Predicted mutation
evidence seq id position mutation freq annotation gene description
MC JC CP000730 2,501,188 Δ3,014 bp 100% USA300HOU_2364 USA300HOU_2364

Missing coverage evidence...
   seq id start end size ←reads reads→ gene description
* * ÷ CP000730 2501188 2504201 3014 54 [1] [1] 54 USA300HOU_2364 USA300HOU_2364

New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP000730 = 25011871 (0.020)45 (1.100) 37/230 NT 97.9% intergenic (+1198/‑290) USA300HOU_2363/USA300HOU_2364 hypothetical protein/AraC transcriptional regulator
?CP000730 2504202 = 1 (0.020)intergenic (+620/‑138) USA300HOU_2364/USA300HOU_2365 AraC transcriptional regulator/hypothetical protein

AATCGATTTATAACACAAAGTGTATATAGGAAATAACTTTTATGAATTCTAGATATAACAATGTTAAATACTTAAAATAACTCGCTATAATTAAAGTGTTTAATATGTTTACAATTCAATTTGCAATGTATTGTTTTTTAGACACACTTTATTCACATTTAACGTGATTAGGGTGTGTCTTTTTAAATTAATTTTATGTAATATAAATACTGCATTTGCAAACTGTTGCACTTTTAGGTATAACAGAATTAACTACATTTAAGGAGATTGATGAACCAT  >  CP000730/2504063‑2504341
                                                                                                                                           |                                                                                                                                           
cgataaaatttaagtcatgggtacatttaatgttttttgattcaaacttccattttggtcaatttgctttttttataacatagttaaataaaaataaaagattttatagttagttcaaaatggctatgtattgtttttta                                                                                                                                             >  2:114058‑M2/140‑140 (MQ=255)
      aatttaagtcatgggtacatttaatgttttttgattcaaacttccattttggtcaatttgctttttttataacatagttgaatatcaataaaagattagcaagttagttcaaaatggctatgtattgttttttAGacaca                                                                                                                                       <  1:263109‑M2/7‑1 (MQ=255)
       atttaagtcatgggtacatttaatgttttttgattcaaacttccattttggtcaatttgctttttttataacatagttgaatatcaataaaagattagcaagttagttcaaaatggctatgtattgttttttAGacacac                                                                                                                                      <  1:245348‑M2/8‑1 (MQ=255)
       atttaagtcatgggcacatttaatgttttttgattcgaacttgcattttggtcaatttgctttttttataacatagttgaatatcaataaaagcttagcaagttagttcaaaatggctacgtattgttttttAGatacac                                                                                                                                      <  1:387269‑M2/8‑1 (MQ=255)
       atttaaataatgggtacatttaatgttttttgagtcaaacttccattgtggtcaatttgctttttttataacatagttgaatatcaagaaaagattagcaagttagttcaaaatggctatgtattgttttttAGacacac                                                                                                                                      <  2:98768‑M2/8‑1 (MQ=255)
         ttaagtcatgggtacatttaatgttttttgattcaaatttccattttggtcaatttgctttttttataacatagttgaatatcaataaaagattagcaagttagttcaaaatggctatgtattgttttttAGACACACtt                                                                                                                                    <  1:220747‑M2/10‑1 (MQ=255)
             gtcatcgttacatttaatgttttttgattcaaacttccattttggtcaatttgctttttttataacatagttgaatatcaataaaagattagcaagttagttcaaaatggctatgtattgttttttAGACACACTTTAtt                                                                                                                                <  1:247692‑M2/14‑1 (MQ=255)
                atgggtatatttaattttttttgattcaaacttccactttggtgaatttgctttttttataacatagttgaatatcaataaaatagtagcaagttagttcaaaatggctatgtattgttttttAGACACACTTTATTcac                                                                                                                             <  1:264191‑M2/17‑1 (MQ=255)
                      acatttaatgttttttgattcaaacttccattttggtcaatttgctttttttataacatagttgaatatcaataaaagattagcaagttagttcaatatggctatgtattgttttttAGACACACTTTATTCACATTTaa                                                                                                                       >  2:352346‑M2/118‑140 (MQ=255)
                      acatttaatgttttttgattcaaacttccattttggtcaatttgctttttttataacatagttaaatatcaataaaagattagcaagttagttcaaaatggctatgtattgttttttAGACACACTTTATTCACATTTaa                                                                                                                       >  1:185378‑M2/118‑140 (MQ=255)
                           taatgttttttgattcaaacttccattttggtcaatttgctttttttataacatagttgaatatcaataaaagattagcaagttagttcaaaatggctatgtattgttttttAGACACACTTTATTCACATTTAACGTGa                                                                                                                  >  1:256815‑M2/113‑140 (MQ=255)
                             atgttttttgattcaaacttccattttggtcaatttgctttttttataacatagttgaatatcaataaaagattagcaagttagttcaaaatggctatgtattgttttttAGACACACTTTATTCACATTTAACGTGAtt                                                                                                                <  2:422495‑M2/30‑1 (MQ=255)
                                   tttgattcaaacttccattttggtcaatttgctttttttataacatagttgaatatcaataaaagattagcaagttagttcaaaatggctatgtattgttttttAGACACACTTTATTCACATTTAACGTGATTAGGgtg                                                                                                          <  1:461645‑M2/36‑1 (MQ=255)
                                    ttgattcaaattaaacttttggttaatttgctttttttaaaacatagttgaatatcaataaaagattagcaagttagttcaaaatgggtatgtattgttttttAGACACACTTTATTCACATTTAACGTGATTAGGgtgt                                                                                                         <  2:414004‑M2/37‑1 (MQ=255)
                                    ttgattcaaacttccattttggttaatttgctttttttataacatagttgaatatcaagaaaagattagcaagttagttcaaaattgctatttattgttttttAGACACACTTTATTCACATTTAACGTGATTAGGgtgt                                                                                                         <  2:130191‑M2/37‑1 (MQ=255)
                                        ttcaaacttccattttggtcaatttgctttttttataacatagttgaatatcaataaaagattagcaagttagttcaaaatggctatgtattgttttttAGACACACTTTATTCACATTTAACGTGATTAGGGTGTGTCt                                                                                                     >  1:57048‑M2/100‑140 (MQ=255)
                                        ttcaaacttccattttggtcaatttgctttttttataacatagttgaatatcaataaaagattagcaagttagttcaaaatggctatgtattgttttttAGACACACTTTATTCACATTTAACGTGATTAGGGTGTGTCt                                                                                                     <  2:210694‑M2/41‑1 (MQ=255)
                                          caaacttccattttggtcaatttgctttttttataacatagttgaatatcaataaaagattagcaagttagttcaaaatggctatgtattgttttttAGACACACTTTATTCACATTTAACGTGATTAGGGTGTGTCttt                                                                                                   <  1:396372‑M2/43‑1 (MQ=255)
                                             actgtcattttggtcaatttgctttttttataacatagttgaatatcaataaaagattagcaagttagttcaaaatggctatgtattgttttttAGACACACTTTATTCACATTTAACGTGATTAGGGTGTGTCTTTTTa                                                                                                <  2:165954‑M2/46‑1 (MQ=255)
                                              cttccattttggtcaatttgctttttttataacatagttgaatatcaataaaagattagcaagttagttcaaaatggctatgtattgttttttAGACACACTTTATTCACATTTAACGTGATTAGGGTGTGTGTTTTTaa                                                                                               >  1:109626‑M2/94‑140 (MQ=255)
                                                 ccattttggtcaatttgctttttttataacatagttgaatatcaataaaagattagtaagttagttcaaaatggctatgtattgttttttAGACACACTTTATTCACATTTAACGTGATTAGGGTGTGTCTTTTTAaatt                                                                                            <  2:59346‑M2/50‑1 (MQ=255)
                                                 ccattttggtcaatttgctttttttataacatagttgaatatcaataaaagattagcaagttagttcaaaatggctatgtattgttttttAGACACACTTTATTCACATTTAACGTGATTAGGGTGTGTCTTTTTAaatt                                                                                            <  2:279231‑M2/50‑1 (MQ=255)
                                                 ccattttggtcaatttgctttttttataacatagttgaatatcaataaaagattagcaagttagttcaaaatggctatgtattgttttttAGACACACTTTATTCACATTTAACGTGATTAGGGTGTGTCTTTTTAaatt                                                                                            >  1:135875‑M2/91‑140 (MQ=255)
                                                 ccattttggtcaatttgctttttttataacatagttgaatatcaataaaagattagcaagttagttcaaaatggctatgtattgttttttAGACACACTTTATTCACATTTAACGTGATTAGGGTGTGTCTTTTTAaatt                                                                                            <  2:457691‑M2/50‑1 (MQ=255)
                                                  cattttggtcaatttgctttttttataacatgtttgaatatcaataaaagattagcaagttagttcaaaatggctatgtattgttttttAGACACACTTTATTCACATTTAACGTGATTAGGGTGTGTCTTTTTAaatta                                                                                           <  1:412733‑M2/51‑1 (MQ=255)
                                                   attttgttcaatttgctttttttataacatagttgaatatcaataaaagattagcaagttagttcaaaatggctatgtattgttttttAGACACACTTTATTCACATTTAACGTGATTAGGGTGTGTCTTTTTAaattaa                                                                                          <  2:280776‑M2/52‑1 (MQ=255)
                                                                tgctttttttataacatagttgaatatcaataaaagattagcaagttagttcaaaatgggtatgtattgttttttAGACACACTTTATTCACATTTAACGTGATTAGGGTGTGTCTTTTTAAATTAATTTTATGTAatat                                                                             >  2:480945‑M2/76‑140 (MQ=255)
                                                                  ctttttttataacatagttgaatatcaataaaagattagcaagttagttcaaaatggctatgtattgttttttAGACACACTTTATTCACATTTAACGTGATTAGGGTGTGTCTTTTTAAATTAATTTTATGTAATATaa                                                                           >  1:19102‑M2/74‑140 (MQ=255)
                                                                              catagttgaatatcaataaaagattagcaagttagttcaaaattgctatgtattgttttttAGACACACTTTATTCACATTTAACGTGATTAGGGTGTGTCTTTTTAAATTAATTTTATGTAATATAAATACTGCATTTg                                                               <  1:85107‑M2/79‑1 (MQ=255)
                                                                                cTCGCTATAATTAAAGTGTTTAATATGTTTACAATTCAATTTGCAATGTATTGTTTTTTAGACACACTTTATTCACATTTAACGTGATTAGGGTGTGTCTTTTTAAATTAATTTTATGTAATATAAATACTGCATTTGCa                                                             >  2:391610/1‑140 (MQ=255)
                                                                                  gttgaatatcaataaaagattagcaagttagttcaaaatggctatgtattgttttttAGACACACTTTATTCACATTTAACGTGATTAGGGTGTGTCTTTTTAAATTAATTTTATGTAATATAAATACTGCATTTGCaaa                                                           <  2:35639‑M2/83‑1 (MQ=255)
                                                                                       atatcaataaaagattagcaagttagttcaaaatggctatgtattgttttttAGACACACTTTATTCACATTTAACGTGATTAGGGTGTGTCTTTTTAAATTAATTTTATGTAATATAAATACTGCATTTGCAAACTGtt                                                      <  2:89170‑M2/88‑1 (MQ=255)
                                                                                       atatcaataaaagattagcaagttagttcaaaatggctatgtattgttttttAGACACACTTTATTCACATTTAACGTGATTAGGGTGTGTCTTTTTAAATTAATTTTATGTAATATAAATACTGCATTTGCAAACTGtt                                                      >  2:301932‑M2/53‑140 (MQ=255)
                                                                                       atatcaataaaagattagcaagttagttcaaaatggctatgtattgttttttAGACACACTTTATTCACATTTAACGTGATTAAGGTGTGTCTTTTTAAATTAATTTTATATAATATAAATACTGCATTTGCAAACTGtt                                                      >  1:236093‑M2/53‑140 (MQ=255)
                                                                                         atcaataaaagattagcaagttagttcaaaatggctatgtattgttttttAGACACACTTTATTCACATTTAACGTGATTAGGGTGTGTCTTTTTAAATTAATTTTATGTAATATAAATACTGCATTTGCAAACTGTTGc                                                    <  2:548672‑M2/90‑1 (MQ=255)
                                                                                           tcataaaagattagcatgttagttcaaaatggctatgtattgttttttAGACACACTTTATTCACATTTAACGTGATTAGGGTGTGTCTTTTTAAATTAATTTTATGTAATATAAATACTGCATTTGCAAACTGTTGCAc                                                  <  2:169495‑M2/92‑1 (MQ=255)
                                                                                           caataaaagattagcaagttagttcaaaatggctatgtattgttttttAGACACACATTATTCAGATTTAACGTGATTAGGGTGTGTCTTTTTAAATTAATTTTATGTAATATAAATACTGCATTTGTAAACTTTTGAAc                                                  >  2:167319‑M2/49‑140 (MQ=255)
                                                                                             ataaaagattagctagttagttcaaaatggctatgtattgttttttAGACACACTTTATTCACATTTAACGTGATTAGGGTGTGTCTTTTTAAATTAATTTTATGTAATATAAATACTGCATTTGCAAACTGTTGCACtt                                                <  1:157950‑M2/94‑1 (MQ=255)
                                                                                              taaaagattagcaagttagttcaaaattgctatgtattgttttttAGACACACTTTATTCACATTTAACGTGATTAGGGTGTGTCTTTTTAAATTAATTTTATGTAATATAAATACTGCATTTGCAAACTGTTGCACttt                                               <  2:352951‑M2/95‑1 (MQ=255)
                                                                                                 aagattagcaagttagttcaaaatggctatgtattgttttttAGACACACTTTATTCACATTTAACGTGATTAGGGTGTGTCTTTTTAAATTAATTTTATGTAATATAAATACTGCATTTGCAAACTGTTGCACTTTTAg                                            <  1:468430‑M2/98‑1 (MQ=255)
                                                                                                     ttagcaagttagttcaaaatggctatgtattgttttttAGACACACTTTATTCACATTTAACGTGATTAGGGTGTGTCTTTTTAAATTAATTTTATGTAATATAAATACTGCATTTGCAAACTGTTGCACTTTTAGGtat                                        <  1:273912‑M2/102‑1 (MQ=255)
                                                                                                       agcaagttagttcaaaatggctatgtattgttttttAGACACACTTTATTCACATTTAACGTGATTAGGGTGTGTCTTTTTAAATTAATTTTATGTAATATAAATACTGCATTTGCAAACTGTTGCACTTTTAGGTATaa                                      <  1:370684‑M2/104‑1 (MQ=255)
                                                                                                          aagttagttcaaaatggctatgtattgttttttAGACACACTTTATTCACATTTAACGTGATTAGGGTGTGTCTTTTTAAATTAATTTTATGTAATATAAATACTGCATTTGCAAACTGTTGCCCTTTTAGGTATAACAg                                   <  1:526917‑M2/107‑1 (MQ=255)
                                                                                                             ttagttcaaaatggctatgtattgttttttAGACACACTTTATTCAACTTTAACGTGATTAGGGTTTGTCTTTTTAAATTAATTTTATGTAATATAAATACTGCATTTGCAAAATGGTGCACTTTTAGGTATAACAGAAt                                >  2:311730‑M2/31‑140 (MQ=255)
                                                                                                                  tcaaaatggctatgtattgttttttAGACACACTTTATTCACATTTAACGTGATTAGGGTGTGTCTTTTTAAATTAATTTTATGTAATATAAATACTGCATTTGCAAACTGTTGCACTTTTAGGTATAACAGAATTAACt                           <  1:167171‑M2/115‑1 (MQ=255)
                                                                                                                  tcaaaatggctatgtattgtctcttAAACACACTTTATTCACATTTAACATGATTAGGGTGTGTCTTTTTAAATTAATTTTATGTAATATAAATACTGCATTTGCAAACTGTTGCACTTTTAGGTATAACAGAATTAACt                           <  1:40410‑M2/115‑1 (MQ=255)
                                                                                                                     atatggctatgtatttttttttAGACACACTTTATTCTCATTTCACCTTATTAGTGTTTGTCTTTTTAAATTAATTTTATGTAATATAAATACTGCATTTGCAAACTGTTGCACTTTTAGGTATAACAGAATTAACTACa                        <  1:452001‑M2/118‑1 (MQ=255)
                                                                                                                           ctatgtattgttttttAGACACTCTTTATTCACATTTAACGTGATTAGGGTGTGTCTTTTTAAATTAATTTTATGTAATATAAATACTGCATTTGCAAACTGTTGCACTTTTAGGTATAACAGAATTAACTACATTTAAg                  <  2:373114‑M2/124‑1 (MQ=255)
                                                                                                                                  ttgttttctTGACTCATTTTATTCACATTTAACGTGATTAGGTTGTGTCTTTTTAAATTAATTTTATGTAATATAAATACTTCATTTGCAAACTGTTGCACTTTTAGGTATAACAGAATTAACTACATTTAAGGAGATtg           <  2:536506‑M2/131‑1 (MQ=255)
                                                                                                                                     ttttttAGACACACTTTATTCACATTTAACGTGATTAGGGTGTGTCTTTTTAAATTAATTTTATGTAATATAAATACTGCATTTGCAAACTGTTGCACTTTTAGGTATAACAGAATTAACTACATTTAAGGAGATtgatg        >  1:376221‑M2/7‑140 (MQ=255)
                                                                                                                                        tttAGACACACTTTATTCACATTTAACGTGATTAGGGTGTGTCTTTTTAAATTAATTTTATGTAATATAAATACTGCATTTGCAAACTGTTGCACTTTTAGGTATAACAGAATTAACTACATTTAAGGAGATTGATGAAc     <  2:100932‑M2/137‑1 (MQ=255)
                                                                                                                                         ttAGACACACTTTATTCACATTTAACGTGATTCGGGTGTGTCTTTTTAAATTAATTTTATGTAATTTAAATACTGCATTTGCAAACTGTTGCACTTTTAGGTATAACAGAATTAACTACATTTAAGGAGATTGATGAAcc    >  1:520679‑M2/3‑140 (MQ=255)
                                                                                                                                         ttAGACACACTTTATTCACATTTAACGTGATTAGGGTGTGTCTTTTTAAATTAATTTTATGTAATATAAATACTGCATTTGCAAACTGTTGCACTTTTAGGTATAACAGAATTAACTACATTTAAGGAGATTGATGAAcc    >  1:39071‑M2/3‑140 (MQ=255)
                                                                                                                                           aGACACACTTTATTCACATTTAACGTGATTAGGGTGTGTCTTTTTAGATTAATTTTATGTAATATAAATACTGCATTTGCAAACTGTTGCACTTTTAGGTATAACAGAATTAACTACATTTAAGGAGATTGATGAACCAt  >  1:155129/1‑140 (MQ=255)
                                                                                                                                           |                                                                                                                                           
AATCGATTTATAACACAAAGTGTATATAGGAAATAACTTTTATGAATTCTAGATATAACAATGTTAAATACTTAAAATAACTCGCTATAATTAAAGTGTTTAATATGTTTACAATTCAATTTGCAATGTATTGTTTTTTAGACACACTTTATTCACATTTAACGTGATTAGGGTGTGTCTTTTTAAATTAATTTTATGTAATATAAATACTGCATTTGCAAACTGTTGCACTTTTAGGTATAACAGAATTAACTACATTTAAGGAGATTGATGAACCAT  >  CP000730/2504063‑2504341

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: