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.