New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	566777 =	NA (NA)	2171 (46.830)	257/262	NT	98.1%	noncoding (1/1258 nt)	IS3	repeat region
	?	NC_000913	= 572471	43 (0.920)					coding (6/456 nt)	ybcN	DLP12 prophage; DNA base‑flipping protein

CGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGC  >  NC_000913/566635‑566909                                                                                                                                               |                                                                                                                                     cGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCt                                                                                                                                      <  1:494348/143‑1 (MQ=255) cGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGCAATCt                                                                                                                                      >  1:751674/1‑143 (MQ=255)  gAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAGCCGGCGCAACCGTACTCTg                                                                                                                                     >  1:18540/1‑143 (MQ=255)  gAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTg                                                                                                                                     >  1:153125/1‑143 (MQ=255)   aaGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGa                                                                                                                                    <  1:454924/143‑1 (MQ=255)     gATCGCAGAAATTAAAGCTAAGTTCTTACTGAAAGGAGCAAGTGTATGGCGGGCAAAGAGGCAATTATGCGTTACCTGGGGACGCAGAAGAGCTTCTGTACACAGTTGGTTTCCGCGGTAACAGGCGCAACCGTAATCTGATc                                                                                                                                  <  1:873802/143‑1 (MQ=255)     gATCGCAGAAATTAAAGCTAAGTTCCGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATc                                                                                                                                  <  1:794325/143‑1 (MQ=255)         gCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTAc                                                                                                                              >  1:837249/1‑143 (MQ=255)         gCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGCAACATCCGCAACCGTAATCTGATCTTAc                                                                                                                              >  1:817290/1‑143 (MQ=255)               aTTAAAGCTAAGTTCGGAATGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTTTTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCa                                                                                                                        <  2:54002/143‑1 (MQ=255)                ttAAAGATAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGCCGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCCGCaa                                                                                                                       >  1:331036/1‑143 (MQ=255)                  aaaGCTGAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATa                                                                                                                     <  2:707233/143‑1 (MQ=255)                       gagtgttggATTGAAAGGAGCATGTTTATGACGGGTCAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGa                                                                                                                <  2:467938/136‑1 (MQ=255)                          gTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGacac                                                                                                             >  1:495123/1‑143 (MQ=255)                             cGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAAATATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACAcgcg                                                                                                          <  1:763199/143‑1 (MQ=255)                              ggACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACCGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCgg                                                                                                         >  2:791230/1‑143 (MQ=255)                                    aaaGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGt                                                                                                   <  2:153125/143‑1 (MQ=255)                                    aaaGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGt                                                                                                   >  1:804867/1‑143 (MQ=255)                                           cAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTTGACACGCGGCTACGTGAggaca                                                                                            >  2:771499/1‑139 (MQ=255)                                            aaGTGTCTGACGGGCAAAGCGGCAATTATTGCTTACCTGGGGACGGATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCCGCTATAGTGGACACGCGGCTAAGTGAGTAAAc                                                                                           <  1:677825/143‑1 (MQ=38)                                            aaGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGACGAAAc                                                                                           >  2:396371/1‑143 (MQ=255)                                             agggtATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTCGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAAct                                                                                          <  1:433161/140‑1 (MQ=255)                                                  aTGACGGGCAAAGAGGCGATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTGGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCtcag                                                                                     <  1:311832/143‑1 (MQ=255)                                                  aTGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAAATCtcag                                                                                     >  1:642292/1‑143 (MQ=255)                                                       gggCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACGGTACGGCAATCTTGCCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCaga                                                                                >  1:910290/1‑143 (MQ=37)                                                            aaGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGa                                                                           >  1:510421/1‑143 (MQ=255)                                                                            ttACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAGTCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTCACCTCTCAGTCAGAGGTGACTCACATGACcaaccc                                                           >  2:285970/1‑140 (MQ=25)                                                                             gaCCTGGAGATGCATAAGATCTTCTGTGAACTGGACGTTGCCGCAGTAACAGGCGCAACAGTAATCTGATACGACCCAGGAATAGTTGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGGCAAAAACa                                                          <  2:83416/142‑1 (MQ=18)                                                                               gctcgggACGCATGAGCGCGTCTGTGCACACGCACTCGCCCCGTTAACAGGCGCAACCGTAATCTGATCGTACCCAAGAATAGTAGACAGGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGt                                                        <  2:164325/139‑1 (MQ=17)                                                                               ccTGCGGCCGCAACAGAGCCTCTGTGCACAGGACGTCGCCGCGGTAACAGGCCCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCCAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGt                                                        <  1:647633/143‑1 (MQ=18)                                                                                    ggACGCATAAGAGATTCTGTGCACAGGACGTTGCCGCGGTAACAGGCACAACCGTAATCTGATCTTACCCAGCAATAGAGGACACGCGGCTAAGTGAGTAAACAATCAGTCAGAGATAACTCGCATGAAAAAAAAAGTAACaa                                                   >  2:250533/1‑143 (MQ=21)                                                                                        gCATAAGAGCTTCTGTGCACAAGAAGTTGCCGTGGTAACAGTGGCAACCGTAATCTGATCTTACCCGGCAATAGTGGACACGCGGCTAAGTGAATAAACTCTCAGTCAGAGGTGCCTCACATGACAAAAACAGTATCAACCAg                                               >  2:18181/1‑143 (MQ=18)                                                                                             agagCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCAAGAAATAGTGGTCACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTaaaa                                          >  1:343667/1‑143 (MQ=255)                                                                                              gagCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACCCACATGACAAAAACAGTATCAACCAGTaaaaa                                         >  2:873194/1‑143 (MQ=255)                                                                                                     tgtgCACAGGACGTTGCCGCGGTAACAGGAGCCAACGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGt                                  <  1:711555/143‑1 (MQ=255)                                                                                                       tgCACAGGACGTTGCCGCGGGAACATGCGCAACCGTAAGCTGATCTTACCCAGCAGTAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGAGTCAGATGACAAAAACAGCATCAACCAGTAACAACACCCGTaa                                >  2:559368/1‑143 (MQ=17)                                                                                                        gCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTaaa                               >  1:211188/1‑143 (MQ=255)                                                                                                          acaGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCCGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACa                             <  1:606586/143‑1 (MQ=255)                                                                                                          aaaGGACGTTGCCGAGGTAACAGGCGCAACGGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACa                             <  2:741064/141‑1 (MQ=255)                                                                                                           caGGACGTGGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAg                            <  1:860169/143‑1 (MQ=255)                                                                                                                 gTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAACCTCTCAGTCAGAGGTGCCTCACATGACAAATACAGTTTCCACCAGTAAAAAACCAAATAAACAGCATTca                      >  1:240141/1‑142 (MQ=17)                                                                                                                 gTTGACTCGGTAACAGTCGCAACCGTTATCTGATCGCACCCAGCAATATGGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTTACATGACAAAAACAGTATCAACCATTAAAAAACCCCGTAAACAGCATTCg                      <  2:23773/143‑1 (MQ=14)                                                                                                                  ttGCCGCGGTAACAGGCGCAATCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGc                     <  1:446274/143‑1 (MQ=255)                                                                                                                      cgcgGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGGCAGAGGTGACTCACATGACAAAAACAGTAGCCACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGa                 >  1:798522/1‑143 (MQ=255)                                                                                                                          gTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTAAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGCAACCACCATACGCCtccatct             >  2:769955/1‑137 (MQ=14)                                                                                                                              cacgcgcAACCGGAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAACCTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCa         <  2:246121/140‑1 (MQ=255)                                                                                                                               aGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAg        >  1:814528/1‑143 (MQ=38)                                                                                                                               aGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAg        >  1:605909/1‑143 (MQ=38)                                                                                                                                 gcgcAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTg      >  1:162527/1‑143 (MQ=35)                                                                                                                                  cgcAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGGCCGAATATCGCAGTGa     >  1:662103/1‑143 (MQ=255)                                                                                                                                   gcAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGaa    <  1:791230/143‑1 (MQ=34)                                                                                                                                   gcAACCGTAATCTCATCTTACCCCGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGaa    <  1:868113/143‑1 (MQ=21)                                                                                                                                    cAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTCAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGacg   >  2:360930/1‑141 (MQ=18)                                                                                                                                     aaCCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGc  <  2:211188/143‑1 (MQ=32)                                                                                                                                               |                                                                                                                                     CGAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGC  >  NC_000913/566635‑566909

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ 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.