New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1433172 =	60 (0.800)	4 (0.060)	4/554	9.1	6.0%	coding (503/591 nt)	pinR	Rac prophage; putative site‑specific recombinase
	?	NC_000913	= 1634197	68 (0.940)					coding (576/591 nt)	pinQ	Qin prophage; putative site‑specific recombinase
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below cutoff threshold.

ATTGATTGTGACAAAACTGGATCGCCTTGGTTGTAATGCAATGGATATCAGGAAAACAGTGGAACAACTGACCGAAACAGGTATCAGAGTGCATTGCTTAGCATTGGGTGGCATTGACCTGACCAGTCCAACAGGAAAAATGATGATGCAAGTAATTTCAGCAGTCGCTGAATTTGAACGAGACCTTTTACTTGAACGCACTCATTCCGGGATAGTAAGAGCCCGCGGCGCAGGGAAACGTTTTGGTCGACCTCCTGTGTTAAATGAAGAACAGAAACAGGTGGTATTCGAACGAATTAAGTCAGGTGT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/1433480‑1433172 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gtcaggtgtCTGAAGTTTTGCTTTGGCTCTTAAAATGGTTTGCCGCGAGGTTTTGAATTCCCGGGCAATGGCACTTATACTTACACCTGACTTAATTCGTTCGAATACCGCCTGTTTCTGTTCTTCATTTAACACAGGTGGTCGACCAAAACGTTTCCCTGCGCCGCGGGCTCTTACTATCCCGGAATGAGTGCGTTCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGTCAGGTCAATGCCCCCCAATGCTAAGCAATGCACTCT  <  NC_000913/1634197‑1633901                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                agTGATTGTGACAAAACGGGAGCGCCTGGGTTGTAATGCAAGGGATATCAGGAAAACAGGGGAACAACTGACCGAAACAGGTATCAGAGTGCATTGCTTAGCATTGGGTGGCATTGACCTGACCAGTCCAACAGGAAAAATGATGATGCAAGTAATTTCAGCAGTCGCTGAATTTGAACGAGACCTTTTACTTGAACGCACTCATTCCGGGATAGTAAGAGCCCGCGGCGCAGGGAAACGTTTTGGTCGACCTCCTGTGTTAAATGAAGAACAGAAACAGGTGGTATTCGAACGAATTAAG                                                                                                                                                                                                                                                                                                                   <  2:149742/299‑1    GATTGTGACAAAACTGGATCGCCTTGGTTGTAATGCAATGGATATCAGGAAAACAGTGGAACAACTGACCGAAACAGGTATCAGAGTGCATTGCTTAGCATTGGGTGGCATTGACCTGACCAGTCCAACAGGAAAAATGATGATGCAAGTAATTTCAGCAGTCGCTGAATTTGAACGAGACCTTTTACTTGAACGCACTCATTCCGGGATAGTAAGAGCCCGCGGCGCAGGGAAACGTTTTGGTCGACCTCCTGTGTTAAATGAAGAACAGAAACAGGTGGTATTCGAACGAATTAAGTC                                                                                                                                                                                                                                                                                                                 >  2:287834/1‑300       TGTGAAAAAACTGGATCGCCTTGGTTGTAATGCAATGGATATCAGGAAAACAGGGGAACAACTGACCGAAACAGGTATCAGAGTGCATTGCTTAGCATTGGGTGGCATTGACCTGACCAGTCCAACAGGAAAAATGATGATGCAAGTAATTTCAGCAGTCGCTGAATTTGAACGAGACCTTTTACTTGAACGCACTCATTCCGGGATAGTAAGAGCCCGCGGCGCAGGGAAACGTTTTGGTCGACCTCCTGTGTTAAATGAAGAACAGAAACAGGTGGTATTCGAACGAATTAAGTCAGG                                                                                                                                                                                                                                                                                                              <  2:548185/300‑1            CAAAACTGGATCGCCTTGGTTGTAATGCAATGGATATCAGGAAAACAGTGGAACAACTGACCGAAACAGGTATCAGAGTGCATTGCTTAGCATTGGGTGGCATTGACCTGACCAGTCCAACAGGAAAAATGATGATGCAAGTAATTTCAGCAGTCGCTGAATTTGAACGAGACCTTTTACTTGAACGCACTCATTCAGGGATAGTAAGAGCCCGAGGCGCCGGGAAACGTTTTGGTCGACATCCTGTGTTAAATGAAGAAAATAAACAGGTGGTATTTGAAGGAATTAAGTCAGGTGaa                                                                                                                                                                                                                                                                                                          >  2:578724/1‑297                                                               AACAACTGACCGAAACAGGTATCAGAGTGCATTGCTTAGCATTGGGTGGCATTGACCTGACCAGTCCAACAGGAAAAATGATGATGCAAGTAATTTCAGCAGTCGCTGAATTTGAACGAGACCTTTTACTTGAACGAACTCATTCCGGGATAGTAAGAGCCCGCGGCGCAGGGAAACGTTTTGGTCGACCTCCTGCGTTAATTGAAGAACAGAAACAGGTGGTATTCGAACGAATTAAGTCAGGTGTCTGAAGTTTTGCTTTGGCTCTTAAAATGGTTTGCCGCGAGGTTTTGAATTCCCG                                                                                                                                                                                                                                                     >  2:630825/1‑301                                                                                                   gacgaggGGGGGGCAGTGAACAGAACAGTAAAACAGGAAAAAAGATGATGAAAGTAAGTTCATCAGTCGCGGAATTTGAACGAGACCTTTTACTTGAACGCACTCATTCCGGGATAGTAAGAGCCCGCGGCGCAGGGAAACGTTTTGGTCGACCTCCTGTGTTAAATGAAGAACAGAAACAGGTGGTATTCGAACGAATTAAGGCAGGTGTCTGAAGTTTTGCTTTGGCTCTTAAAATGGTTTGCCGCGAGGTTTTGAATTCCCGGGCAATGGCACTTATACTTACACCTGACTTAATTC                                                                                                                                                                                                                  <  1:630648/293‑1                                                                                                                                                                   AGTCGCTGAATTTGAACGAGACCTTTTACTTGAACGCACTCATTCCGGGATAGTAAGAGCCCGCGGCGCAGGGAAACGTTTTGGTCGACCTCCTGTGTTAAATGAAGAACAGAAACAGGTGGTATTCGAACGAATTAAGTCAGGTGTCTGAAGTTTTGCTTTGGCTCTTAAAATGGTTTGCCGCGAGGTTTTGAATTCCCGGGCAATGGCACTTATACTTACACCTGACTT                                                                                                                                                                                                                       <  1:482684/231‑1                                                                                                                                                                   AGTCGCTGAATTTGAACGAGACCTTTTACTTGAACGCACTCATTCCGGGATAGTAAGAGCCCGCGGCGCAGGGAAACGTTTTGGTCGACCTCCTGTGTTAAATGAAGAACAGAAACAGGTGGTATTCGAACGAATTAAGTCAGGTGTCTGAAGTTTTGCTTTGGCTCTTAAAATGGTTTGCCGCGAGGTTTTGAATTCCCGGGCAATGGCACTTATACTTACACCTGACTT                                                                                                                                                                                                                       >  2:482816/1‑231                                                                                                                                                                                                                                                                                                     tttccggtaTCAGGTGTCTGATGTTTTGCTTTGGCTCTTAAAATGGTTTGCCGCGAGGTTTTTAATTCCCGGGCAATGGCACTTATACTTACACCTGACTTAATTCGTTCGAATACCGCCTGTTTCTGTTCTTCATTTAACACAGGTGGTCGACCAAAACGTTTCCCTGCGCCGCGGGCTCTTACTATCCCGGAATGAGTGCGTTCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGTCAGGTCAATGCCCCCCAATGCT                <  1:544897/291‑1                                                                                                                                                                                                                                                                                                               CAGGTGTCTGAAGTTTTGCTTTGGCTCTTAAAATGGTTTGCCGCGAGGTTTTGAATTCCCGGGCAATGGCACTTATACTTACACCTGACTTAATTCGTTCGAATACCGCCTGTTTCTGTTCTTCATTTAACACAGGTGGTCGACCAAAACGTTTCCCTGCGCCGCGGGCTCTTACTATCCCGGAATGAGTGCGTTCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGTCAGGTCAATGCCCCCCAATGCT                >  2:545046/1‑290                                                                                                                                                                                                                                                                                                                 GGTGTCTGAAGTTTTGCTTTGGCTCTTAAAATGGTTTGCCGCGAGGTTTTGAATTCCCGGGCAATGGCACTTATACTTACACCTGACTTAATTCGTTCGAATACCGCCTGTTTCTGTTCTTCATTTAACACAGGTGGTCGACCAAAACGTTTCCCTGCGCCGCGGGCTCTTACTATCCCGGAATGAGTGCGTTCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGG                                            <  2:268230/260‑1                                                                                                                                                                                                                                                                                                                  GTGTTTGCATTTTTGCTTTGTCGCTTAAAATGGTTTGCCGCGAGTTTTTTAATTTCCGGGCCATGGCACTTATACTTACACCTGACTTAATTCGTTCGAATACCGCCTGTTTCTGTTCTTCATTTAACACAGGTGGTCGACCAAACCGTTTCCCTGCGCCTCGGGCTCTTACTATCCCGGAATGAGTGCGTTCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGTCAGGTCAATGCCCCCCAATGCTAAGCAATGCACTCT  <  1:97712/301‑1                                                                                                                                                                                                                                                                                                                  GTGTCATAAGTTTTGCTTTGGCTCTTAAAATGGGTTGCCGCGAGGTTTTGAATTCCCAAGCAATGGCACTTATACGTACACCTGACTGAATTAGTTCGAAGACCGCCTGTTTCTGTTCTTCATTTAACACAGGTGGTCGACCAAAACGTTTCCCTGCGACGCGGGCTCTTACTATCCCGGAATGAGTGCGTTCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGTCAGGTCAATGCCCCCCAATGCTAAGCAATGCACTCT  <  2:568955/301‑1                                                                                                                                                                                                                                                                                                                   TGTTTGAAGTTTTGCTTTGTCTCTTAAGATGGTTGTCCGCGAGTTTTTGAAGTCCCGGTCAATGGCGCTTATACTTACCCCTTACTTAATTCTTTCGAATACCGCCTGTTTCTGTTCTTCATTTAACACAGGTGGTCGACCAAAACGTTTCCCTGCGCCGCGGGCTCTTACTATCCCGGAATGAGTGCGTTCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGTCAGGTCAATGCCCCCCAATGCTAAGCAATGCACTCT  <  2:114990/300‑1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                ATTGATTGTGACAAAACTGGATCGCCTTGGTTGTAATGCAATGGATATCAGGAAAACAGTGGAACAACTGACCGAAACAGGTATCAGAGTGCATTGCTTAGCATTGGGTGGCATTGACCTGACCAGTCCAACAGGAAAAATGATGATGCAAGTAATTTCAGCAGTCGCTGAATTTGAACGAGACCTTTTACTTGAACGCACTCATTCCGGGATAGTAAGAGCCCGCGGCGCAGGGAAACGTTTTGGTCGACCTCCTGTGTTAAATGAAGAACAGAAACAGGTGGTATTCGAACGAATTAAGTCAGGTGT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/1433480‑1433172 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gtcaggtgtCTGAAGTTTTGCTTTGGCTCTTAAAATGGTTTGCCGCGAGGTTTTGAATTCCCGGGCAATGGCACTTATACTTACACCTGACTTAATTCGTTCGAATACCGCCTGTTTCTGTTCTTCATTTAACACAGGTGGTCGACCAAAACGTTTCCCTGCGCCGCGGGCTCTTACTATCCCGGAATGAGTGCGTTCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGTCAGGTCAATGCCCCCCAATGCTAAGCAATGCACTCT  <  NC_000913/1634197‑1633901

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 34 ≤ 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.