New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1413022 =	309 (1.350)	8 (0.040)	8/566	26.7	2.6%	coding (214/1236 nt)	intR	Rac prophage; integrase
	?	NC_000913	1413041 =	295 (1.320)					coding (195/1236 nt)	intR	Rac prophage; integrase
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below cutoff threshold.

AGTATCTCCTTTAGGTAAGCCAGACAGCAAACGAGGGATTATCTGGTACAACTATCCAAAGATAAATCAGTTTATCAAAGACTCATGATATGTCTAAATTACCAACAGGTGTCGAGATTAGAGGTAGATACATTCGCATCTGGTTCATGTTTCGAGGAAAACGATGTCGGGAAACATTAAAAGGCTGGGAGATTACAAACAGTAATATTAAAAAGGCCGGAAATTTAAGAGCGCTGATAGTTCATGAAATAAACTCCGGTGAATTTGAGTATTTAAGACGTTTTCCCCAGTCCAGCACTGGGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/1413324‑1413022 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑actggggAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGCGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGGATAGTTGTACCAGATAATCCCTCGTTTGCTGTCTGGCTTACCTAAAGGAGATACTCGTTTGAAGTGGAAGC  >  NC_000913/1413041‑1413340                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             aaTATCTCATTAAGGTAAGCCAGAAAGCAAACAAGGGATTTGCTGGAACAACTATCAAAAGATAAATCAGTTTATCAAAGACTCATGATATGTCTAAATTACCAACAGGTGTCGAGATTAGAGGTAGATACATTCGCATCTGGTTCATGTTTCGAGGAAAACGATGTCGGGAAACATTAAAAGGCTGGGAGATTACAAACAGTAATATTAAAAAGGCCGGAAATTTAAGAGCGCTGATAGTTCATGAAATAAACTCCGGTGAATTTGAGTATTTAAGACGTTTTCCCCAGTCCAGCACTGG                                                                                                                                                                                                                                                                                                                <  1:14902/299‑1  GTATCTCCTTTAGGTAAGCCAGACAGCAAACGAGGGATTATCTGGTACAACTATCCAAAGATAAATCAGTTTATCAAAGACTCATGATATGTCTAAATTACCAACAGGTGTCGAGATTAGAGGTAGATACATTCGCATCTGGTTCATGTTTCGAGGAAAACGATGTCGGGAAACATTAAAAGGCTGGGAGATTACAAACAGTAATATTAAAAAGGCGGGAAATTTAAGAGCGCTGATAGGTCATGAAATAAACTACGGTGACTTTGAGTATTGAAGACGTTTTCCCCAGTCCAGCACTGGG                                                                                                                                                                                                                                                                                                               >  2:160929/1‑301         CTTTAGGTAAGCCAGACAGCAAACGAGGGATTATCTGGTACAACTATCCAAAGATAAATCAGTTTATCAAAGACTCATGATATGTCTAAATTACCAACAGGTGTCGAGATTAGAGGTAGATACATTCGCATCTGGTTCATGTTTCGAGGAAAACGATGTCGGGAAACATTAAAAGGCTGGGAGATTACAAACAGTAATATTAAAAAGGCCGGAAATTTAAGAGCGCTGATAGTTCATGAAATAAACTCCGGTGAATTTGAGTAATTAAGACGTTTTCCCCAGTCCAGCACTGGGGAAAAa                                                                                                                                                                                                                                                                                                         >  1:1339608/1‑299          TTTAGGTAAGCCAGACAGCAAACGAGGGATTATCTGGTACAACTATCCAAAGATAAATCAGTTTATCAAAGACTCATGATATGTCTAAATTACCAACAGGTGTCGAGATTAGAGGTAGATACATTCGCATCTGGTTCATGTTTCGAGGAAAACGATGTCGGGAAACATTAAAAGGCTGGGAGATTACAAACAGTAATATTAAAAAGGCCGGAAATTTAAGAGCGCTGATAGTTCATGAAATAAACTCCGGTGAATTGGAGTATTTCAGACGTTTTCCCCAGTCCAGCACTGGatagcgga                                                                                                                                                                                                                                                                                                        >  1:1210043/1‑292          TTTAGGTAAGCCAGACAGCAAACGAGGGATTATCTGGTACAACTATCCAAAGATAAATCAGTTTAACAAAGACTCATGATATGTCTAAATTACCAACAGGTGTCGAGATTAGAGGTAGATACATTCGCATCTGGTTCATGTTTCGAGGAAAACGATGTCGGGAAACATTAAAAGGCTGGGAGATTACAAACAGTAATATTAAAAAGGCCGGAAATTTAAGAGCGCTGATAGTTCATGAAATAAACTCCGGTGAATTTGAGTATTTAAGACGTTTTCCCCAGTCCAGCACTGG                                                                                                                                                                                                                                                                                                                <  2:1210381/292‑1              GGTAAGCCAGACAGCAAACGAGGGATTATCTGGTACAACTATCCAAAGATAAATCAGTTTATCAAAGACTCATGATATGTCTAAATTACCAACAGGTGTCGAGATTAGAGGTAGATACATTCGCATCTGGTTCATGTTTCGAGGAAAACGATGTCGGGAAACATTAAAAGGCTGGGAGATTACAAACAGTAATATTAAAAAGGCCGGAAATTTAAGAGCGATGATAGTTCATGAAATAAACTCCGGTGAATTTGAGAATTTAAGACGTGTTGCCAAGTCAAGCACTGGGGAAAgaatgat                                                                                                                                                                                                                                                                                                    >  2:1785041/1‑293                                                      ATCCAAAGATAAATCAGTTTATCAAAGACTCATGATATGTCTAAATTACCAACAGGTGTCGAGATTAGAGGTAGATACATTCGCATCTGGTTCATGTTTCGAGGAAAACGATGTCGGGAAACATTAAAAGGCTGGGAGATTACAAACAGTAATATTAAAAAGGCCGGAAATTTAAGAGCGCTGATAGTTCATGAAATAAACTCCGGTGAATTTGAGTATTTAAGACGTTTTCCCCAGTCCAGCACT                                                                                                                                                                                                                                                                                                                  <  2:1819270/246‑1                                                                                                                                                                                         CTGGGAGATTACAAACAGTAATATTAAAAAGGCCGGAAATTTAAGAGCGCTGATAGTTCATGAAATAAACTCCGGTGAATTTGAGTATTTAAGACGTTTTCCCCAGTCCAGCACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGCGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATTTTTCCCGACATCGTTTTTCTCGAAACATTAACCATATGCGAATGTATCTACCTTTAATCTCGACAACTGTTt                                                                                                                        >  2:1639939/1‑300                                                                                                                                                                                                                               ATTTAAGAGCGCTGATAGTTCATGAAATAAACTCCGGTGAATTTGAGTATTTAAGACGTTTTCCCCAGTCCAGTACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTCTCAGCTCTCTTAAATTTACGGCCTTTTTAATATTATTTTTTGTACTCTCCCAGCCTTTTAATGTTTCGCGACATCTATTTCCTAGAAACATCACACATCTGCGTCTGTATCTACGTCTATTTTAGACAACTGTTGATTATTTTGACATATCATGAGTTTTTGATAAACTGATT                                                                                  >  1:1203811/1‑301                                                                                                                                                                                                                                TTTAAGAGCGCTGATAGTTCATGAAATAAACTCCGGTGAATTTGAGTATTTAAGACGTTTTCCCCAGTCCAGCACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGCGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTA                                                                                                                                                                                                   <  2:911391/187‑1                                                                                                                                                                                                                                TTTAAGAGCGCTGATAGTTCATGAAATAAACTCCGGTGAATTTGAGTATTTAAGACGTTTTCCCCAGTCCAGCACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGCGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTA                                                                                                                                                                                                   >  1:911142/1‑187                                                                                                                                                                                                                                                                          TGAGTATTTAAGACGTTTTCCCCAGTCCAGCACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGCGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATTTCATTAGTCTTTGATAAACTGATTTATCTTTGGATAGTTGTACCAGATAATCTCTCGTTTGCTGTCT                                       >  1:637419/1‑301                                                                                                                                                                                                                                                                               ATTTAATACGTTTGCCCCAGTCCAGCACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGCGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGGATAGTTGTACCAGATAATCCCTCGTTTGCTGTCTGGCT                                   <  2:637590/300‑1                                                                                                                                                                                                                                                                                                        ggtctaGGAAAACTACTTTAATACTCAAATTCACCGAAGGTTATTTCATTAACTAGCAGCGATCTTAAATTTCCGGCCTTTTTAAAATTCCTGTTTGTAATCTCCCATCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGGATAGTTGTACCAGATAATCCCTCGTTTGCTGTCTGGCTTACCTAAAGGAGATACTCGTTTGAAG         <  2:484598/295‑1                                                                                                                                                                                                                                                                                                          CTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGCGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATTCGAATGTATCTACCTCTAATCTCGACACCTTTTGGTAATTTAGACATATAATGAGTCTTTTATAAACTGATTTATCTTTGGCTAGTTGTCACAGATAATCCCTCGTTTGCTGTCTGGCTTACCTAAAGTCATTACTCTTTTGAAttt       >  1:503110/1‑298                                                                                                                                                                                                                                                                                                            GGGGAAAACGTCTTAAATACTCAAATTCTCCGGAGTTTATTTCATGAACTATCAGCGTTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTCTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGTTAAACTGATTTATCTTTGGATAGTTGTACCAGATAATCCCTCGTTTGCTGTCTGGCTTACCTAAAGGAGATACTCGTTTGAAGTGGA     <  2:1276524/301‑1                                                                                                                                                                                                                                                                                                            GGGGAAAACGTCTTAAATACTCAAATTCACCGGATTTTATTTCATGAACTATCAGCGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGGATAGTTGTACCAGATAATCCCTCGTTTGCTGTCTGGCTTACCTAAAGGAGATACTCGTTTGAAGTG       <  1:1132370/299‑1                                                                                                                                                                                                                                                                                                            GGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGCGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGGATAGTTTTACCAGATAATCCCTCTTTTGCTGTCTGGCTTACCTAAAGGAGATACTCGTTTGAAGTtg      >  2:1664690/1‑298                                                                                                                                                                                                                                                                                                              GGAAAACGTTTTAAATACTCAAATTCACCGATATTTATTTCATGTACTTTCAGCGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACTTCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGGATAGTTGTACCAGATAATCCCTCGTTTGCTGTCTGGCTTACCTAAAGGAGATACTCGTTTGAAGTGGAA    <  1:603423/300‑1                                                                                                                                                                                                                                                                                                               GAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGCGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGGATAGTTGTACCAGATAATCTCTCGTTTGCTGTCTGGCTTACCTATAGGAGATACTCGTTTGTATTGGAAGC  >  2:184992/1‑301                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             AGTATCTCCTTTAGGTAAGCCAGACAGCAAACGAGGGATTATCTGGTACAACTATCCAAAGATAAATCAGTTTATCAAAGACTCATGATATGTCTAAATTACCAACAGGTGTCGAGATTAGAGGTAGATACATTCGCATCTGGTTCATGTTTCGAGGAAAACGATGTCGGGAAACATTAAAAGGCTGGGAGATTACAAACAGTAATATTAAAAAGGCCGGAAATTTAAGAGCGCTGATAGTTCATGAAATAAACTCCGGTGAATTTGAGTATTTAAGACGTTTTCCCCAGTCCAGCACTGGGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/1413324‑1413022 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑actggggAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGCGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGGATAGTTGTACCAGATAATCCCTCGTTTGCTGTCTGGCTTACCTAAAGGAGATACTCGTTTGAAGTGGAAGC  >  NC_000913/1413041‑1413340

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 32 ≤ 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.