New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP000730 512620 =49 (1.060)26 (0.820)
+TTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAA
19/178 NT 43.6% intergenic (+688/‑173) recR/rrs1 recombination protein RecR/16S ribosomal RNA
?CP000730 1998278 = NA (NA)intergenic (‑6/+5) USA300HOU_t0050/rrf4 tRNA‑Val/5S ribosomal RNA

CTGATTACAAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAATTTAT  >  CP000730/1998139‑1998416
                                                                                                                                           |                                                                                                                                          
cTGATTACAAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTa                                                                                                                                            >  1:49325/1‑140 (MQ=37)
cTGAGTACAAGTCAGTTGCTCTACCAGTTGAGCTAGGCCGGCAATTTGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTa                                                                                                                                            <  2:508603/140‑1 (MQ=255)
  gATCACCAGTCAGTTGCTCGACCAATTGGGCTAGGCCGGCAAGATGTAAGAATAAATGGTGGAGAATGACGGGTTCGGCCCGCCGCCCCTCTGCCTGTACGGCAGACGCTCTCCCAGCTGTGCTAATTCTCCGATTTaaa                                                                                                                                          <  2:266580/140‑1 (MQ=11)
      aCAAGTCAGTTGCTCTACCAATTGGGCTAGGCCGGTAATATGTAAGAATAAAAGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTg                                                                                                                                      <  1:17253/140‑1 (MQ=255)
       cAAGTCAGTTGCTCTACCAATTGGGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGATCCGCCGACCCTCTGCTTGTAAGGCAGACGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGc                                                                                                                                     <  1:307748/140‑1 (MQ=255)
        aaGTCAGTTGCTCTACCAATTGAGCTAGGCCCCCAATGCAATTTTCTAAATAGTGGATAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGcc                                                                                                                                    >  1:541732/1‑140 (MQ=14)
              gTTGCTCGTCCAACTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCaa                                                                                                                              <  1:469736/140‑1 (MQ=255)
               ttGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATTACGGGTTCGTACCGTCTACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAAc                                                                                                                             <  1:168562/140‑1 (MQ=255)
               tggCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAAc                                                                                                                             <  2:44669/138‑1 (MQ=255)
                tGCTTTACCAATTGCGCTAGGCCTGCTATATGTAAGAATAAATGGTGGGGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACg                                                                                                                            <  1:191598/140‑1 (MQ=14)
                tGCTCTGCCAATTTGGCTGGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGTCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCCGCTGAGATAATTCTCCGATTTAAAACTGCCTGGCAACg                                                                                                                            <  1:80881/140‑1 (MQ=17)
                 gCTCTACCAATTGTGCTAGGCTGGAAACATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTCAGGCAGATGTTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGt                                                                                                                           <  2:350726/140‑1 (MQ=17)
                             taGCTAGGCCGGAAATATGTAAGAATAAATTGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGTTTGTAAGGGAGATGATCTCCCAGCTGAGCTAATTCTCCGATTTAAACCTGCCTGGCAACGTTCTACTCTAGCg                                                                                                               <  1:227001/139‑1 (MQ=17)
                             gatcTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACAGGCTGGGAACGTTCTACTCTAGCg                                                                                                               <  1:405132/137‑1 (MQ=255)
                                  aGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTACTTCGCCGATTTGAAACTGCCTGGCAACGTTCTACTCTAGCGGAACg                                                                                                          >  2:315946/1‑140 (MQ=255)
                                   gtccGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCCGGCAACGTTCTACTCTAACGGAACGt                                                                                                         >  2:477385/3‑140 (MQ=255)
                                            tatGTAAGAATAAATGGTGGCGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCATATGCTCTCTCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCAAGCGGAACGTAAGTTCGAc                                                                                                <  1:161904/140‑1 (MQ=255)
                                            tatGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCTGTTGCTTTCCCAGCTGAGCTAATTATCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGAc                                                                                                <  1:23173/140‑1 (MQ=255)
                                            tatGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCACAGTTCTACTCTAGCGGAAGGTAAGttgcgc                                                                                                >  2:232371/1‑136 (MQ=255)
                                             atttAAGAATTAGTGGTGGAGAATGACGGGTTTGATCCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACt                                                                                               <  1:122709/137‑1 (MQ=14)
                                               ggaaGAATAAATGGTGGGGAATGACGGGTTCGCACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTAc                                                                                             <  1:314814/138‑1 (MQ=255)
                                                        aaTGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAGGTTCAACTACCATCGACGc                                                                                    >  1:62742/1‑140 (MQ=255)
                                                            ttggATAATGACGTGTTCGACACGCCGACCCCCCTCTTGTAAGGCAGATCCTCTCCGCGCTGAGCTAATTCACCGATTTAAAACGTCCTTGCAACGTTCTCCTCTAGCGGAACGTAAGTTCGACTTCCATCGAGGCTAAg                                                                                <  2:129970/139‑1 (MQ=14)
                                                             tggAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAAATGCCTGGCAACGTTCTACCCTAGCGGAACGTAAGTTCGACTACCATCGAGGCTAAgg                                                                               >  2:110086/1‑140 (MQ=255)
                                                                agaATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGc                                                                            <  2:101712/140‑1 (MQ=255)
                                                                 gaATGACGGGTTCGAACCGCCTATCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCt                                                                           <  2:53194/140‑1 (MQ=255)
                                                                  gaTGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCtt                                                                          <  1:71189/139‑1 (MQ=255)
                                                                  aaTGACGGGTTCGAACCGCCGACCTTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCtt                                                                          <  2:437373/140‑1 (MQ=255)
                                                                      aCGGCTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACt                                                                      <  2:75061/140‑1 (MQ=255)
                                                                       cGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACtt                                                                     >  1:355872/1‑140 (MQ=255)
                                                                       cGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGATCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAGGGAGCTTAACtt                                                                     >  1:197262/1‑140 (MQ=255)
                                                                                   gccgACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGCCa                                                         >  2:119696/1‑140 (MQ=255)
                                                                                      gccccTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCGGGCAACGTTCTACTCTAGCGGGACGTAAGTGCGAGTACCCTCGCCGCTCAGGCGCTTAACTTCTGTGTACAGCATgg                                                      >  2:331886/3‑140 (MQ=14)
                                                                                      gACCCTCTCCTTGGAATGCAGCTGCTCTCCCAGCTTAGCTAATTCTCCGATTTAAAACTGCCTGGCCACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATgg                                                      <  1:57541/140‑1 (MQ=14)
                                                                                        cccTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGCTTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGa                                                    >  1:62022/1‑140 (MQ=255)
                                                                                        cccTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGa                                                    >  1:203726/1‑140 (MQ=255)
                                                                                           tctGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACa                                                 <  1:477972/140‑1 (MQ=255)
                                                                                                ttGTAAGGCGGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTATGTTCTACTACCTTCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGgtgt                                            <  1:39015/140‑1 (MQ=255)
                                                                                                  gtgaGGCAGATGCTCGCCCAGCTGAGTTAATTCTCCGATTTAAGACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTCAACTTTTTTTGTCGGCATGGGAACAGGTGTGa                                          <  2:118016/137‑1 (MQ=14)
                                                                                                  gTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGa                                          <  2:548675/140‑1 (MQ=255)
                                                                                                   tAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGTAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGAc                                         <  1:251220/140‑1 (MQ=255)
                                                                                                    aaGGCAGATGGTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGAcc                                        >  2:372660/1‑140 (MQ=255)
                                                                                                       gctgATGCTCCCCCAGTGGAGCTAATTCACCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGATTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGAcctcc                                     <  2:369005/137‑1 (MQ=14)
                                                                                                       gCAGATGCTCCCCCAGCTGAGCTAATTCTCCGATTTAAACCTGCATGGCAACGTTCTGATCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGGGAcctcc                                     <  1:111960/140‑1 (MQ=14)
                                                                                                           aTGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGc                                 >  1:195240/1‑140 (MQ=255)
                                                                                                                        tGAGCTAATTCTCCGATTTAAATCTGCCTGGCAACGTTCTACTCTGGCTGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGa                    <  1:103225/140‑1 (MQ=255)
                                                                                                                          aGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACa                  >  1:337219/1‑140 (MQ=255)
                                                                                                                          aGCTAATCCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACa                  <  1:459707/140‑1 (MQ=255)
                                                                                                                           gCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACat                 >  2:316175/1‑140 (MQ=255)
                                                                                                                                     cGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTaa       >  1:545667/1‑140 (MQ=39)
                                                                                                                                       aTTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAAtt     >  1:60211/1‑140 (MQ=37)
                                                                                                                                        tttAAAACTGCCTGGCAACGTTCTACTCTCGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAAttt    >  1:155034/1‑140 (MQ=37)
                                                                                                                                          tAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTAGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAATTtat  >  2:422871/1‑140 (MQ=21)
                                                                                                                                           |                                                                                                                                          
CTGATTACAAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAATTTAT  >  CP000730/1998139‑1998416

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.