New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1646853 =	67 (0.490)	3 (0.020)	3/498	NT	2.9%	intergenic (+116/+321)	flxA/intK	Qin prophage; uncharacterized protein/pseudogene, integrase fragment, Qin prophage;Phage or Prophage Related
	?	NC_000913	1649105 =	138 (1.040)					intergenic (+64/‑277)	ydfC/dicF	uncharacterized protein, Qin prophage/sRNA antisense regulator, inhibits ftsZ, Hfq‑dependent; Qin prophage
Rejected: Frequency below/above cutoff threshold.

ATCCATTCATAGGGTAGATTCTTAAGTCGCGTTTCTGGTGTTCATTTTCGGGTGGTTTGTTACTTGTTTTACCGGGGATATGCCAGAAACGCGCTGAGTCAGTCTGGGCGGTGCGCGTAATGAGGCGTTATGGTAAATAGCCTATGCTAATGTCCGCTAAGAGCAAGAAGCGGAAGTTGGCAGTTTTGTGGACTGTCCCCACAAAAGTGACTACAGAAATAGTTGCAATTCATAATTGATCATGGGTTGTCAGTTAAACTCGTGGCGATTTAAATAGACTAATTGGGAGTGCGT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/1647146‑1646853 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ggagtgcgtGCGCCGGACACGGGTGCGCATCCGGAACTGACAGTTTACTGAAAGGATATTTCCCTGAAAAGTCAGACCATAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGCGGGGTTATTCCTTCCCCGTTGAGGACACCGGGTTGTCAGGTTGACCATACGCT  >  NC_000913/1649105‑1649343                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       ATCCATTCATAGGGTAGATTCTTAAGTCGCGTTTCTGGTGTTCATTTTCGGGTGGTTTGTTACTTGTTTTACCGGGGATATGCCAGAAACGCGCTGAGTCAGTCTGGGCGGTGCGCGTAATGAGGCGTTATGGTAAATAGCCTATGCTAATGTCCGCTAAGAGCAAGAAGCGGAAGTTGGCAGTTTTGTGGACTGTCCCCACAAAAGTGACTACAGAAATAGTTGCAATTCATAATTGATCATGGGTTGTCAGTTAAACTCGTGGCGATTTAAATAGACTAATTGGGAG                                                                                                                                                                                                                                                      >  2:272374/1‑289  TCCATTCCTAGGGTAGATTCTTAAGTCGCGTTTCTGGTGTTCATTTTCGGGTGGTTTGTTACTTGGTTTACCGGGGATATGCCAGAAACGCGCTGAGTCAGTCTGGGCGGTGCGCGTAATGAGGCGTTATGGTAAATAGCCTATGCTAATGTCCGCTAAGAGCAAGAAGCGGAAGTTGGCAGTTTTGTGGACTGTCCCCACAAAAGTGACTACAGAAATAGTTGCAATTCATAATTGATCATGGGTTGTCAGTTAAGCTCGTGGCGATTTAAATAGACTAATTGGGAGT                                                                                                                                                                                                                                                     <  2:731295/289‑1  TCCATTCATAGGGTAGATTCTTAAGTCGCGTTTCTGGTGTTCATTTTCGGGTGGTTTGTTACTTGTTTTACCGGGGATATGCCAGAAACGCGCTGAGTCAGTCTGGGCGGTGCGCGTAATGAGGCGTTATGGTAAATAGCCTATGCTAATGTCCGCTAAGAGCAAGAAGCGGAAGTTGGCAGTTTTGTGGACTGTCCCCACAAAAGTGACTACAGAAATAGTTGCAATTCATAATTGATCATGGGTTGTCAGTTAAACTCGTGGCGATTTAAATAGACTAATTGGGAGT                                                                                                                                                                                                                                                     <  1:810530/289‑1  TCCATTCATAGGGTAGATTCTTAAGTCGCGTTTCTGGTGTTCATTTTCGGGTGGTTTGTTACTTGTTTTACCGGGGATATGCCAGAAACGCGCTGAGTCAGTCTGGGCGGTGCGCGTAATGAGGCGTTATGGTAAATAGCCTATGCTAATGTCCGCTAAGAGCAAGAAGCGGAAGTTGGCAGTTTTGTGGACTGTCCCCACAAAAGTGACTACAGAAATAGTTGCAATTCATAATTGATCATGGGTTGTCAGTTAAACTCGTGGCGATTTAAATAGACTAATTGGGAGT                                                                                                                                                                                                                                                     <  2:269902/289‑1      TTCATAGGGTAGATTCTTAAGTCGCGTTTCTGGTGTTCATTTTCGGGTGGTTTGTTACTTGTTTTACCGGGGATATGCCAGAAACGCGCTGAGTCAGTCTGGGCGGTGCGCGTAATGAGGCGTTATGGTAAATAGCCTATGCTAATGTCCGCTAAGAGCAAGAAGCGGAAGTTGGCAGTTTTGTGGACTGTCCCCACAAAAGTGACTACAGAAATAGTTGCAATTCATAATTGATCATGGGTTGTCAGTTAAACTCGTGGCGATTTAAATAGACTAATTGGGAGTGCG                                                                                                                                                                                                                                                  >  1:201747/1‑288      TTCATAGGGTAGATTCTTAAGTCGCGTTTCTGGTGTTCATTTTCGGGTGGTTTGTTACTTGTTTTACCGGGGATATGCCAGAAACGCGCTGAGTCAGTCTGGGCGGTGCGCGTAATGAGGCGTTATGGTAAATAGCCTATGCTAATGTCCGCTAAGAGCAAGAAGCGGAAGTTGGCAGTTTTGTGGACTGTCCCCACAAAAGTGACTACAGAAATAGTTGCAATTCATAATTGATCATGGGTTGTCAGTTAAACTCGTGGCGATTTAAATAGACTAATTGGGAGTGCG                                                                                                                                                                                                                                                  >  1:382038/1‑288      TTCATAGGGTAGATTCTTAAGTCGCGTTTCTGGTGTTCATTTTCGGGTGGTTTGTTACTTGTTTTACCGGGGATATGCCAGAAACGCGCTGAGTCAGTCTGGGCGGTACGCGTAATGAGGCGTTATGGTAAATAGCCTATGCTAATGTCCGCTAAGAGCAAGAAGCGGAAGTTGGCAGTTTTGTGGACTGTCCCCACAAAAGTGACTACAGAAATAGTTGCAATTCATAATTGATCATGGGTTGTCAGTTAAACTCGTGGCGATTTAAATAGACTAATTGGGAGTGCG                                                                                                                                                                                                                                                  >  1:785736/1‑288                                                                                                     AGTCTGGGCGGTGCGCGTAATGAGGCGTTATGGTAAATAGCCTATGCTAATGTCCGCTAAGAGCAAGAAGCGGAAGTTGGCAGTTTTGTGGACTGTCCCCACAAAAGTGACTACAGAAATAGTTGCAATTCATAATTGATCATGGGTTGTCAGTTAAACTCGTGGCGATTTAAATAGACTAATTGGGAGTGCGTGCGCCGGACACGGGTGCGCATCCGGAACTGACAGTTTACTGAAAGGATATTTCCCTGAAAAGTCAGCCCATAACGCGAAAGCGCATGGCTGGGTA                                                                                                                                                  >  2:18549/1‑289                                                                                                                                                                                                                     ACAGAAATAGTTGCAATTCATAATTGATCATGGGTTGTCAGTTAAACTCGTGGCGATTTAAATAGACTAATTGGGAGTGCGTGCGCCGGACACGGGTGCGCATCCGGAACTGACAGTTTACTGAAAGGATATTTCCCTGAAAAGTCAGACCATAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGCGGGGTTATTCCTTCCCCGTTG                                  <  1:514472/289‑1                                                                                                                                                                                                                                                      GTTGTCAGTTAAACTCGTGGCGATTTAAATAGACTAATTGGGAGTGCGTGCGCCGGACACGGGTGCGCATCCGGAACTGACAGTTTACTGAAAGGATATTTCCCTGAAAAGTCAGACCATAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGCGGGGTTATTCCTTCCCCGTTGAGGACACCGGGTTGTCAGGTTGACCATACGCT  <  1:18549/288‑1                                                                                                                                                                                                                                                                                                    CGTGCGCCGGACACGGGTGCGCATCCGGAACTGACAGTTTACTGAAAGGATATTTCCCTGAAAAGTCAGACCATAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGC                                                                                       <  1:667570/157‑1                                                                                                                                                                                                                                                                                                    CGTGCGCCGGACACGGGTGCGCATCCGGAACTGACAGTTTACTGAAAGGATATTTCCCTGAAAAGTCAGACCATAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGC                                                                                       >  2:667570/1‑157                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       ATCCATTCATAGGGTAGATTCTTAAGTCGCGTTTCTGGTGTTCATTTTCGGGTGGTTTGTTACTTGTTTTACCGGGGATATGCCAGAAACGCGCTGAGTCAGTCTGGGCGGTGCGCGTAATGAGGCGTTATGGTAAATAGCCTATGCTAATGTCCGCTAAGAGCAAGAAGCGGAAGTTGGCAGTTTTGTGGACTGTCCCCACAAAAGTGACTACAGAAATAGTTGCAATTCATAATTGATCATGGGTTGTCAGTTAAACTCGTGGCGATTTAAATAGACTAATTGGGAGTGCGT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/1647146‑1646853 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ggagtgcgtGCGCCGGACACGGGTGCGCATCCGGAACTGACAGTTTACTGAAAGGATATTTCCCTGAAAAGTCAGACCATAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGCGGGGTTATTCCTTCCCCGTTGAGGACACCGGGTTGTCAGGTTGACCATACGCT  >  NC_000913/1649105‑1649343

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 28 ≤ 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.