New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1633479 =	0 (0.000)	4 (0.140)	4/208	2.9	72.7%	intergenic (+174/‑143)	ydfK/pinQ	cold shock protein, function unknown, Qin prophage/Qin prophage; putative site‑specific recombinase
	?	NC_000913	1633499 =	3 (0.110)					intergenic (+194/‑123)	ydfK/pinQ	cold shock protein, function unknown, Qin prophage/Qin prophage; putative site‑specific recombinase

ATTCTTCTTCCTTGAGTCCGCCCGGAACTCGAAAAACAAACCGAGTTAAAGCCATTTTTCACAAAATCGATTTTGGGTCTCACCAAAATTACGGGGTTGCATACGCATTCGTTTATTTTCGAACGTGTACATACAAATATGCACAAAAATAATCATAATTATTTTCTGAGATGCATTATGATATGAACACCAATTTCGTATAGAGTCTCACTATGTCTCAAATTTTTGCTTA  >  NC_000913/1633410‑1633641                                                                                          |                                                                                                                                               ttatgattatttttgtgcatatttgtatgtacacgttcgaaaataaacgaatgcgtatgcaaccccgtaATTTTGGGTCTCACCAAAATTACggg                                                                                                                                           <  2:71760‑M1/26‑1 (MQ=255) ttatgattatttttgtgcatatttgtatgtacacgttcgaaaataaacgaatgcctatgcaaccccgtaATTTTGGGTCTCACCAAAATTACggg                                                                                                                                           >  1:71760‑M1/70‑95 (MQ=255)                   atatttgtatgtacacgttcgaaaataaacgaatgcgtatgcaaccccgtaATTTTGGGTCTCACCAAAATTACgg                                                                                                                                            <  6:18901‑M1/25‑1 (MQ=255)                   atatttgtatgtacacgttcgaaaataaacgaatgcgtatgcaaccccgtaATTTTGGGTCTCACCAAAATTACgg                                                                                                                                            >  5:18901‑M1/52‑76 (MQ=255)                                                                cccgtaattttggtgagacccaaaatTACGGGGTTGCATAGGCATTCGTTTATTTTCGAACGTGTACATACAAATATGCACAAAAATAATCATaa                                                                            >  1:71760‑M2/27‑95 (MQ=255)                                                                cccgtaattttggtgagacccaaaatTACGGGGTTGCATACGCATTCGTTTATTTTCGAACGTGTACATACAAATATGCACAAAAATAATCATaa                                                                            <  2:71760‑M2/69‑1 (MQ=255)                                                                 ccgtaattttggtgagacccaaaatTACGGGGTTGCATACGCATTCGTTTATTTTCGAACGTGTACATACAAatat                                                                                              <  6:18901‑M2/51‑1 (MQ=255)                                                                 ccgtaattttggtgagacccaaaatTACGGGGTTGCATACGCATTCGTTTATTTTCGAACGTGTACATACAAatat                                                                                              >  5:18901‑M2/26‑76 (MQ=255)                                                                       TTTTGGGTCTCACCAAAATTACGGGGTTGCATACGCATTCGTTTATTTTCGAACGTGTACATACAAATATGCACAAAAATAATCATAATTATTTTCTGAGATGCATTATGATATGAACACCAATTTCGTATAGAGTCTCACTATGtctc               >  3:53998‑M1/1‑149 (MQ=255)                                                                           GGGTCTCACCAAAATTACGGGGTTGCATACGCATTCGTTTATTTTCGAACGTGTACATACAAata                                                                                               <  8:65698‑M1/65‑1 (MQ=255)                                                                           GGGTCTCACCAAAATTACGGGGTTGCATACGCATTCGTTTATTTTCGAACGTGTACATACAAata                                                                                               >  7:65698‑M1/1‑65 (MQ=255)                                                                              tctcACCAAAATTACGGGGTTGCATACGCATTCGTTTATTTTCGAACGTGTACATACAAATATGCACAAAAATAATCATAATTATTTTCTGAGATGCATTATGATATGAACACCAATTTCGTATAGAGTCTCACTATGTCTCAAAtttt        <  5:18295/149‑1 (MQ=32)                                                                                  aCCAAAATTACGGGGTTGCATACGCATTCGTTTATTTTCGAACGTGTACATACAAATATGCACAAAAATAATCATAATTATTTTCTGAGATGCATTATGATATGAACACCAATTTCGTATAGAGTCTCACTATGTCTCAAATTTTTGCt    >  3:154023/1‑149 (MQ=32)                                                                                  aCCAAAATTACGGGGTTGCATACGCATTCGTTTATTTTCGAACGTGTACATACAAATATGCACAAAAATAATCATAATTATTTTCTGAGATGCATTATGATATGAACACCAATTTCGTATAGAGTCTCACTATGTCTCAAATTTTTGCt    >  1:188325/1‑149 (MQ=32)                                                                                   ccaaaatTACGGGGTTGCATACGCATTCGTTTAtttt                                                                                                                   >  4:60717‑M2/8‑37 (MQ=255)                                                                                   ccaaaatTACGGGGTTGCATACGCATTCGTTTAtttt                                                                                                                   <  3:60717‑M2/30‑1 (MQ=255)                                                                                   ccaaaatTACGGGGTTGCATACGCATTCGTTTATTTTCGAACgtg                                                                                                           <  2:27277‑M2/38‑1 (MQ=255)                                                                                   ccaaaatTACGGGGTTGCATACGCATTCGTTTATTTTCGAACGTGTACATACAAATATGCACAAAAATAATCATAATTATTTTCTgaga                                                               <  4:24543‑M2/82‑1 (MQ=255)                                                                                   ccaaaatTACGGGGTTGCATACGCATTCGTTTATTTTCGAACGTGTACATACAAATATGCACAAAAATAATCATAATTATTTTCTgaga                                                               >  3:24543‑M2/8‑89 (MQ=255)                                                                                   ccaaaatTACGGGGTTGCATACGCATTCGTTTATTTTCGAACGTGTACATACAAATATGCACAAAAATAATCATAATTATTTTCTGAGATGCATTATGATATGAACACCATTTTCGTATAGAGTCTCACTATGTCTCAAATTTTTGCtt   <  4:154023‑M2/142‑1 (MQ=255)                                                                                    caaaatTACGGGGTTGCATACGCATTCGTTTATTTTCGAACGTGTACATACAAATATGCACAAAAATAATCATAATTATTTTCTGAGATGCATTATGATATGAACACCAATTTCGTATAGAGTCTCACTATGTCTCAAATTTTTGCTTa  >  5:39900‑M2/7‑149 (MQ=255)                                                                                          |                                                                                                                                               ATTCTTCTTCCTTGAGTCCGCCCGGAACTCGAAAAACAAACCGAGTTAAAGCCATTTTTCACAAAATCGATTTTGGGTCTCACCAAAATTACGGGGTTGCATACGCATTCGTTTATTTTCGAACGTGTACATACAAATATGCACAAAAATAATCATAATTATTTTCTGAGATGCATTATGATATGAACACCAATTTCGTATAGAGTCTCACTATGTCTCAAATTTTTGCTTA  >  NC_000913/1633410‑1633641

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ 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.