New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	566777 =	NA (NA)	1275 (30.790)	248/282	-0.0	97.6%	noncoding (1/1258 nt)	IS3	repeat region
	?	NC_000913	= 572471	31 (0.740)					coding (6/456 nt)	ybcN	DLP12 prophage; DNA base‑flipping protein

AAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGCC  >  NC_000913/566647‑566910                                                                                                                                   |                                                                                                                                      ataTTGAAGCTAAGTTAGGATTGAAAGGAGTAAGTGTATGACGGGCAAAGAGGCAATTATTTATTACCTGGGGACGCATAAGAGCTTCTGTGGACAGGACGTTGCCGTGGTAACAGGCGCAACCGTAATCTGATCTTACCCAg                                                                                                                           <  1:501440/141‑1 (MQ=255) aaaTTAAAGCGAATGTCGGTAGTACAGGAGCTAGTGTATGACGGGCAAAGAGGCAAGTATTCATTACCTGGGTGCGCATAAGAGCTTCTGTGTACAGGACGTTGCCGTGGTAATAGGCGCAACCGTAATCTGATCTTACCCAg                                                                                                                           <  2:678083/143‑1 (MQ=255)   aTTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCa                                                                                                                         >  1:510832/1‑143 (MQ=255)          cTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATAATTCATTACCTGGGGACGCATAAGCGCTGCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTACTCTGATCTTACCCAGCACGAGTgg                                                                                                                  >  2:463127/1‑143 (MQ=255)           tAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGa                                                                                                                 <  2:113343/143‑1 (MQ=255)               ttCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAGCCGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACAcg                                                                                                             >  1:58381/1‑143 (MQ=255)                tCGGAGTGATAGGAGCATGTGTATGCCGTGCAAAGTGGCCATTAGTCATTTCCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACAcgc                                                                                                            <  2:624171/143‑1 (MQ=38)                  ggACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGTTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGAACACGCgg                                                                                                          >  1:219328/1‑143 (MQ=255)                   gACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCGCAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGc                                                                                                         >  1:698638/1‑143 (MQ=255)                   gACTGAAAGGAGCAAGTGTATGACGCGCAACGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGCTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTCACCCCGCAATAGTGGACAcacgcc                                                                                                         >  2:346800/1‑141 (MQ=255)                        aaaGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCCGCAGTCGCGGCCACGCGGCtgcag                                                                                                    >  1:708592/1‑139 (MQ=255)                        aaaGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGCAATCTGATCTTACCCAGCAATAATGGACAAGAGGCTAAGt                                                                                                    >  1:377493/1‑143 (MQ=255)                         aaGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCACAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTg                                                                                                   >  1:154112/1‑143 (MQ=255)                          aGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGa                                                                                                  >  1:296706/1‑143 (MQ=255)                            gAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCACCCGTAATCTGATCTTACCCAACAAAAGTGAACACGCAGCTAAGTGAGt                                                                                                >  1:199275/1‑143 (MQ=255)                                   tgtATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAActct                                                                                         <  2:296706/143‑1 (MQ=255)                                     tacgACGGGTAAAGAGGTAATTATGCATTACTTGGGGACGCATAAGAGCTGCTGGGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCTGCTAAGTGAGTAAACTCtca                                                                                       <  2:214880/140‑1 (MQ=37)                                       tGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCtcagt                                                                                     <  2:339435/143‑1 (MQ=255)                                        gACGGGCAAAGAGGCAATTATTCATTACCTGCAGACGCAGAAGAGCGTCTGTGCACAGGACGTTGCCGCGGTAACAAGCACAACCGTAACCTGAACTTACCCAACAAAAGTAAACACGCCGCTAAGTAAGTAAACTCtcagtc                                                                                    >  2:526344/1‑143 (MQ=255)                                                  gagGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACt                                                                          >  1:557433/1‑143 (MQ=255)                                                    ggCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTca                                                                        <  2:103086/143‑1 (MQ=255)                                                       aaTTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAATCTCTCAGTCAGAGGTAACTCAAAt                                                                     >  1:226766/1‑143 (MQ=255)                                                       aaTTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAAAGGTGACTcacgt                                                                     >  1:80431/1‑141 (MQ=255)                                                         ttattCATTACCTGGAGACGCATAAGAGCTTCGGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAAGCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGa                                                                   <  1:245007/143‑1 (MQ=255)                                                             tCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGCTCTTACCCAGCAATAGTGGACTCGCGGCTAAGTGAGAAAAATCTCAGTAAGAGGGAACAAACATGACaaa                                                               >  1:295126/1‑143 (MQ=25)                                                                gtACCTGATGACGGATAAGAGCTTCTGTGCATAGGACGATGCCGCGGTAACAGGCGCAAAGGTAATCTCGTGTTACCCAGCAATAGTGGACACGCTGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCAAATGAGAAAAAc                                                            <  2:152806/142‑1 (MQ=18)                                                                               tAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGAGACTCACATGACAAAAACAGTAGCCACCAGTaa                                             >  2:596725/1‑143 (MQ=255)                                                                                   agCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTagacaa                                         >  2:169978/1‑138 (MQ=255)                                                                                    gCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAACTGAGTAAACTCTCAGTCATAGGTGACTCACATAACAAAAAAAGTATCAACAAGTAAAAAAc                                        >  1:106966/1‑143 (MQ=18)                                                                                     cTTTTGTGCACAGGCCGTTTGCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAAcc                                       <  2:623232/143‑1 (MQ=255)                                                                                       tCTGTGCACAGTACGTTGTCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAAcccc                                     <  1:7827/143‑1 (MQ=255)                                                                                              acaGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCCACCAGTAAAAAACCCCGTAcaca                              >  1:457916/1‑143 (MQ=255)                                                                                                    cgtaaccGCGGTAACAGGCGCAACCGTAATCTGATATTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGACAGAGGGGACTCACATGAAAAAAACAGTATCAACCAGTAAAAAACACCGAAAACAGCATTc                        >  2:637676/6‑143 (MQ=14)                                                                                                               tAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCATATGACAAAAACAGAATCAATCAGTAAAAAAAACTGTAAACAACATTAgaatgaatata             >  1:303988/1‑140 (MQ=14)                                                                                                                   aGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCGAAGTGAATAAACTCCCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTACACCGCAGTCGCCCGAAGTTCGCAg         >  2:630796/1‑143 (MQ=11)                                                                                                                        cAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTAACAAAAAAAAAAAAACCACGTAAACAGCATTCGCCTGAATTTCGCAGTGAAg    >  1:249471/1‑143 (MQ=11)                                                                                                                          aCCGTAATATGATCTTACCCAGCAATAGGGGACACGCGGCTAAGTGAGTAAACTCTCAGCCAGAGGTGACTCACATGACAATAACAGTATCAACCCGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGcc  <  2:245150/143‑1 (MQ=11)                                                                                                                                   |                                                                                                                                      AAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGCC  >  NC_000913/566647‑566910

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ 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.