New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP000730 512620 =25 (1.030)16 (0.950)
+TTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAA
15/180 NT 45.7% intergenic (+688/‑173) recR/rrs1 recombination protein RecR/16S ribosomal RNA
?CP000730 1998278 = 30 (1.230)intergenic (‑6/+5) USA300HOU_t0050/rrf4 tRNA‑Val/5S ribosomal RNA

ACTGATTACAAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAATTTA  >  CP000730/1998138‑1998415
                                                                                                                                             |                                                                                                                                         
aCTGATTACAAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTa                                                                                                                                           >  2:109204/1‑141 (MQ=35)
 ccgcttACAATTCAGCTGCTCTACCAATTGCGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGTCCCGCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTaa                                                                                                                                          <  1:86968/137‑1 (MQ=11)
  tGATTACAAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTaaa                                                                                                                                         <  1:62186/141‑1 (MQ=38)
    attatcaGTCAGTTGCTCTACCAATTGAGTTAGGTCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAAc                                                                                                                                       <  2:223150/135‑1 (MQ=255)
     ttACAAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACt                                                                                                                                      <  1:38334/141‑1 (MQ=40)
       aCAAGTCAGTTGCCCTACCGAAAGAGGTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACGGc                                                                                                                                    >  1:135906/1‑141 (MQ=14)
         aaGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAAAATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTGATTCTCCGATTTAAAACTGCCt                                                                                                                                  >  1:194032/1‑141 (MQ=255)
           gacatattgtcattcagttttcaatgttcatttttcttaccgacaagaattaattatacattttatcaacatttaagtcaataactttttttatcttgtccattttattttttaaccaaaatttgattaaAAAACTGCCTg                                                                                                                                 <  1:259290‑M2/11‑1 (MQ=255)
                      tACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTAc                                                                                                                     <  1:132572/141‑1 (MQ=255)
                        tcagttttcaatgttcatttttcttaccgacaagaattaattatacattttatcaacatttaagtcaataactttttttatcttgtccattttattttttaaccaaaatttgattaaAAAACTGCCTGGCAACGTTCTAct                                                                                                                    >  1:266687‑M2/118‑141 (MQ=255)
                        tcagttttcaatgttcatttttcttaccgacaagaattaattatacattttatcaacatttaagtcaataactttttttatcttgtccattttattttttaaccaaaatttgattaaAAAACTGCCTGGCAACGTTCTAct                                                                                                                    <  1:238755‑M2/24‑1 (MQ=255)
                            ttGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGc                                                                                                               >  1:151353/1‑141 (MQ=255)
                               aGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCACCGTTCTACTCTAGCGGa                                                                                                            >  1:136461/1‑141 (MQ=255)
                                taatgttaatttttcttaccgacaagaattaattatacattttatcaacatttaagtcaataactttttttatcttgtccattttattttttaaccaaaatttgattaaAAAACTGCCTGGCAACGTTCTACTCTAGCGGa                                                                                                            <  2:30455‑M2/32‑1 (MQ=255)
                                 cttcaccGGCAATATGTAAGAATAAATGGTGGAGAATGCCGGGTTCGAAGCGCCGACCCTCTGCGTGTAAGGCAGATGCTCTCCCAGCTGAGCTAAGTCTACGATTTAAACCTGCCTGGAAACGTTGTAatctctaggcac                                                                                                          >  2:212126/6‑133 (MQ=14)
                                 ctgggCCGGCTAGGTGGAAGAGGAAATGTTGTAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAAc                                                                                                          >  2:234617/4‑141 (MQ=17)
                                 aatgttcatttttcttaacgacaaaaattaattatacattttatcaacatttaagtcaataactttttttatcttgtccattttattttttaaccaaaattttattaaAAAACAGCTTTGCAACTTTCTACTCTAGCGGaa                                                                                                           >  2:126435‑M2/109‑141 (MQ=255)
                                  tAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACg                                                                                                         >  1:197423/1‑141 (MQ=255)
                                  atgttcatttttcttaccgacaagaattaattatacattttatcaacatttaagtcaataactttttttatcttgtccattttattttttaaccaaaatttgattaaAAAACTGCCTGGCAACGTTCTACTCTAGCGGAAc                                                                                                          >  1:45885‑M2/108‑141 (MQ=255)
                                   tgttcatttttcttaccgacaagaattaattatacattttatcaacatttaagtcaataactttttttatcttgtccattttattttttaaccaaaatttgattaaAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACg                                                                                                         <  1:19814‑M2/35‑1 (MQ=255)
                                     ttcatttttcttaccgacaagaattaattatacattttatcaacatttaagtcaataactttttttatcttgtccattttattttttaaccaaaatttgattaaAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTa                                                                                                       >  1:216542‑M2/105‑141 (MQ=255)
                                          ttttcttaacgacaagaattaattatacattttatcaacatttaagtcaataactttttttatcttgtccattttattttttaaccaacgtttgattaaACAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTc                                                                                                  <  1:108802‑M2/42‑1 (MQ=255)
                                          cattttttAAGAATAAATGGTGGCGAATGACGGGTTCGAACCGCCGACCATCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCg                                                                                                 <  1:34212/134‑1 (MQ=255)
                                          cAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTca                                                                                                 >  1:113375/1‑140 (MQ=255)
                                             tatGTAAGAATAAATGGTGGAGAATGACGGGTTCGACCCGCCGCCCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACt                                                                                              <  2:246555/141‑1 (MQ=255)
                                                    gacaagaattaattatacattttatcaacatttaagtcaataactttttttatcttgtccattttattttttaaccaaaatttgattaaAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATc                                                                                        <  2:177176‑M2/52‑1 (MQ=255)
                                                         aaTGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGCTCGACTACCATCGACGCt                                                                                  <  2:256989/141‑1 (MQ=255)
                                                                ttatacattttatcaacatttaagtcaataactttttttatcttgtccattttattttttaaccaaaatttgattaaAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAg                                                                            >  1:253272‑M2/78‑141 (MQ=255)
                                                                gagaATGCCGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGc                                                                           <  1:253055/141‑1 (MQ=255)
                                                                  gaATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCCGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTCCGACTACCACCGACGCTAGGGAGCtt                                                                         >  2:12476/1‑141 (MQ=255)
                                                                         ttatcaacatttaagtcaataactttttttatcttgtccattttattttttaaccaaaatttgattaaAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTc                                                                   <  2:17851‑M2/73‑1 (MQ=255)
                                                                          ggTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCtg                                                                 <  1:76462/141‑1 (MQ=255)
                                                                           atcaacatttaagtcaataactttttttatcttgtccattttattttttaaccaaaatttgattaaAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCtg                                                                 >  1:138642‑M2/67‑141 (MQ=255)
                                                                            ttCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCtgtg                                                               >  1:116421/1‑141 (MQ=255)
                                                                             tCGAACCGCCGACCCGCTGCTTGTAAGGCAGATGCTCTCCCGGCTTGGCTAATTCTCCGATTTAAAACTGCCTGGCAACCTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTgtgt                                                              <  1:48001/141‑1 (MQ=17)
                                                                                    taagtcaataactttttttatcttgtccattttattttttaaccaaaatttgattacAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGGTTAACTTCTGTGTTCGGCa                                                        >  2:49501‑M2/58‑141 (MQ=255)
                                                                                      agtcaataactttttttatcttgtccattttattttttaaccaaaatttgattaaAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATg                                                      >  1:230752‑M2/56‑141 (MQ=255)
                                                                                       gtcaataactttttttatcttgtccattttattttttaaccaaaatttgattaaAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATgg                                                     >  1:227988‑M2/55‑141 (MQ=255)
                                                                                       caCCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATggg                                                    <  1:25826/140‑1 (MQ=255)
                                                                                         cccTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTATGTTCGGCATGGGaa                                                  >  1:14029/1‑141 (MQ=255)
                                                                                                     aaGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGAcct                                      >  2:272216/1‑141 (MQ=255)
                                                                                                       atcttgtccattttattttttaaccaaaatttgattaaAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGAcctc                                     >  1:258056‑M2/39‑141 (MQ=255)
                                                                                                           gATGCTCTCCCAGCTGAGCTAATTGCGAATAGAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGc                                >  1:67209/1‑141 (MQ=14)
                                                                                                           gATGCTCCCCCAACCGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGc                                <  2:121748/141‑1 (MQ=255)
                                                                                                            gtccattttattttttaaccaaaatttgattaaAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCGTGGGACCAGGTGTGACGTCCTTGc                                >  2:11522‑M2/34‑141 (MQ=255)
                                                                                                            ggccattttattttttaaccaaaatttgattaaAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGc                                <  1:78742‑M2/108‑1 (MQ=255)
                                                                                                              ccattttattttttaaccaaaatttgattaaAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGACCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCta                              <  1:266047‑M2/110‑1 (MQ=255)
                                                                                                               ctctCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCtata                            >  2:26432/1‑141 (MQ=255)
                                                                                                               ctctCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCtata                            >  1:172816/1‑141 (MQ=255)
                                                                                                                 ctcCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTGCTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGCCCTCCTTGCGATAGt                          >  2:213710/1‑141 (MQ=255)
                                                                                                                     tttttttaaccaaaatttgattaaAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCAc                       <  2:40686‑M2/117‑1 (MQ=255)
                                                                                                                       tttttaaccaaaatttgattaaAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAATTCGACTACCATCGACGCTAAGGAGCTCAACTTCTGTGTTCGGCATAGGAACAGGTGTGACCTACTTGCGATAGTCACCa                     >  2:156209‑M2/23‑141 (MQ=255)
                                                                                                                       gCTGAGCTAATTCTCCGATTTAAAACGGCCTGGCAACGTGCTGCTCTAGCGTAACTTAAGTTCGACTACCTTCGACGCTAAGGATCTTAACTTCTGTGTTCGGCATGTGAACAGGTGTGACCTCCTTGCTATAGTCACCAg                    <  2:75676/141‑1 (MQ=14)
                                                                                                                        cTGAGCTAATTCTCCGATTTAAAACTGCCTGGCTACGTTCGACTCTAGCGGAAGGCAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTATTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGa                   <  2:153279/141‑1 (MQ=14)
                                                                                                                        cTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGa                   <  1:211193/141‑1 (MQ=255)
                                                                                                                                aTTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGaa           <  2:116421/141‑1 (MQ=255)
                                                                                                                                         ttaaAAAACTGCCTGGCAATGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTACTATAGTCACCAGACATATGAATGTAAttt   >  1:156260‑M2/5‑141 (MQ=255)
                                                                                                                                         tttAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTAAGATTGTGATCAAAGGTGGTTAGCTTGACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAATTta  <  2:197423/141‑1 (MQ=11)
                                                                                                                                             |                                                                                                                                         
ACTGATTACAAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAATTTA  >  CP000730/1998138‑1998415

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.