Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
JC	CP000730	2,501,544	Δ108 bp	9.8%	coding (68‑175/2106 nt)	USA300HOU_2364 →	AraC transcriptional regulator

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	= 2501543	45 (0.700)	5 (0.080)	3/240	NT	9.8%	coding (67/2106 nt)	USA300HOU_2364	AraC transcriptional regulator
	?	CP000730	2501652 =	50 (0.840)					coding (176/2106 nt)	USA300HOU_2364	AraC transcriptional regulator

ACAATACCAAGTCGTAATATTAATAATATTATGGTGCTATTTTCACTTACAAGTAAACTCAATATTACGATTAATGGTGAAACCAAAGACGTAAGTAATTATATTATCTTAATTAACCATGGTGATATTTATAATATTAACCACGGCGAAAATATAATCGAATTAATGATACCCGTTTTTTATTTTTATCAACAAGATGATGATTTCTTTAATGGTTATTTAGATCGTCATTTATTACAATCAAGTAATTATATTAAGTCATTAATTGCCGATT  >  CP000730/2501513‑2501786                                                                                                                                            |                                                                                                                                       aCAATACCAAGTCGTAATATTACTAATATCATGGGGCTATTTTCACTTACAAGTAAACTCAATATTACGATTAATGGTGAAACCAAAGACGTAAGTAATTATATTATCTTAATTAACCATGGTGATATTTATAATATTaa                                                                                                                                        >  2:162234/1‑140 (MQ=255)  ccaaaCCAAGTCGTAATATTAATAATACTATGGTGCTATTATCACTTACAAGTAAACTCAATATTACGATTAATGGTGAAACCAAAGACGTAAGTAATTATATTAGCTTAATTAACCATGGTTATATTTATAATATTAAc                                                                                                                                       <  2:747802/136‑1 (MQ=255)      aCCAAGTCGTAATATTAATAATATTATGGTGCTATTTTCACTTACAAGTAAACTCAATATTACGATTAATGGTGAAACCAAAGACGTAAGTAATTATATTATCTTAATTAACCATGGTGATATTTATAATATTAACCACg                                                                                                                                   >  2:126648/1‑140 (MQ=255)       ccAAGTCGTAATATTAATAATATTATGGTGCTATTTTCACGTACAAGTAAACTCAATATTACGATTAATGGTGAAACCAAAGACGTAAGTAATTATATTATCTTAATTAACCATGGTGATATTTATAATATTAACCACgg                                                                                                                                  >  2:493774/1‑140 (MQ=255)       ccAAGTCGTAATATTAATAATATTATGGTGATATTTTCACTTACAAGTAAACTCAATATTACGATTAATGGTGAAACCAAAGACGTAAGTAATTATATTATCTTAATTAACCATGGTGATATTTATAATATTAACCACgg                                                                                                                                  >  2:403747/1‑140 (MQ=255)          aaaatttccatgttttacatttaaatgatagatttcaatatatattaggcaggggagagaaatatgacatgccaacttaaaatacatcatacattatcgacaataccaagtggtaatattaataatattaACCACagcaa                                                                                                                               >  2:379239‑M2/131‑138 (MQ=255)                                 ggTGCTATTTTCACTTACAAGTAAACTCAATATTACGATTAATGGTGAAACCAAAGACGTAAGTAATTATATTATCTTAATTAACCATTGTGATATTTATAATATTAACCACGGCGAAACTATAATCGAATTAATGATAc                                                                                                        <  1:525661/140‑1 (MQ=255)                                 ggTGCTATTTTCACTTACAAGTAAACTCAATATTACGATTAATGGTGAAACCAAAGACGTAAGTAATTATATTATCTTAATTAACCATGGTGATATTTATAATATTAACCACGGCGAAAATATAATCGAATTAATGATAc                                                                                                        <  1:620371/140‑1 (MQ=255)                                  gTGCTATTTTCACTTACAAGTAAACTCAATATTACGATTAATGGTGAAACCAAAGACGTAAGTAATTATATTATCTTAATTAACCATGGTGATATTTATAATATTAACCACGGCGAAAATATAATCGAATTACTGATccc                                                                                                       >  2:724217/1‑140 (MQ=255)                                    gCTATTTTCACTTACAAGTAAACTCAATATTACGATTAATGGTGAAACCAAAGACGTAAGTAATTATATTATCTTAATTAACCATGGTGATATTTATAATATTAACAACGGCGAAAATATAATCGAATTAATGATACCCg                                                                                                     >  2:29660/1‑140 (MQ=255)                                        ttttCACTTACAAGTAAACTCAATATTACGATTAATGGTGAAACCAAAGACGTAAGTAATTATATTATCTTAATTAACCATGGTGATATTTATAATATTAACCACGGCGAAAATATAATCAAATTAATAATACCCGtttt                                                                                                 >  1:327904/1‑140 (MQ=255)                                            cACTTACAAGTAAAATAAATATTACGATTAATGGTGAAATCAAAGACGTAAGTCATTATATTATCTTAATTAACCATGGTGATATTTATAATATTAACTAAGGCAAGAAAATAAACGAATTAATAAAACCAGTttttaat                                                                                             >  2:177742/1‑140 (MQ=255)                                             aCTTACAAGTAAACTCAATATTACGATTAATGGTGAAACCAAAGACGTAAGTAATTATATTATCTTAATTAACCATGGTGATATTTATAATATTAACCACGGCGAAAATATAATCGAATTAATGATACCCGTtttttatt                                                                                            >  1:183415/1‑140 (MQ=255)                                                    aGTAAATCCAATATTACGATTAATGGTGAAACCACAGACGTAAGTAATTATATTACCTTAATTAAACATGGTGATATTTATAATATTAACCACGGTGAAAATATAATCGAATTAATGATACCCGTTTTTTATTTTTATca                                                                                     >  2:38570/1‑140 (MQ=255)                                                    aGTAAACTCAATATTAGGAGTAATGGTGAAACCAAAGATGTAAGTAATTATATTATCTTAATTAACCATGGTGATATTTATAATATTAACCACGGCGAAAATATAATCGAATTAATGATACCCGTTTTTTATTTTTATca                                                                                     >  1:424149/1‑140 (MQ=255)                                                    aGTAAACTCAATATTACGATTAATGGTGAAACCAAAGACGTAAGTAATTATATTATCTTAATTAACCATGGTGATATTTATAATATTAACCACGGCGAAAATATAATCGAATTAATGATACCCGTTTTTTATTTTTATca                                                                                     >  2:150335/1‑140 (MQ=255)                                                          cTCAATATTACGATTAATGGTGAAACCAAAGACGTAAGTAATTATATTATCTTAATTAACCATGGTGATATTTATAATATTAACTACGGTGAAAATATAATCGAATTAATGATACCATTTTTTTATTATTATCAACAAga                                                                               >  1:396769/1‑140 (MQ=255)                                                          cTCAATATTACGATTAATGGTGAAACCAAAGACGTAAGTAATTATATTATCTTAATTAACCATGGTGATATTTATAATATTAACCACGGCGAAAATATAATCGAATTAATGATACCCGTTTTTTATTTTTATCAACAAga                                                                               >  1:421185/1‑140 (MQ=255)                                                           tCAATATTACGATTAATGGTGAAACCAAAGACGTAAGTAATTATATTATCTTAATTAACCATGGTGATATTTATAATATTAACCACGGCGAAAATATAATCGAATTAATGATACCCGTTTTTTATTTTTATCAACAAgat                                                                              <  1:446586/140‑1 (MQ=255)                                                           tCAATATTACGATTAATGGTGAAACCAAAGACGTAAGTAATTATATTATCTTAATTAACCATGGTGATATTTATAATATTAACCACGGCGAAAATATAATCGAATTAATGATACCCGTTTTTTATTTTTATCAACAAgat                                                                              <  1:69621/140‑1 (MQ=255)                                                             aaTATTACGATTAATGGTGAAACCAAAGACGTAAGTAATTATATTATCTTAATTAACCATGGTGATATTTATAATATTAACCACGGCGAAAATATAATCGAATTAATGATACCCGTTTTTTATTTTTATCAACAAgatga                                                                            <  1:126562/140‑1 (MQ=255)                                                              atatTACGATTAATGGTGAAACCAAAGACGTAAGTAATTATATTATCTTAATTACCCATGGTGATATTTATAATATTAACCACGGCGAAAATATAATCGAATTCATGATACCCGCTTTTTATTTTTATCAACAAgttgat                                                                           >  2:321536/1‑140 (MQ=255)                                                                  tACGATTAATGGTGAAACCAAAGACGTAAGTAATTATATTATCTTAATTAACCATGGTGATATTTATAATATTAACCACGGCGAAAATATAATCGAATTAATGATACCCGTTTTTTTTTTTTTTTTTCAAGTTGATGttt                                                                       >  2:408312/1‑140 (MQ=255)                                                                    cGATTAATGGTGAAACCAAAGACGTAAGTAATTATATTATCTTAATTAACCATGGTGATATTTATAATATTAACCACGGCGAAAATATAATCGAATTAATGATACCCGTTTTTTATTTTTATCAACAAGATGATGATTTc                                                                     >  1:723773/1‑140 (MQ=255)                                                                       ttAATTGTGAAACCAAAGACTTAATTAATTATATTACCCTAAGTCACCGAGGACATATTGACAATATTCACCACGGCCAAAATATAATCGAATTAATGATACCGGTTTTTTATTTTTATCAACAAGATGATGATTTCttt                                                                  <  2:82898/140‑1 (MQ=255)                                                                            acatgccaacttaaaatacatcatacattatcgacaataccaagtcgtaatattaataatattaACCACGGCGAAAATATAATCGAATTAATGAAAACCGTTTTTTATTTTTATCAACAAGATGATGATTTCTTTAATgg                                                             >  1:317044‑M2/65‑140 (MQ=255)                                                                                gctaacttaaaatacatcatacattatcgacaataccaagtcgtaatattaataatattaACCACGGCGAAAATATAATCGAATTAATGATACCCGTTTTTTATTTTTATCAACAAGATGATGATTTCTTTAATTGTTAt                                                         <  2:383107‑M2/80‑1 (MQ=255)                                                                                gccaacttaaaatacatcatacattatcgacaataccaagtcgtaatattaataatattaACCACGGCGAAAATATAATCGAATTAATGATACCCGTTTTTTATTTTTATCAACAAGATGATGATTTCTTTAATGGTTAt                                                         <  2:99695‑M2/80‑1 (MQ=255)                                                                                actaacttaatatacaacatacattagctacaagaccaagtcgtaatattaataatattaACCACGGCGAAAATATAATCGAATTAATGATACCCGTTTTTTATTTTTATCAACAAGATGATGATTTCTTTAATGGTTAt                                                         <  2:593578‑M2/80‑1 (MQ=255)                                                                                  aCCAAAGACGTAAGTAATTATATTATCTTAATTAACCATGGTGATATTTATAATATTAACCACGGCGAAAATATAATCGAATTAATGATACCCGTTTTTTATTTTTATCAACAAGATGATGATTTCTTTAATGGTTAttt                                                       <  2:611252/140‑1 (MQ=255)                                                                                   ccAAAGACGTAAGTAATTATATTATCTTAATTAACCATGGTGATATTTATAATATTAACCACGGCGAAAATATAATCGAATTAATGTTACCCGTTTTTTATTTTTATCATCAAGTTGATGATTTCTTTAATGGttttttt                                                      >  2:627682/1‑139 (MQ=255)                                                                                     gaaGACGTAAGTAATTATATTTTCTTAATTAACCATGGTGATATTTATAACATTAACCACGGCGAAAATATAATCGAATTAATGGTATCCGTTTTTTATTTTTATCAACCAGACGATGATTTCTTTAATGGTTATTTAGa                                                    <  2:1441/139‑1 (MQ=255)                                                                                     aaaGACGTAAGTAATTATATTATCTTAATTAACCATGGTGATATTTATAATATTAACCACGGCGAAAATATAATCGAATTAATGATACCCGTTTTTTATTTTTATCAACAAGATGATGATTTCTTTAATGGTTATTTAGa                                                    >  1:240484/1‑140 (MQ=255)                                                                                      aaGACGTAAGTAAGTATACTATGTTAACTAACCCTGGTGATATGTATAATATTAACCACGGCGAAAATATAATCGAATTAACGATACCCGTTTTTTATTTTTATCACCCAGATGATGATTTCTTTAATGGTTATTTAgct                                                   <  2:1798/140‑3 (MQ=255)                                                                                         aCGTAAGTAATTATATTATCTTAATTAACCATGGTGATATTTATAATATTAACCACGGCGAAAATATAATTGAATTAATGATACCCGTTTTTTATTTTTATTAACAAGATGATGATTTCTTTAATGGTTATTTAGATCGt                                                <  1:401589/140‑1 (MQ=255)                                                                                         aCGTAAGTAATTATATTATCTTAATTAACCATGGTCATATTTATAATATTAACCACGGCGAAAATATAATCGAATTAATGATACCCGTTTTTTATTTTTATCAACAAGATGATGATTTCTTTAATGGTTATTTAGATCGt                                                <  1:12424/140‑1 (MQ=255)                                                                                         aCGTAAGTAAATATATTATCTTAATTAACCATGGTGATATTTATAATATTAACCACGGCGAAAATATAATCGAATTAATGATACCCGTTTTTTATTTTTATCAACAAGATGATGATTTCTTTAATGGTTATTTAGATCGt                                                <  2:14247/140‑1 (MQ=255)                                                                                          cGTAAGTAATTATATTATCTTCATTAACCATGGTGATATTTATAATATTAACCACGGTGAAAATATAATCGAATTAATGATACACGTTTTTTATTTTTATCAACAAGATGATGATTTCTTTAATGGTTATTTAGATCGTc                                               <  2:194494/140‑1 (MQ=255)                                                                                           gtaagtaaTTATATTATCTTAATTAACCATGGTGATATTTATAATATTAACCACGGCGAAAATATAATCGAATTAATGATACCCGTTTTTTATTTTTATCAACAAGATGATAATTTCTTTAATGGTTATTTAGATTGTCa                                              >  2:642166/1‑140 (MQ=255)                                                                                                     atattatCTTAATTAACCATGGTGATATTTATAATATTAACCACGGCGAAAATATAATCGAATTAATGATACCCGTTTTTTATTTTTTTTAACAAAATAATGATTTCTTTACTTTTTATTTAGATTGTTATTTATTaaaa                                    >  2:67071/1‑140 (MQ=255)                                                                                                     atattatCTTAATTAACCATGGTGATATGTATAGTAGTAACCACGGCGAAAATATAATCGAATTAATGATACCCGTTTTTTATTTTTATCAACAAGATGATGATTTCTTTAATGGTTATTTAGATCGTCATTTATTACaa                                    >  1:753833/1‑140 (MQ=255)                                                                                                       attatCTTAATTAACCATGGTGATATTTATAATATTAACCACGGCGAAAATATAATCGAATTAATGATACCCGTTTTTTATTTTTATCAACAAGATGATGATTTCTTTAATGGTTATTTAGATCGTCATTTATTACAATc                                  >  1:337136/1‑140 (MQ=255)                                                                                                       attatCTTAATTAACCATGGTGATATTTATAATATTAACCACGGCGAAAATATAATCGAATTAATGATACCCGTTTTTTATTTTTATCAACAAGATGATGATTTCTTTAATGGTTATTTAGATCGTCATTTATTACAATc                                  >  1:83320/1‑140 (MQ=255)                                                                                                          atCTTAATTAACCATGGTGATATTTATAATATTAACCACGGCGAAAATATAATCGAATTAATGATACCCGTTTTTTATTTTTATAAACAAGATGATGATTTCTTTAATGGTTATTTAGATTGTCATTTATTACAATCAAg                               >  2:733909/1‑140 (MQ=255)                                                                                                             ttaattaaCCATGGTGATATTTATAATATTAACCACGGCGAAAATATAATCGAATTAATGATACCCGTTTTTTATTTTTATCAACAAGATGATGATTTCTTTAATGGTTATTTAGATCGTCATTTATTACAATCAAGTaa                            <  2:421185/140‑1 (MQ=255)                                                                                                                attaaCCGTGGGGATATTTATAATATTAAGCACGGCTAAAATATAATCGAATTAATGATACCCGTTTTTTATTTTTATCAACAAGATGATGATTTCTTTAATGGTTATTTAGATCGTCATTTATTACAATCAAGTAATta                         <  2:214969/140‑1 (MQ=255)                                                                                                                 ttaaCCATGGTGATATTTATAATATTAACCACGGCGAAATTATAATCGAATTAATGATACCCGTTTTTTATTTTTATCAACAAAATGATGATTTCTTTAATGATTATTTAGATCGTCATTTATTACAATCAAGTAATtat                        >  1:365479/1‑140 (MQ=255)                                                                                                                   aaCCATGGTGATATTTATAAGATTAACCACGGCGAAAATATAATCGAATTAATGATACCCGTTTTTTATTTTTATCAACAAGATGATGATTTCTTTAATGATTATTTAGGTGGTCATTTATTACAATAAAGTAATTatat                      >  1:496083/1‑140 (MQ=255)                                                                                                                      cATGGTGATATTTATAATATTAACCACGGCGAAAATATAATCGAATTAATGATACCCGTTTTTTATTTTTATCAACAAGATGATGATTTCTTTAATGGTTATTTAGATCGTCATTTATTACAATCCAGTAATTATATTaa                   >  1:136607/1‑140 (MQ=255)                                                                                                                      cATGGTGATATTTATAATATTAACCACGGCGAAAATATAATCGAATTAATGATACCCGTTTTTTATTTTTATCAACAAGATGATGATTTCTTTAATGGTTATTTAGATCGTCATTTATTACAATCAAGTAATTATATTaa                   >  1:10332/1‑140 (MQ=255)                                                                                                                      cATGGTGATATTTATAATATTAACCACGGCGAAAATATAATCGAATTAATGATACCCGTTTTTTATTTTTATCAACAAGATGATGATTTCTTTAATGGTTATTTAGATCGTCATTTATTACAATCAAGTAATTATATTaa                   >  1:626732/1‑140 (MQ=255)                                                                                                                      cATGGTGATATTTATAATATTAACCACGGCGAAAATATAATCGAATTAATGATACCCGTTTTTTATTTTTATCAACAAGATGATGATTTCTTTAATGGTTATTTAGATCGTCATTTATTACAATCAAGTAATTATATTaa                   >  1:756775/1‑140 (MQ=255)                                                                                                                       aTGGTGATATTTATAATTTTAACCACGGCGAATATATTATCGAATTAATGATTCCCGTTTTTTATTTTTATCAACTAGATGATGATTTCTTTAATGGTTATTTAGATCGTCATTTATTACAATCAAGTAATTATATTAAg                  <  1:150335/140‑1 (MQ=255)                                                                                                                       aTGGTGATATTTATAATATTAACCACGGCGAATATATAATCGAATTAATGATACCCGTTTTTTATTTTTATCAACAAGATTATGATTTCTTTAATGGTTATTTAGATCGTCATTTATTACAATCAAGTAATTATATTAAg                  <  2:424149/140‑1 (MQ=255)                                                                                                                       aTGGTGATATGTATAATATTAACCACGGCGAAAATATAATCGAATTAATGATACCCGTTTTTTATTTTTATCAACAAGATGATGATTTCTTTAATGGTTATTTAGATCGTCATTTATTACAATCAAGTAATTATATTAAg                  <  1:38570/140‑1 (MQ=255)                                                                                                                          gTGATATTTATAATATTAACCACGGCGAAAATATAATCGAATTAATGATACCCGTTTTTTATTTTTATCAACAAGATGATGATTTCTTTAATGGTTATTTAGATCGTCATTTATTACAATCAAGTAATCATATTAAGTCa               <  2:723773/140‑1 (MQ=255)                                                                                                                             atatTTATAATATTAACCACGGCGAAAATATAATCGAATTAATGATACCCGTTTTTTTTTTTTTTTTACAAGATGATGATTTCTTTAATTGTTATTTTGTTCGTCATTTATTACAATCAAGTAATTCTATTAAGTCATTa            >  2:625266/1‑140 (MQ=255)                                                                                                                                    taatattaACCACGGCGAAAATATAATCGAATTAATGATACCCGTTTTTTATTTTTATTAACAAGATGATGATTTCTTTAATTGTTATTTAGATCGTCATTTATTACAATCAATTAATTATATGAATTCATTAATTgcca     >  2:75380‑M2/9‑139 (MQ=255)                                                                                                                                    taatattaACCACGGCGAAAATATAATCGAATTAATGATACCCGTTTTTTATTTTTATCAACAAGATGATGATTTCTTTAATTGTTATTTAGATCGTCATTTATTACAATCAAGTAATTATATTAAGTCATTAATTgcct     >  2:485232‑M2/9‑139 (MQ=255)                                                                                                                                       tattaACCACGGCTAATATATAATCGAATTAATGTTACCCGTTTTTTATTTTTATCAACAAGATGATGATTTCTTTAATGGTTATTTAGATCGTCATTTATTACAATCAAGTAATTATATTAAGTCATTAATTGCCGAtt  <  2:434256‑M2/135‑1 (MQ=255)                                                                                                                                            |                                                                                                                                       ACAATACCAAGTCGTAATATTAATAATATTATGGTGCTATTTTCACTTACAAGTAAACTCAATATTACGATTAATGGTGAAACCAAAGACGTAAGTAATTATATTATCTTAATTAACCATGGTGATATTTATAATATTAACCACGGCGAAAATATAATCGAATTAATGATACCCGTTTTTTATTTTTATCAACAAGATGATGATTTCTTTAATGGTTATTTAGATCGTCATTTATTACAATCAAGTAATTATATTAAGTCATTAATTGCCGATT  >  CP000730/2501513‑2501786

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