New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	566777 =	NA (NA)	2154 (34.830)	266/280	0.0	97.1%	noncoding (1/1258 nt)	IS3	repeat region
	?	NC_000913	= 572471	64 (1.030)					coding (6/456 nt)	ybcN	DLP12 prophage; DNA base‑flipping protein

AAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGCCC  >  NC_000913/566637‑566911                                                                                                                                             |                                                                                                                                       aaGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGa                                                                                                                                      <  2:629421/143‑1 (MQ=255)      cGCAGCAATTAGAGCGAAGTTCGGACTGCAAGGAGCAAGCGTATGACTTGCAAAGAGGCAATTATTCAGTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTa                                                                                                                                 <  2:1105655/143‑1 (MQ=255)       gCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTAc                                                                                                                                >  1:994393/1‑143 (MQ=255)       gCAAAAATTAAAGCTAAGATCGGACTGAAAGGAGCCAGTGTATGACGGGCAAAGAGGCAATAATGCATTACCTGGGGACGCATAAGAGCCTCTGTGCACAGGACGTTGCAGCGGTACCAGGCGCAAACGAACGCTGATCTGAc                                                                                                                                >  2:327777/1‑143 (MQ=255)              ttAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGGCGCGGCAACAGGCGACAACGGAAACGGATCTTACCCAGCaa                                                                                                                         >  2:897097/1‑143 (MQ=255)                aacgcgaaGTTCGGACTGAAAGGAGCGAGTGTATGACGGGCAAAGAAGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATa                                                                                                                       <  2:1026396/137‑1 (MQ=255)                         ttCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGCTCTTACCCAGCACTATGCGACAcg                                                                                                              >  1:457469/1‑143 (MQ=255)                         ttCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGaccag                                                                                                              >  2:674861/1‑140 (MQ=255)                                  aaaGGAGCAAGTGTATGACGGGCAAAGATGCAATTATTCATTACCTGGGGACGCATAAGAGCATCTGTGCACAGGACGTTGCGGCGGTAACAGGCGCAACCGTAATCTGATCTTACGCAGCAAGAGTGGACCCTCGGCTACGt                                                                                                     >  2:88516/1‑143 (MQ=255)                                  aaaGGAGCAAGCGGATGACGGGCAAAGAGGCAATTATTCATTACCTGGGTACGCAGAAGAGCGTCTGTGCACAGGCCGTTGCCGCGGGGCGAGGCGCAACCGTAATCCAATCTTACCCAGCAATAGGGCACCAGCGGCTAAGt                                                                                                     >  2:1107724/1‑143 (MQ=255)                                    aagggCACGTGTAGGACGGGGAAAGAGGCAATTAGTCGTTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAAGCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGa                                                                                                   <  2:888122/139‑1 (MQ=38)                                    aGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCCAAGTGa                                                                                                   >  1:191077/1‑143 (MQ=255)                                     ggAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAg                                                                                                  >  1:164689/1‑143 (MQ=255)                                      gAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGt                                                                                                 >  1:205341/1‑143 (MQ=255)                                         cAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATCGTGGACACGCGGCTACGTGACTaaa                                                                                              >  1:195383/1‑143 (MQ=255)                                               tacgACGGGCAAAGAGGCGATTATCCACCACCTTCGGACGCATAAGAGCTTCTGTGCACAGGTCGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCtca                                                                                        <  1:575313/140‑1 (MQ=25)                                               tATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCtca                                                                                        <  1:885929/143‑1 (MQ=255)                                               tATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCtca                                                                                        <  2:72431/143‑1 (MQ=255)                                               tATGACGGGCAAACGGGCAATTATTCCTTACCTGGGGACGCATAAGAGCTTCTGCAGAAATACCGGTTTCGCGGTAACAGGGGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCtca                                                                                        <  1:525766/143‑1 (MQ=21)                                                aTGGCGGGCAAAGAGGCAATTATTCATTGCCTGCGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCtcag                                                                                       <  2:469723/143‑1 (MQ=255)                                                         aaaGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTg                                                                              >  1:997206/1‑143 (MQ=255)                                                           agagGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCCACCGTAATCTGATCTTACCCAACAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGAc                                                                            >  1:698919/1‑143 (MQ=255)                                                            gacgccattcttCTTTACCTGGGGACGCATAATAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCCGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACt                                                                           <  2:389041/137‑1 (MQ=25)                                                               gCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGGAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAGCTCTCAGTCAGAGGTGACTcac                                                                        >  2:721423/1‑143 (MQ=255)                                                                cAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACCGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGCGAGTAAACACTCAGTCAGAGGTGAcacaca                                                                       >  2:738489/1‑143 (MQ=255)                                                                cAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTcaca                                                                       <  1:979481/143‑1 (MQ=255)                                                                   ttattCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGa                                                                    <  2:691180/143‑1 (MQ=255)                                                                    tattCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGAACGTTGCCGCGGAAACAGGCGCAACCGGAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAACCTCTCAGTCAAAGGTGACACACCTGAc                                                                   >  2:105690/1‑143 (MQ=25)                                                                      ttCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCACCCGTAATCTGATCTTACCCAGCACTCGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGGGCCTAACATGACaa                                                                 >  2:168446/1‑143 (MQ=25)                                                                         aTTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACaaaaa                                                              >  2:966875/1‑143 (MQ=255)                                                                         aTTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCCTACCCAGCAAAAATGGACACGCCGCTAAGTGAGCAAACTCGCAGTCAGAGGTGACTAACAAGACcaaaa                                                              >  2:625499/1‑143 (MQ=255)                                                                           ttccTGGGTACGCATATGAGCTTCTGTGCACAGGATGTTGCCGCGGTAACAGGCGCAACAGTAATCTGATCTTACCCAGCAATACTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACa                                                            <  2:565416/141‑1 (MQ=21)                                                                                 gggACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGa                                                                             <  1:186934/120‑1 (MQ=255)                                                                                 gggACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGa                                                                             >  2:186934/1‑120 (MQ=255)                                                                                     cGCATAGGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCa                                                  <  2:199281/143‑1 (MQ=255)                                                                                               cgtCTGTGCACAGGACCTTGCCGCAGTAACTGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAAcc                                        <  2:663696/141‑1 (MQ=255)                                                                                                        acaGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACa                               >  2:133579/1‑143 (MQ=255)                                                                                                        acaGGACGTGGCCGCGGTAACAGGCGCAACCGTAAGCTGATCTTACCCAGCAATAGTGGACACGCGGCGAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACa                               <  1:256677/143‑1 (MQ=255)                                                                                                         caGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAg                              >  1:33853/1‑143 (MQ=255)                                                                                                                ttGCCGCGGTAACAGGCGCACCCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGc                       <  1:960881/143‑1 (MQ=255)                                                                                                                 tgcgggggTAACAGGCGCTACTGTAATCTTATGTTACCCAGCAAGAGTGGACACGCGGATAAGTGAGTAAACTCTCAGTGAGAGGTGACTCACATGACAAAAACAGGATCAACCAGTAAAAAACCCCGTAAACAGCATTCGcc                      <  2:383927/137‑1 (MQ=11)                                                                                                                  gCCGCGGTAACAGGCGCAACCGTAACCCGATCCTACCCAGGAATAGGGGACACGCGGCTAAGTGAGTGAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCt                     <  1:997571/143‑1 (MQ=14)                                                                                                                    cgcgGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGa                   >  1:910452/1‑143 (MQ=255)                                                                                                                        gcaaCATGCGCAACCGTAAGCGAATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTACACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAAttt               <  1:569815/141‑1 (MQ=11)                                                                                                                        gTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAAttt               <  2:151664/143‑1 (MQ=255)                                                                                                                         tAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAACCAGCATTCGCCTGAATTTc              >  1:916840/1‑143 (MQ=255)                                                                                                                           aCAGGCGCAACCGTACGCTGATCTTACCCAGCCTTGCTGGACACTCGGGTGCGTGAGCAAACTCTCAGGCAGGGGTGTGTCGCAGTACAGATACAGGATCAACCAGTAAAAAACCCCGGAAAGAGCATTCGCGTGAATTTCGc            >  2:1057584/1‑143 (MQ=9)                                                                                                                            cAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCa           <  2:875567/143‑1 (MQ=38)                                                                                                                            cAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCa           <  1:1106948/143‑1 (MQ=38)                                                                                                                               gcgcAACCGTAATCCGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTg        <  1:46584/143‑1 (MQ=25)                                                                                                                                cgcAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGTCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTGGCCTGAATTTCGCAGTGa       >  2:425325/1‑143 (MQ=25)                                                                                                                                 gcAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACGCACATGACAAAAACAGTATCAACCCGTCAACACCCCCGTAGCCCGCATTCGCCTGAATATCGCAGTGaa      >  1:905634/1‑143 (MQ=11)                                                                                                                                    aCCGTTATCTGTTCTTTCCTAGCAATAGCGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGcc   <  1:442720/143‑1 (MQ=11)                                                                                                                                    aCCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGcc   <  1:88516/143‑1 (MQ=32)                                                                                                                                     ccGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGAAGTGAAGccc  >  2:37926/1‑143 (MQ=14)                                                                                                                                             |                                                                                                                                       AAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGCCC  >  NC_000913/566637‑566911

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