New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	566777 =	NA (NA)	2880 (43.040)	275/280	0.0	97.9%	noncoding (1/1258 nt)	IS3	repeat region
	?	NC_000913	= 572471	63 (0.930)					coding (6/456 nt)	ybcN	DLP12 prophage; DNA base‑flipping protein

GAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGCCCT  >  NC_000913/566636‑566912                                                                                                                                              |                                                                                                                                        gAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGTGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTACCAGGCGCAACCGTAATCTg                                                                                                                                        >  1:643133/1‑143 (MQ=255)  aaGACCGCAGAAATTCAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCCGGGGAAGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGa                                                                                                                                       <  1:403555/143‑1 (MQ=255)   aGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGAt                                                                                                                                      >  1:1077163/1‑143 (MQ=255)          aGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATTACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCACCGGTAATCTGATCTTAccc                                                                                                                               >  2:266054/1‑143 (MQ=255)          aGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCGTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTaaca                                                                                                                               >  2:454491/1‑140 (MQ=255)            aaaTTAAAGCTAATTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGCGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAg                                                                                                                             <  1:115760/143‑1 (MQ=255)            aaaTTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAg                                                                                                                             >  1:814941/1‑143 (MQ=255)            aaaTGAAGGCTAAGGTCTGACTGAAAGGAGCAAGTGTAGGACGGGCAAAGAGGCGATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAg                                                                                                                             <  2:989591/143‑1 (MQ=255)                   ggCTAAGGTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGt                                                                                                                      <  1:579870/142‑1 (MQ=255)                   aGCTAAGTTCGGAGTGACAGGAGCAAGTGGATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGGAGAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGt                                                                                                                      <  2:528523/143‑1 (MQ=255)                   aGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAATAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGt                                                                                                                      >  1:651331/1‑143 (MQ=255)                            cggagcgAAGGGAGCAAGCGTATGACGGGCAAAAAGGCCATTATTCATTACCTGGGTACGCATAAGAGCTTCTGCGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACAcgcg                                                                                                             <  2:93528/137‑1 (MQ=38)                             ggACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCgg                                                                                                            >  1:872094/1‑143 (MQ=255)                                cTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTa                                                                                                         >  1:1218271/1‑143 (MQ=255)                                 tGAAAGTAGCTATTGTATGACGGGCAATGATGCAATTATTCATTACCTGTGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGTACACGCGGCTaa                                                                                                        <  2:121988/143‑1 (MQ=38)                                 tGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTaa                                                                                                        <  1:380471/143‑1 (MQ=255)                                   aaaGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGt                                                                                                      <  2:563830/143‑1 (MQ=255)                                     tggAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGa                                                                                                    <  2:507482/142‑1 (MQ=255)                                            aGTGGATGACGGGCAAGGGGGGAATGATTCATGGCCTGGGGAGGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAAct                                                                                             <  1:277859/143‑1 (MQ=37)                                             gtgtATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATCGTGGATACGCGGCTAAGTGAGTAAActc                                                                                            >  2:414101/1‑143 (MQ=255)                                              tgtATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAActct                                                                                           <  2:956807/143‑1 (MQ=255)                                                  tGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCtgagt                                                                                       >  1:324738/1‑143 (MQ=255)                                                  tGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCtcagt                                                                                       >  1:81667/1‑143 (MQ=255)                                                    aCGGGCACAGGAGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGGAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCtcagtca                                                                                     <  1:734496/143‑1 (MQ=255)                                                      gggCACAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCaga                                                                                   <  2:108893/143‑1 (MQ=255)                                                      gggCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTATTTGTTTTTGTCCCCACCACAATAACAGGCGCAACCGTAATGTGATCTTACCCAGGAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCaga                                                                                   <  1:901857/143‑1 (MQ=18)                                                                gCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCACGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCGAAGTGAGTAAACTCTCAGTCAGAGGTGACTcac                                                                         >  1:646149/1‑143 (MQ=255)                                                                  aaTTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGCCTCACAt                                                                       >  1:387089/1‑143 (MQ=255)                                                                  aaTTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTcacct                                                                       >  1:272699/1‑141 (MQ=255)                                                                               cTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTGACATGACAAAAACAGTa                                                          >  2:331671/1‑143 (MQ=255)                                                                               cTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTa                                                          >  1:1179591/1‑143 (MQ=255)                                                                                gggggCCGCAGAAGAGTTTCTGTGCACAGGACGTCCACACGGTAACAGGCGCAACCGTAATCTGATCTTACCTAGCAATAGTGGACAGGCGGGTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTAt                                                         <  2:111709/142‑1 (MQ=18)                                                                                    gACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAAc                                                     <  1:1212973/143‑1 (MQ=255)                                                                                    gACGCACAAGAGCTTCTGCGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAAc                                                     <  1:58082/143‑1 (MQ=255)                                                                                       gCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTcaca                                                                        >  2:1234270/1‑121 (MQ=255)                                                                                       gCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTcaca                                                                        <  1:1234270/121‑1 (MQ=255)                                                                                       gCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAg                                                  >  1:1048444/1‑143 (MQ=255)                                                                                       gCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTAACATGACAAAAACAGTATCAACCAg                                                  >  2:992474/1‑143 (MQ=255)                                                                                        cATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTATACTTTCAGTCAGTGGTGACTCACATGACAAAAACAGTATCAACCAGt                                                 <  1:607557/143‑1 (MQ=255)                                                                                         aTAAGAGCTTCTGTGCACAGGACGTTGCCGCGTTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATACTAGACACGCGGCTAAGTGAGTAAACACTCAGGAAGAGGAAAATAAAAAGAAAAAAACAAAAACAACCAGTa                                                >  2:648609/1‑143 (MQ=21)                                                                                          tAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTaa                                               >  1:578875/1‑143 (MQ=255)                                                                                            agagCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTaaaa                                             >  1:832379/1‑143 (MQ=255)                                                                                             gagCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAGAACAGTATCAACCAGTaaaaa                                            >  1:454558/1‑143 (MQ=255)                                                                                                 ttCTGTGCACAGGACGTTGCGCCGGTAACAGGCGCAAACGTAATCTGATCTGACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAAccc                                        <  2:948501/143‑1 (MQ=255)                                                                                                      tgCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGGAATCGTGCACACGCGGCTAAGTGCGAAAACACACAGTCAGAGGTGACTCCCATGACAACAACAGTAACAACCAGAAAAAAACCCCGaaa                                   >  2:742758/1‑143 (MQ=255)                                                                                                      tgCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTaa                                   >  1:1088679/1‑143 (MQ=255)                                                                                                         acaGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGCCAAGAACACGAACAACCAGGAAAAAAACACGTAAACa                                >  2:6232/1‑143 (MQ=17)                                                                                                                 ttGCCGCGGTAACAGGGGGAACCGTAATCTGATCTTACGCAGCAATAGTGGACAGGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGc                        <  2:406305/143‑1 (MQ=255)                                                                                                                 ttGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGc                        <  1:537045/143‑1 (MQ=255)                                                                                                                      gcgGTAACAGGCGCAAGCGTAATCTGATCTGACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGaa                   <  2:1104633/143‑1 (MQ=255)                                                                                                                         gTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTCAAttt                <  2:564697/143‑1 (MQ=255)                                                                                                                           aaCAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCg              <  2:1179591/143‑1 (MQ=40)                                                                                                                             cAGGCGCGACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCACACGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCa            <  2:879566/143‑1 (MQ=255)                                                                                                                              aGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAg           >  2:418655/1‑143 (MQ=38)                                                                                                                               ggCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGt          <  2:832379/143‑1 (MQ=37)                                                                                                                                     aCCGTAATCTGATCTTACCCAGCAATAGTGGACCCGCCACTCATTCATGATACTCTCAGTCAGAGGTGACGCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGcc    <  1:1223045/143‑1 (MQ=11)                                                                                                                                      ccGTAATCTGATCTTACCCAGCAATAATGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTAGCCTGAATTTCGCAGTGAAGccc   >  1:372301/1‑143 (MQ=14)                                                                                                                                       cGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGCCCt  >  1:289862/1‑143 (MQ=11)                                                                                                                                              |                                                                                                                                        GAAGATCGCAGAAATTAAAGCTAAGTTCGGACTGAAAGGAGCAAGTGTATGACGGGCAAAGAGGCAATTATTCATTACCTGGGGACGCATAAGAGCTTCTGTGCACAGGACGTTGCCGCGGTAACAGGCGCAACCGTAATCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTCACATGACAAAAACAGTATCAACCAGTAAAAAACCCCGTAAACAGCATTCGCCTGAATTTCGCAGTGAAGCCCT  >  NC_000913/566636‑566912

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ 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.