New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1647054 =22 (0.840)3 (0.120) 3/276 2.8 14.2% intergenic (+317/+120) flxA/intK Qin prophage; uncharacterized protein/pseudogene, integrase fragment, Qin prophage;Phage or Prophage Related
?NC_000913 1647120 = 16 (0.660)intergenic (+383/+54) flxA/intK Qin prophage; uncharacterized protein/pseudogene, integrase fragment, Qin prophage;Phage or Prophage Related
Rejected: Frequency below cutoff threshold.

CTTCCGCTTCTTGCTCTTAGCGGACATTAGCATAGGCTATTTACCATAACGCCTCATTACGCGCACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGTAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTATGAATGGATATGCACTCAACCGAATCGATCTTGGTTTCAATCTTTTTTATCGGGATCAGGCTTCTTTTTAGGTAACTTCGGGGGCTTAACTTGCTGATGACTTTGCGTTCGGCGCGTAAGCCAGGGA  >  NC_000913/1646971‑1647264
                                                                                                                                                     |                                                                                                                                                
cTTCCGCTTCTTGCTCTTAGCGGACATTAGCATAGGCTATTTACCATAACGCCTCATTACGCGCACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGTAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGa                                                                                                                                                  >  1:28982/1‑150 (MQ=255)
                 tAGCGGACATTAGCATAGGCTATTTACCATAACGCCTCATTACGCGCACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGTAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTAt                                                                                                                                >  2:174597/1‑151 (MQ=255)
                        cATTAGCATAGGCTATTTACCATAACGCCTCATTACGCGCACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGTAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTATGAATGGa                                                                                                                         <  1:114712/151‑1 (MQ=255)
                         ttgaaaccaagatcgattcggttgagtgcatatccattcatagggtagattcttaagtcgcgtttctggtgttcattttcgggtggtttgttacttgttttaccggggatatgccagaaacgcgACTTAAGAATCTACCCTATGAATGGat                                                                                                                        <  1:410852‑M2/27‑1 (MQ=255)
                            aGCATAGGCTATTTACCATAACGCCTCATTACGCGCACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGTAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTATGAATGGATATg                                                                                                                     >  1:412492/1‑151 (MQ=255)
                            aGCATAGGCTATTTACCATAACGCCTCATTACGCGCACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGTAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTATGAATGGAAATg                                                                                                                     >  2:177387/1‑151 (MQ=255)
                              cATAGGCTATTTACCATAACGCCTCATTACGCGCACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGTAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTATGAATGGATATg                                                                                                                     <  1:83742/149‑1 (MQ=255)
                               ccaagatcgattcggttgagtgcatatccattcatagggtagattcttaagtcgcgtttctggtgttaattttcgggtggtttgttacttgttttaccggggatatgccagaaacgcgACTTAAGAATCTACCCTATGAATGGATATGCAc                                                                                                                  <  1:157974‑M2/33‑1 (MQ=255)
                               aTAGGCTATTTACCATAACGCCTCATTACGCGCACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGTAAAACAAGTAACAAACCCCCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTATGAATGGATATGCAc                                                                                                                  <  2:318263/151‑1 (MQ=255)
                                tAGGCTATTTACCATAACGCCTCATTACGCGCACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGTAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTATGAATGGATATGCACt                                                                                                                 <  2:61767/151‑1 (MQ=255)
                                    cTATTTACCATAACGCCTCATTACGCGCACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGTAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTATGAATGGATATGCACTCAAc                                                                                                             <  2:410295/151‑1 (MQ=255)
                                        attcggttgagtgcatatccattcatagggtagattcttaagtCGCGTTTCTGGCATATCCCCGGTAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTATGAATGGATATGCACTCAACCGaa                                                                                                         <  1:317220‑M1/108‑1 (MQ=255)
                                         ttcggttgagtgcatatccattcatagggtagattcttaagtcgcgtttctggtgttcattttcgggtggtttgttacttgttttaccggggatatgccagaaacgcgACTTAAGAATCTACCCTATGAATGGATATGCACTCAACCGAAt                                                                                                        <  1:317220‑M2/43‑1 (MQ=255)
                                             aTAACGCCTCATTACGCGCACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGTAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTATGAATGGATATGCACTCAACCGAATCGAt                                                                                                    >  2:255077/1‑151 (MQ=255)
                                                  gtgcatatccattcatagggtagattcttaagtCGCGTTTCTGGCATATCCCCGGTAAAACAAGTAACAAACCACCCGAAAATTAACACCAGAAACGCGACTTAAGAATCTACCCTATGAATGGATATGCACTCAACCGAATCGATCTTgg                                                                                               <  1:157974‑M1/118‑1 (MQ=255)
                                                        atccattcatagggtagattcttaagtCGCGTTTCTGGCATATCCCCGGTAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTATGAATGGATATGCACTCAACCGAATCGATCTTGGTTTCaa                                                                                         <  1:410852‑M1/124‑1 (MQ=255)
                                                                            gactCAGCGCGTTTCTGGCATATCCCCGGTAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTATGAATGGATATGCACTCAACCGAATCGATCTTGGTTTCAATCTTTTTTATCGGGATCAgg                                                                     >  1:72152/1‑151 (MQ=255)
                                                                                            GGCATATCCCCGGTAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTATGAATGGATATGCACTCAACCGAATCGATCTTGGTTTCAATCTTTTTTATCGGGATCAGGCTTCTTTTTAGGTaa                                                      <  2:122391‑M1/150‑1 (MQ=255)
                                                                                                   ccccGGTAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTATGAATGGATATGCACTCAACCGAATCGATCTTGGTTTCAATCTTTTTTATCGGGATCAGGCTTCTTTTTAGGTAACTTCgggg                                              >  2:82532/1‑151 (MQ=255)
                                                                                                    cccGGTAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTTCCCTATGAATGGATATGCACTCAACCGAATCGATCTTGGTTTCAATCTTTTTTATCGGGATCAGGCTTCTTTTTAGGTACCTTCggggg                                             <  2:222125/151‑1 (MQ=255)
                                                                                                        gTAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTATGAATGGATATGCACTCAACCGAATCGATCTTGGTTTCAATCTTTTTTATCGGGATCAGGCTTCTTTTTAGGTAACTTCGGGGGCTTa                                         >  1:41054/1‑151 (MQ=255)
                                                                                                                 gTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTATGAATGGATATGCACTCAACCGAATCGATCTTGGTTTCAATCTTTTTTATCGGGATCAGGCTTCTTTTTAGGTAACTTCGGGGGCTTAACTTGCtga                                >  2:381387/1‑151 (MQ=255)
                                                                                                                  tAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTATGAATTGATATGCACTCAACCGAATCGATCTTGGTTTCAATCTTTTTTATCGGGATCAGGCTTCTTTTTAGGTAACTTCGGGGGCTTAACTTGCtg                                 <  2:184975/149‑1 (MQ=255)
                                                                                                                                             gaaacgcgACTTAAGAATCTACCCTATGAATGGATATGCACTCAACCGAATCGATCTTGGTTTCAATCTTTTTTATCGGGATCAGGCTTCTTTTTAGGTAACTTCGGGGGCTTAACTTGCTGATGACTTTGCGTTCGGCGCGTAAGCCAgg    >  1:139370‑M2/9‑151 (MQ=255)
                                                                                                                                               aacgcgACTTAAGAATCTACCCTATGAATGGATATGCACTCAACCGAATCGATCTTGGTTTCAATCTTTTTTATCGGGATCAGGCTTCTTTTTAGGTAACTTCGGGGGCTTAACTTGCTGATGACTTTGCGTTCGGCGCGTAAGCCAGGGa  <  1:142869‑M2/145‑1 (MQ=255)
                                                                                                                                               aacgcgACTTAAGAATCTACCCTATGAATGGATATGCACTCAACCGAATCGATCTTGGTTTCAATCTTTTTTATCGGGATCAGGCTTCTTTTTAGGTAACTTCGGGGGCTTAACTTGCTGATGACTTTGCGTTCGGCGCGTAAGCCAGGGa  <  2:139403‑M2/145‑1 (MQ=255)
                                                                                                                                                     |                                                                                                                                                
CTTCCGCTTCTTGCTCTTAGCGGACATTAGCATAGGCTATTTACCATAACGCCTCATTACGCGCACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGTAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTATGAATGGATATGCACTCAACCGAATCGATCTTGGTTTCAATCTTTTTTATCGGGATCAGGCTTCTTTTTAGGTAACTTCGGGGGCTTAACTTGCTGATGACTTTGCGTTCGGCGCGTAAGCCAGGGA  >  NC_000913/1646971‑1647264

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ 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.