tGATAACATCCTGGTAAAATACCATTTCAGCAATGAAACTGAGTTCAAACTTAAAGCGGCAGCGGTCAGAGAATGCGCCAACGTAGCAGAAAACAACGGCTTTGTTTTGGTAGGTAGAGTATTTGAAAAACGTAATTGATTGCGAATAGCAACAACTAAACAACCAATACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCAGGAGTTACGaa                                                                                                                                                                                               >  1:254776/1‑301 (MQ=255)                                                                                        aTAACATCCTGGTAAAATACCATTTCAGCAATGAAACTGAGTTCAAACTTAAAGCGGCAGCGGTCAGAGAATGCGCCAACGTAGCAGAAAACAACGGCTTTGTTTTGGTAGGTAGAGTATTTGAAAAACGTAATTGATTGCGAATAGCAACAACTAAACAACCAATACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCTATGAGATggagatcggaagagcgtcgtgtagggaa                                                                                                                                                                                             >  1:16902/1‑275 (MQ=255)                                                                                                        aTACCATTTCAGCAATGAAACTGAGTTCAAACTTAAAGCGGCAGCGGTCAGAGAATGCGCCAACGTAGCAGAAAACAACGGCTTTGTTTTGGTAGGTAGAGTATTTGAAAAACGTAATTGATTGCGAATAGCAACAACTAAACAACCAATACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGCGACAt                                                                                                                                                                              >  1:65330/1‑300 (MQ=255)                                                                                                            cATTTCCACAATGAAACTGAGTTCAAACTTAAAGCGGCAGCGGTCAGAGAATGCGCCAACGTAGCAGAAAACAACGGCTTTGTTTTGGTAGGTAGAGTATTTGAAAAACGTAATTGATTGCGAATAGCAACAACTAAACAACCAATACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGCGACATCCTCa                                                                                                                                                                         <  1:15587/301‑1 (MQ=255)                                                                                                                   gCAATGAAACTGAGTTCAAACTTAAAGCGGCAGCGGTCAGAGAATGCGCCAACGTAGCAGAAAACAACGGCTTTGTTTTGGTAGGTAGAGTATTTGAAAAACGTAATTGATTGCGAATAGCAACAACTAAACAACCAATACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGCGACATCCTCAAAGgcgg                                                                                                                                                                  >  1:68019/1‑300 (MQ=255)                                                                                                                               tgggctcttccgatctggCAGCGGTCAGAGAATGCGCCAACGTAGCAGAAAACAACGGCTTTGTTTTGGTAGGTAGAGTATTTGAAAAACGTAATTGATTGCGAATAGCAACAACTAAACAACCAATACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAgg                                                                                                                                                      <  2:267628/285‑1 (MQ=255)                                                                                                                                gTTCAAACTTAAAGCGGCAGCGGTCAGAGAATGCGCCAACGTAGCAGAAAACAACGGCTTTGTTTTGGTAGGTAGAGTATTTGAAAAACGTAATTGATTGCGAATAGCAACAACTAAACAACCAATACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCTATGAGATGGGAGATACAAATCATGAGTTACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGa                                                                                                                                                     >  1:136597/1‑301 (MQ=255)                                                                                                                                               ggCAGCGGTCAGAGAATGCGCCAACGTAGCAGAAAACAACGGCTTTGTTTTGGTAGGTAGAGTATTTGAAAAACGTAATTGATTGCGAATAGCAACAACTAAACAACCAATACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGagatcggaagagcgt                                                                                                                                       >  1:267296/1‑286 (MQ=255)                                                                                                                                                                   ccAACGTAGCAGAAAACAACGGCTTTGTTTTGGTAGGTAGAGTATTTGAAAAACGTAATTGATTGCGAATAGCAACAACTAAACAACCAATACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGACAATATAAGGGCGCTCAACGTGGGGCCAAATGCga                                                                                                                  >  1:71335/1‑301 (MQ=255)                                                                                                                                                                             ccaaaaCAAAGCCGTTGTTTTGGTAGGTAGAGTATTTGAAAAACGTAATTGATTGCGAATAGCAACAACTAAACAACCAATACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGCGACATCCCCAAAGGCTCTGCGATGGAAGGACAATATAAGGGCGCTCAACGTGGGGCCAAATGCgaggaactagca                                                                                                        >  1:14361/3‑294 (MQ=255)                                                                                                                                                                                                    taggtagAGTATTTGAAAAACGTAATTGATTGCGAATAGCAACAACTAAACAACCAATACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGACAATATAAGGGCGCTCAACGTGGGGCCAAATGCGAGGAGATCGCAAACGAGTTAACTCGCCGGGGAg                                                                                  <  2:71404/300‑1 (MQ=255)                                                                                                                                                                                                             tATTTGAAAAACGTAATTGATTGCGAATAGCAACAACTAAACAACCAATACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGCGACATCCTCAGAGGCGCTGCGATGGAAGGACAATATAAGGGCGCTCAACGTGGGGCCAAATGCGAGGAGATCGCAAACGAGTTAACTCGCCGGGGAGTTAAAaaca                                                                         <  2:14371/300‑1 (MQ=255)                                                                                                                                                                                                                                                                         cTCGCCGGGTTTTGTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGACAATATAAGGGCGCTCAACGTGGGGCCAAATGCGAGGAGATCGCAAACGAGTTAACTCGCCGGGGAGTTAAAAACAACAAGGGAGAGGTTATTACTAAGGGCGGCGTTAGCCATTGGCTGGAAGGTAGACGGGAGcc            <  2:68088/301‑1 (MQ=255)                                                                                                                                                                                                                                                                                   tttttGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGACAATATAAGGGCGCTCAACGTGGGGCCAAATGCGAGGAGATCGCAAACGAGTTAACTCGCCGGGGAGTTAAAAACAACAAGGGAGAGGTTATTACTAAGGGCGGCGTTAGCCATTGGCTGGAAGGTAGACGGGAGCCAAATTTCGac  <  2:65392/301‑1 (MQ=255)                                                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                                                                                             CCGCAAAAATAATGGGTCGCGACTACGCATGGAAACATGTAAAAGAAGACAGGTTGCCATGTCTGTTTGCCGCCGGGGTTGTTGCTGATAACATCCTGGTAAAATACCATTTCAGCAATGAAACTGAGTTCAAACTTAAAGCGGCAGCGGTCAGAGAATGCGCCAACGTAGCAGAAAACAACGGCTTTGTTTTGGTAGGTAGAGTATTTGAAAAACGTAATTGATTGCGAATAGCAACAACTAAACAACCAATACACCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTTACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGACAATATAAGGGCGCTCAACGTGGGGCCAAATGCGAGGAGATCGCAAACGAGTTAACTCGCCGGGGAGTTAAAAACAACAAGGGAGAGGTTATTACTAAGGGCGGCGTTAGCCATTGGCTGGAAGGTAGACGGGAGCCAAATTTCGAC  >  NC_000913/2564149‑2564723

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ 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.