New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 574464	27 (0.170)	4 (0.030)	4/250	NT	13.3%	intergenic (+125/+65)	quuD/nmpC	DLP12 prophage; putative antitermination protein/DLP12 prophage; truncated outer membrane porin (pseudogene);IS, phage, Tn; Phage or Prophage Related; outer membrane porin protein; locus of qsr prophage
	?	NC_000913	= 574470	27 (0.180)					intergenic (+131/+59)	quuD/nmpC	DLP12 prophage; putative antitermination protein/DLP12 prophage; truncated outer membrane porin (pseudogene);IS, phage, Tn; Phage or Prophage Related; outer membrane porin protein; locus of qsr prophage

GCTGCTCTGATGGTTATATCGGGAAAAGGTTACAGAAGGCTGAGGGCATAATTGAAGGGATGTTAATGGCATTAGATATCCGGTTAGAGATGGATATCGTTGTTAATAACTCTAATTAATATGCCAATTGTTTACTAAAAATTATTAAAAATGGGGCGTTGAGACGCCCCCAAAAATAAAGGGTAATATATAACAGAAGGTTTATATAGTTAGAAGCAAGGTTGTGCTTCTAAAGGAAGTGGCTTGAGGGAGCCACTTATATGTTGGGGAGGCAACGCCTCCCGCAACATATCTTTTTCGTAATCAGATTAGAACTGGTAAACCAGACCTACAGCAACGATGTCATCAGTGCTTACACCGAGTGCTTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCAGTTT  >  NC_000913/574221‑574736                                                                                                                                                                                                                                                          |                                                                                                                                                                                                                                                                           gctggtCTGATGGTTATAGCGTGAAAATGGTACAGAAGGCTTAGGGCATAAGTGAAGGGATGTTAATGACATTAGATATCCGGTTAGAGATGGATATCGTTGTTAATAACTCTAATTAATATGCAAATTGTTTACTAAAAATTATTAAAAATGGGGCGTTGATACGCCCCCAAAAATAAAGGGTAATATATAACAGAAGGTTTATATAGTTAGAAGCAAGGTTGTGCTTCTAAAGGAAGTGGCTTGAGGGAGCCACTTATATGTTGGGGAGGCaa                                                                                                                                                                                                                                                   <  1:19158/275‑1 (MQ=255)                                                                                                                                                             cGTTGAGACTCCCCCAAAAATAAAGGGTAATATATAACAGAAGGTTTATATAGTTAGAAGCAAGGCTGTGCTTCTAAAGGAAGTGGCTTGAggg                                                                                                                                                                                                                                                                            >  8:990135/1‑94 (MQ=255)                                                                                                                                                             cGTTGAGACGCCCCCAAAAATAAAGGGTAATATATAACAGAAGGTTTATATAGTTAGAAGCAAGGTTGTGCTTCTAAAGGAAGTGGCTTGAggg                                                                                                                                                                                                                                                                            <  7:990135/94‑1 (MQ=255)                                                                                                                                                                             aaaaTAAAGGGTAATATATAACAGAAGGTTTATATAGTTAGAAGCAAGGTTGTGCTTCTAAAGGAAGTGGCTTGAGGGAGCCACTTATATg                                                                                                                                                                                                                                                               >  8:637532/1‑91 (MQ=255)                                                                                                                                                                             aaaaTAAAGGGTAATATATAACAGAAGGTTTATATAGTTAGAAGCAAGGTTGTGCTTCTAAAGGAAGTGGCTTGAGGGAGCCACTTATATg                                                                                                                                                                                                                                                               <  7:637532/91‑1 (MQ=255)                                                                                                                                                                                               taACAGAAGGTTTATATAGTTAGAAGCAAGGTTGTGCTTCTAAAGGAAGTGGCTTGAGGGAGCCACTTATATGTTGGGGAGGCaa                                                                                                                                                                                                                                                   <  7:1013517/85‑1 (MQ=255)                                                                                                                                                                                               taACAGAAGGTTTATATAGTTAGAAGCAAGGTTGTGCTTCTAAAGGAAGTGGCTTGAGGGAGCCACTTATATGTTGGGGAGGCaa                                                                                                                                                                                                                                                   >  8:1013517/1‑85 (MQ=255)                                                                                                                                                                                                    gAAGGTTTATATAGTTAGAAGCAAGGTTGTGCTTCTAAAGGAAGTGGCTTGAGGGAGCCACTTATATGTTgg                                                                                                                                                                                                                                                           >  5:184275/1‑72 (MQ=255)                                                                                                                                                                                                    gAAGGTTTATATAGTTAGAAGCAAGGTTGTGCTTCTAAAGGAAGTGGCTTGAGGGAGCCACTTATATGTTgg                                                                                                                                                                                                                                                           <  6:184275/72‑1 (MQ=255)                                                                                                                                                                                                       ggTTTATATAGTTAGAAGCAAGGTTGTGCTTCTAAAGGAAGTGGCTTGAGGGAGCCACTTATATGTTGGGGAGGCAACGCCTCCCGCAACATATCTTTTTCGTAATCAGATTAGAACTGGTAAACCAGACCTACAGCAACGATGTCATCAGTGCTTACACCGAGTGCTTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGc                                               >  2:24962/1‑273 (MQ=255)                                                                                                                                                                                                                  ttAGAAGCAAGGTTGTGCTTCTAAAGGAAGTGGCTTGAGGGAGCCACTTATATGTTGGGGAGGCAACGCCTCCCGCAACATATCTTTTTCGTAATCAGATTAGAACTGGTAAACCAGACCTACAGCAACGATGTCATCAGTTCTTACACCGAGTGCTTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCTGTAAATGCCTTGAATCAGCCTATTTAGACCGt                                  >  2:142890/1‑275 (MQ=255)                                                                                                                                                                                                                  ttAGAAGCAAGGTTGTGCTTCTAAAGGAAGTGGCTTGAGGGAGCCACTTATATGTTGGGGAGGCAACGCCTCCCGCAACATATCTTTTTCGTAATCAGATTAGAACTGGTAAACCAGACCTACAGCAACGATGTCATCAGTGCTTACACCGAGTGCTTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCCGCCTATTTAGACCGt                                  >  4:76587/1‑275 (MQ=255)                                                                                                                                                                                                                   tAGAAGCAAGGTTGTGCTTCTAAAGGAAGTGGCTTGAGGGAGCCACTTATATGTTGGGGAGGCAACGCCTCCCGCAACa                                                                                                                                                                                                                                     >  8:369279/1‑79 (MQ=255)                                                                                                                                                                                                                   tAGAAGCAAGGTTGTGCTTCTAAAGGAAGTGGCTTGAGGGAGCCACTTATATGTTGGGGAGGCAACGCCTCCCGCAACa                                                                                                                                                                                                                                     <  7:369279/79‑1 (MQ=255)                                                                                                                                                                                                                   tAGAAGCAAGGTTGTGCTTCTAAAGGAAGTGGCTTGAGGGAGCCACTTATATGTTGGGGAGGCAACGCCTCCCGCAACATATCTTTTTCGTAATCAGATTAGAACTGGTAAACCAGACCTACAGCAACGATGt                                                                                                                                                                               >  1:88593/1‑133 (MQ=255)                                                                                                                                                                                                                   tAGAAGCAAGGTTGTGCTTCTAAAGGAAGTGGCTTGAGGGAGCCACTTATATGTTGGGGAGGCAACGCCTCCCGCAACATATCTTTTTCGTAATCAGATTAGAACTGGTAAACCAGACCTACAGCAACGATGTCATCAGTGCTTACACCGAGTGCTTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGtt                                 >  4:33653/1‑275 (MQ=255)                                                                                                                                                                                                                      aaGCAAGGTTGTGCTTCTAAAGGAAGTGGCTTGAGGGagc                                                                                                                                                                                                                                                                         >  4:184249‑M2/1‑37 (MQ=255)                                                                                                                                                                                                                       aGCAAGGTTGTGCTTCTAAAGGAAGTGGCTTGAGGGAGCCACTTATATGTTGGGGAGGCAACGCCTCCCGCAACATATCTTTTTCGTAATCAGATTAGAACTGGTAAACCAGACCTACAGCAACGATGtcatc                                                                                                                                                                           <  3:88593/133‑1 (MQ=255)                                                                                                                                                                                                                           aGGTTGTGCTTCTAAAGGAAGTGGCTTGAGGGAGCCACTTATATGTTgggg                                                                                                                                                                                                                                                         <  8:631169/51‑1 (MQ=255)                                                                                                                                                                                                                           aGGTTGTGCTTCTAAAGGAAGTGGCTTGAGGGAGCCACTTATATGTTgggg                                                                                                                                                                                                                                                         >  7:631169/1‑51 (MQ=255)                                                                                                                                                                                                                            ggTTGTGCTTCTAAAGGAAGTGGCTTGAGGGAGCCACTTATATGTTGGGGAGGCAACGCCTCCCGCAACATATCTTTTTCGTAATCAGATTAGAACTGGTAAACCAGACCTACAGCAACGATGTCATCAGTGCTTACACCGAGTGCTTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTTGcc                         >  1:73225/1‑274 (MQ=255)                                                                                                                                                                                                                                 tgCTTCTAAAGGAAGTGGCTTGAGGGAGCCACTTATATGTTGGGGAGGCAACGCCTCCCGCAACATATCTTTTTCGTAATCAGATTAGAACTGGTAAACCAGACCTACAGCAACGATGTCATCAGTGCTTaca                                                                                                                                                                 >  4:570019/1‑133 (MQ=255)                                                                                                                                                                                                                                 tgCTTCTAAAGGAAGTGGCTTGAGGGAGCCACTTATATGTTGGGGAGGCAACGCCTCCCGCAACATATCTTTTTCGTAATCAGATTAGAACTGGTAAACCAGACCTACAGCAACGATGTCATCAGTGCTTACACCGAGTGCTTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCt                                                                                                                >  4:444636/1‑182 (MQ=255)                                                                                                                                                                                                                                 tgCTTCTAAAGGAAGTGGCTTGAGGGAGCCACTTATATGTTGGGGAGGCAACGCCTCCCGCAACATATCTTTTTCGTAATCAGATTAGAACTGGTAAACCAGACCTACAGCAACGATGTCATCAGTGCTTACACCGAGTGCTTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTaa                   >  2:453523/1‑275 (MQ=255)                                                                                                                                                                                                                                   cTTCTAAAGGAAGTGGCTTGAGGGAGCCACTTATATGTTGGGGAGGCAACGCCTCCCGCAACATATCTTTTTCGTAATCAGATTAGAACTGGTAAACCAGACCTACAGCAACGATGTCATCAGTGCTTACACCGAGTGNTTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCTTTTCTTCATGTTTGAGCCGATTTTNGCTCCCGTAAATGCCTTGAATAAGTNTCTGTAGACCTTTTCTTTTCCATTTACgg                 >  3:98493/1‑275 (MQ=37)                                                                                                                                                                                                                                     tCTAAAGGAAGTGGCTTGAGGGAGCCACTTATATGTTGGGGAGGCAACGCCTCCCGCAACATATCTTTTTCGTAATCAGATTAGAACTGGTAAACCAGACCTACAGCAACGATGTCATCAGTGCTTACACCGa                                                                                                                                                             <  2:570020/133‑1 (MQ=255)                                                                                                                                                                                                                                     tCTAAAGGAAGTGGCTTGAGGGAGCCACTTATATGTTGGGGAGGCAACGCCTCCCGCAACATATCTTTTTCGTAATCAGATTAGAACTGGTAAACCAGACCTACAGCAACGATGTCATCAGTGCTTACACCGAGTGCTTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACt                                                                                                            <  2:444637/182‑1 (MQ=255)                                                                                                                                                                                                                                         aaGGAAGTGGCTTGAGGGagccacttcctttagaagcacaaccttgcttc                                                                                                                                                                                                                                            >  5:783995‑M2/1‑18 (MQ=255)                                                                                                                                                                                                                                         aaGGAAGTGGCTTGAGGGagccacttcctttagaagcacaaccttgcttc                                                                                                                                                                                                                                            <  6:783995‑M2/50‑33 (MQ=255)                                                                                                                                                                                                                                             aaGTGGCTTGAGGGAGCCACTTAAAAGTTGGGGAGGCAAAGCCTCCCGCAAAATATCTTTTTCGTAATCAGAGTAGAACTGGTAAACCAGACCTACAGCAACGATGTCATCAGTGCTTACACCGAGTGCTTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATcccc       <  4:453522/275‑1 (MQ=255)                                                                                                                                                                                                                                                tGGCTTGAGGGagccacttcctttagaagcacaaccttgcttcta                                                                                                                                                                                                                                          <  5:507928‑M2/45‑35 (MQ=255)                                                                                                                                                                                                                                                tGGCTTGAGGGagccacttcctttagaagcacaaccttgcttcta                                                                                                                                                                                                                                          >  6:507928‑M2/1‑11 (MQ=255)                                                                                                                                                                                                                                                tGGCTTGAGGGAGCCACTTATATGTTGGGGAGGCAACGCCTCCCGCAACATATCTTTTTCGTAATCAGATTAGAACTGGTAAACCAGACCTACAGCAACGATGTCATCAGTGCTTa                                                                                                                                                                   >  4:545042/1‑116 (MQ=255)                                                                                                                                                                                                                                                   cTTGAGGGAGCCACTTATATGTTGGGGAGGCAACGCCTCCCGCAACATATCTTTTTCGTAATCAGATTAGAACTGGTAAACCAGACCTACAGCAACGATGTCATCAGTGCTTACACCGAGTGCTTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCAGttt  >  2:546116/1‑274 (MQ=255)                                                                                                                                                                                                                                                   cTTGAGGGAGCCACTTATATGTTGGGGAGGCAACGCCTCCCGCAACATATCTTTTTCGTAATCAGATTAGAACTGGTAAACCAGACCTACAGCAACGATGTCATCAGTGCTTACACCGAGTGCTTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCAGttt  >  1:75215/1‑274 (MQ=255)                                                                                                                                                                                                                                                    ttGAGGGAGCCACTTATATGTTGGGGAGGCAACGCCTCCCGCAACATATCTTTTTCGTAATCAGATTAGAACTGGTAAACCAGACCTACAGCAACGATGTCATCAGTGCTTACAcc                                                                                                                                                               <  2:545043/116‑1 (MQ=255)                                                                                                                                                                                                                                                          |                                                                                                                                                                                                                                                                           GCTGCTCTGATGGTTATATCGGGAAAAGGTTACAGAAGGCTGAGGGCATAATTGAAGGGATGTTAATGGCATTAGATATCCGGTTAGAGATGGATATCGTTGTTAATAACTCTAATTAATATGCCAATTGTTTACTAAAAATTATTAAAAATGGGGCGTTGAGACGCCCCCAAAAATAAAGGGTAATATATAACAGAAGGTTTATATAGTTAGAAGCAAGGTTGTGCTTCTAAAGGAAGTGGCTTGAGGGAGCCACTTATATGTTGGGGAGGCAACGCCTCCCGCAACATATCTTTTTCGTAATCAGATTAGAACTGGTAAACCAGACCTACAGCAACGATGTCATCAGTGCTTACACCGAGTGCTTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCAGTTT  >  NC_000913/574221‑574736

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 24 ≤ 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.