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	= 2501187	1 (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

CGATAAAATTTAAGTCATGGGTACATTTAATGTTTTTTGATTCAAACTTCCATTTTGGTCAATTTGCTTTTTTTATAACATAGTTGAATATCAATAAAAGATTAGCAAGTTAGTTCAAAATGGCTATGTATTGTTTTTTGAAATACATAGGTTTGAAATCTATATTAATTATGCACCAAATAATTTAATTAGACTCTATCGAAAATTTCCAAATTTTGCTTACTATCTTTCTAATTTTACTTTTATATTGTTCGCAATGCATAAAAACAAGCGTTTT  >  CP000730/2501049‑2501325                                                                                                                                           |                                                                                                                                           cGATAAAATTTAAGTCATGGGTACATTTAATGTTTTTTGATTCAAACTTCCATTTTGGTCAATTTGCTTTTTTTATAACATAGTTAAATAAAAATAAAAGATTTTATAGTTAGTTCAAAATGGCTATGTATTGTTTTTTa                                                                                                                                           >  2:114058‑M1/1‑139 (MQ=255)       aaTTTAAGTCATGGGTACATTTAATGTTTTTTGATTCAAACTTCCATTTTGGTCAATTTGCTTTTTTTATAACATAGTTGAATATCAATAAAAGATTAGCAAGTTAGTTCAAAATGGCTATGTATTGTTTTTTagacaca                                                                                                                                     <  1:263109‑M1/140‑8 (MQ=255)        aTTTAAGTCATGGGTACATTTAATGTTTTTTGATTCAAACTTCCATTTTGGTCAATTTGCTTTTTTTATAACATAGTTGAATATCAATAAAAGATTAGCAAGTTAGTTCAAAATGGCTATGTATTGTTTTTTagacacac                                                                                                                                    <  1:245348‑M1/140‑9 (MQ=255)        aTTTAAGTCATGGGCACATTTAATGTTTTTTGATTCGAACTTGCATTTTGGTCAATTTGCTTTTTTTATAACATAGTTGAATATCAATAAAAGCTTAGCAAGTTAGTTCAAAATGGCTACGTATTGTTTTTTagatacac                                                                                                                                    <  1:387269‑M1/140‑9 (MQ=255)        aTTTAAATAATGGGTACATTTAATGTTTTTTGAGTCAAACTTCCATTGTGGTCAATTTGCTTTTTTTATAACATAGTTGAATATCAAGAAAAGATTAGCAAGTTAGTTCAAAATGGCTATGTATTGTTTTTTagacacac                                                                                                                                    <  2:98768‑M1/140‑9 (MQ=255)         tttAAGTCATGGATACATTTAATGTTTTTTGATTCAAATTTCCATTTTGGTGAATTTGCTTTTTTTATAACATAGTTGAAGATCAATAAAAGATTCGCAAGTTACTTCAAAATAGCAATGTATTGttttttagtgcacat                                                                                                                                   >  2:347341/1‑131 (MQ=255)          ttAAGTCATGGGTACATTTAATGTTTTTTGATTCAAATTTCCATTTTGGTCAATTTGCTTTTTTTATAACATAGTTGAATATCAATAAAAGATTAGCAAGTTAGTTCAAAATGGCTATGTATTGTTTTTTagacacactt                                                                                                                                  <  1:220747‑M1/140‑11 (MQ=255)              gTCATCGTTACATTTAATGTTTTTTGATTCAAACTTCCATTTTGGTCAATTTGCTTTTTTTATAACATAGTTGAATATCAATAAAAGATTAGCAAGTTAGTTCAAAATGGCTATGTATTGTTTTTTagacacactttatt                                                                                                                              <  1:247692‑M1/140‑15 (MQ=255)                 aTGGGTATATTTAATTTTTTTTGATTCAAACTTCCACTTTGGTGAATTTGCTTTTTTTATAACATAGTTGAATATCAATAAAATAGTAGCAAGTTAGTTCAAAATGGCTATGTATTGTTTTTTagacacactttattcac                                                                                                                           <  1:264191‑M1/140‑18 (MQ=255)                       aCATTTAATGTTTTTTGATTCAAACTTCCATTTTGGTCAATTTGCTTTTTTTATAACATAGTTGAATATCAATAAAAGATTAGCAAGTTAGTTCAATATGGCTATGTATTGTTTTTTagacacactttattcacatttaa                                                                                                                     >  2:352346‑M1/1‑117 (MQ=255)                       aCATTTAATGTTTTTTGATTCAAACTTCCATTTTGGTCAATTTGCTTTTTTTATAACATAGTTAAATATCAATAAAAGATTAGCAAGTTAGTTCAAAATGGCTATGTATTGTTTTTTagacacactttattcacatttaa                                                                                                                     >  1:185378‑M1/1‑117 (MQ=255)                            tAATGTTTTTTGATTCAAACTTCCATTTTGGTCAATTTGCTTTTTTTATAACATAGTTGAATATCAATAAAAGATTAGCAAGTTAGTTCAAAATGGCTATGTATTGTTTTTTagacacactttattcacatttaacgtga                                                                                                                >  1:256815‑M1/1‑112 (MQ=255)                              aTGTTTTTTGATTCAAACTTCCATTTTGGTCAATTTGCTTTTTTTATAACATAGTTGAATATCAATAAAAGATTAGCAAGTTAGTTCAAAATGGCTATGTATTGTTTTTTagacacactttattcacatttaacgtgatt                                                                                                              <  2:422495‑M1/140‑31 (MQ=255)                                    tttGATTCAAACTTCCATTTTGGTCAATTTGCTTTTTTTATAACATAGTTGAATATCAATAAAAGATTAGCAAGTTAGTTCAAAATGGCTATGTATTGTTTTTTagacacactttattcacatttaacgtgattagggtg                                                                                                        <  1:461645‑M1/140‑37 (MQ=255)                                     ttGATTCAAATTAAACTTTTGGTTAATTTGCTTTTTTTAAAACATAGTTGAATATCAATAAAAGATTAGCAAGTTAGTTCAAAATGGGTATGTATTGTTTTTTagacacactttattcacatttaacgtgattagggtgt                                                                                                       <  2:414004‑M1/140‑38 (MQ=255)                                     ttGATTCAAACTTCCATTTTGGTTAATTTGCTTTTTTTATAACATAGTTGAATATCAAGAAAAGATTAGCAAGTTAGTTCAAAATTGCTATTTATTGTTTTTTagacacactttattcacatttaacgtgattagggtgt                                                                                                       <  2:130191‑M1/140‑38 (MQ=255)                                         ttCAAACTTCCATTTTGGTCAATTTGCTTTTTTTATAACATAGTTGAATATCAATAAAAGATTAGCAAGTTAGTTCAAAATGGCTATGTATTGTTTTTTagacacactttattcacatttaacgtgattagggtgtgtct                                                                                                   >  1:57048‑M1/1‑99 (MQ=255)                                         ttCAAACTTCCATTTTGGTCAATTTGCTTTTTTTATAACATAGTTGAATATCAATAAAAGATTAGCAAGTTAGTTCAAAATGGCTATGTATTGTTTTTTagacacactttattcacatttaacgtgattagggtgtgtct                                                                                                   <  2:210694‑M1/140‑42 (MQ=255)                                           cAAACTTCCATTTTGGTCAATTTGCTTTTTTTATAACATAGTTGAATATCAATAAAAGATTAGCAAGTTAGTTCAAAATGGCTATGTATTGTTTTTTagacacactttattcacatttaacgtgattagggtgtgtcttt                                                                                                 <  1:396372‑M1/140‑44 (MQ=255)                                              actgtcattttGGTCAATTTGCTTTTTTTATAACATAGTTGAATATCAATAAAAGATTAGCAAGTTAGTTCAAAATGGCTATGTATTGTTTTTTagacacactttattcacatttaacgtgattagggtgtgtcttttta                                                                                              <  2:165954‑M1/135‑47 (MQ=255)                                               cTTCCATTTTGGTCAATTTGCTTTTTTTATAACATAGTTGAATATCAATAAAAGATTAGCAAGTTAGTTCAAAATGGCTATGTATTGTTTTTTagacacactttattcacatttaacgtgattagggtgtgtgtttttaa                                                                                             >  1:109626‑M1/1‑93 (MQ=255)                                                  ccATTTTGGTCAATTTGCTTTTTTTATAACATAGTTGAATATCAATAAAAGATTAGTAAGTTAGTTCAAAATGGCTATGTATTGTTTTTTagacacactttattcacatttaacgtgattagggtgtgtctttttaaatt                                                                                          <  2:59346‑M1/140‑51 (MQ=255)                                                  ccATTTTGGTCAATTTGCTTTTTTTATAACATAGTTGAATATCAATAAAAGATTAGCACGTTAGTTCAAAATGGCTATGTATTGTTTTTTGAAATACATAGGTTTGAAATCTATATTAATTATGCACCAAAtaatttaat                                                                                          <  1:400841/140‑1 (MQ=255)                                                  ccATTTTGGTCAATTTGCTTTTTTTATAACATAGTTGAATATCAATAAAAGATTAGCAAGTTAGTTCAAAATGGCTATGTATTGTTTTTTagacacactttattcacatttaacgtgattagggtgtgtctttttaaatt                                                                                          <  2:457691‑M1/140‑51 (MQ=255)                                                  ccATTTTGGTCAATTTGCTTTTTTTATAACATAGTTGAATATCAATAAAAGATTAGCAAGTTAGTTCAAAATGGCTATGTATTGTTTTTTagacacactttattcacatttaacgtgattagggtgtgtctttttaaatt                                                                                          >  1:135875‑M1/1‑90 (MQ=255)                                                  ccATTTTGGTCAATTTGCTTTTTTTATAACATAGTTGAATATCAATAAAAGATTAGCAAGTTAGTTCAAAATGGCTATGTATTGTTTTTTagacacactttattcacatttaacgtgattagggtgtgtctttttaaatt                                                                                          <  2:279231‑M1/140‑51 (MQ=255)                                                   cATTTTGGTCAATTTGCTTTTTTTATAACATGTTTGAATATCAATAAAAGATTAGCAAGTTAGTTCAAAATGGCTATGTATTGTTTTTTagacacactttattcacatttaacgtgattagggtgtgtctttttaaatta                                                                                         <  1:412733‑M1/140‑52 (MQ=255)                                                    aTTTTGTTCAATTTGCTTTTTTTATAACATAGTTGAATATCAATAAAAGATTAGCAAGTTAGTTCAAAATGGCTATGTATTGTTTTTTagacacactttattcacatttaacgtgattagggtgtgtctttttaaattaa                                                                                        <  2:280776‑M1/140‑53 (MQ=255)                                                                 tGCTTTTTTTATAACATAGTTGAATATCAATAAAAGATTAGCAAGTTAGTTCAAAATGGGTATGTATTGTTTTTTagacacactttattcacatttaacgtgattagggtgtgtctttttaaattaattttatgtaatat                                                                           >  2:480945‑M1/1‑75 (MQ=255)                                                                   cTTTTTTTATAACATAGTTGAATATCAATAAAAGATTAGCAAGTTAGTTCAAAATGGCTATGTATTGTTTTTTagacacactttattcacatttaacgtgattagggtgtgtctttttaaattaattttatgtaatataa                                                                         >  1:19102‑M1/1‑73 (MQ=255)                                                                               cATAGTTGAATATCAATAAAAGATTAGCAAGTTAGTTCAAAATTGCTATGTATTGTTTTTTagacacactttattcacatttaacgtgattagggtgtgtctttttaaattaattttatgtaatataaatactgcatttg                                                             <  1:85107‑M1/140‑80 (MQ=255)                                                                                   gTTGAATATCAATAAAAGATTAGCAAGTTAGTTCAAAATGGCTATGTATTGTTTTTTagacacactttattcacatttaacgtgattagggtgtgtctttttaaattaattttatgtaatataaatactgcatttgcaaa                                                         <  2:35639‑M1/140‑84 (MQ=255)                                                                                        atatCAATAAAAGATTAGCAAGTTAGTTCAAAATGGCTATGTATTGTTTTTTagacacactttattcacatttaacgtgattagggtgtgtctttttaaattaattttatgtaatataaatactgcatttgcaaactgtt                                                    >  2:301932‑M1/1‑52 (MQ=255)                                                                                        atatCAATAAAAGATTAGCAAGTTAGTTCAAAATGGCTATGTATTGTTTTTTagacacactttattcacatttaacgtgattagggtgtgtctttttaaattaattttatgtaatataaatactgcatttgcaaactgtt                                                    <  2:89170‑M1/140‑89 (MQ=255)                                                                                        atatCAATAAAAGATTAGCAAGTTAGTTCAAAATGGCTATGTATTGTTTTTTagacacactttattcacatttaacgtgattaaggtgtgtctttttaaattaattttatataatataaatactgcatttgcaaactgtt                                                    >  1:236093‑M1/1‑52 (MQ=255)                                                                                          atCAATAAAAGATTAGCAAGTTAGTTCAAAATGGCTATGTATTGTTTTTTagacacactttattcacatttaacgtgattagggtgtgtctttttaaattaattttatgtaatataaatactgcatttgcaaactgttgc                                                  <  2:548672‑M1/140‑91 (MQ=255)                                                                                            tcataAAAGATTAGCATGTTAGTTCAAAATGGCTATGTATTGTTTTTTagacacactttattcacatttaacgtgattagggtgtgtctttttaaattaattttatgtaatataaatactgcatttgcaaactgttgcac                                                <  2:169495‑M1/138‑93 (MQ=255)                                                                                            cAATAAAAGATTAGCAAGTTAGTTCAAAATGGCTATGTATTGTTTTTTagacacacattattcagatttaacgtgattagggtgtgtctttttaaattaattttatgtaatataaatactgcatttgtaaacttttgaac                                                >  2:167319‑M1/1‑48 (MQ=255)                                                                                              aTAAAAGATTAGCTAGTTAGTTCAAAATGGCTATGTATTGTTTTTTagacacactttattcacatttaacgtgattagggtgtgtctttttaaattaattttatgtaatataaatactgcatttgcaaactgttgcactt                                              <  1:157950‑M1/140‑95 (MQ=255)                                                                                               tAAAAGATTAGCAAGTTAGTTCAAAATTGCTATGTATTGTTTTTTagacacactttattcacatttaacgtgattagggtgtgtctttttaaattaattttatgtaatataaatactgcatttgcaaactgttgcacttt                                             <  2:352951‑M1/140‑96 (MQ=255)                                                                                                  aaGATTAGCAAGTTAGTTCAAAATGGCTATGTATTGTTTTTTagacacactttattcacatttaacgtgattagggtgtgtctttttaaattaattttatgtaatataaatactgcatttgcaaactgttgcacttttag                                          <  1:468430‑M1/140‑99 (MQ=255)                                                                                                      ttAGCAAGTTAGTTCAAAATGGCTATGTATTGTTTTTTagacacactttattcacatttaacgtgattagggtgtgtctttttaaattaattttatgtaatataaatactgcatttgcaaactgttgcacttttaggtat                                      <  1:273912‑M1/140‑103 (MQ=255)                                                                                                        aGCAAGTTAGTTCAAAATGGCTATGTATTGTTTTTTagacacactttattcacatttaacgtgattagggtgtgtctttttaaattaattttatgtaatataaatactgcatttgcaaactgttgcacttttaggtataa                                    <  1:370684‑M1/140‑105 (MQ=255)                                                                                                           aaGTTAGTTCAAAATGGCTATGTATTGTTTTTTagacacactttattcacatttaacgtgattagggtgtgtctttttaaattaattttatgtaatataaatactgcatttgcaaactgttgcccttttaggtataacag                                 <  1:526917‑M1/140‑108 (MQ=255)                                                                                                              ttagttCAAAATGGCTATGTATTGTTTTTTagacacactttattcaactttaacgtgattagggtttgtctttttaaattaattttatgtaatataaatactgcatttgcaaaatggtgcacttttaggtataacagaat                              >  2:311730‑M1/1‑30 (MQ=255)                                                                                                                   tCAAAATGGCTATGTATTGTTTTTTagacacactttattcacatttaacgtgattagggtgtgtctttttaaattaattttatgtaatataaatactgcatttgcaaactgttgcacttttaggtataacagaattaact                         <  1:167171‑M1/140‑116 (MQ=255)                                                                                                                   tCAAAATGGCTATGTATTGTCTCTTaaacacactttattcacatttaacatgattagggtgtgtctttttaaattaattttatgtaatataaatactgcatttgcaaactgttgcacttttaggtataacagaattaact                         <  1:40410‑M1/140‑116 (MQ=255)                                                                                                                      atatgGCTATGTATTTTTTTTTagacacactttattctcatttcaccttattagtgtttgtctttttaaattaattttatgtaatataaatactgcatttgcaaactgttgcacttttaggtataacagaattaactaca                      <  1:452001‑M1/138‑119 (MQ=255)                                                                                                                            cTATGTATTGTTTTTTagacactctttattcacatttaacgtgattagggtgtgtctttttaaattaattttatgtaatataaatactgcatttgcaaactgttgcacttttaggtataacagaattaactacatttaag                <  2:373114‑M1/140‑125 (MQ=255)                                                                                                                                   ttGTTTTCTtgactcattttattcacatttaacgtgattaggttgtgtctttttaaattaattttatgtaatataaatacttcatttgcaaactgttgcacttttaggtataacagaattaactacatttaaggagattg         <  2:536506‑M1/140‑132 (MQ=255)                                                                                                                                      ttttttagacacactttattcacatttaacgtgattagggtgtgtctttttaaattaattttatgtaatataaatactgcatttgcaaactgttgcacttttaggtataacagaattaactacatttaaggagattgatg      >  1:376221‑M1/1‑6 (MQ=255)                                                                                                                                         tttagacacactttattcacatttaacgtgattagggtgtgtctttttaaattaattttatgtaatataaatactgcatttgcaaactgttgcacttttaggtataacagaattaactacatttaaggagattgatgaac   <  2:100932‑M1/140‑138 (MQ=255)                                                                                                                                          ttagacacactttattcacatttaacgtgattcgggtgtgtctttttaaattaattttatgtaatttaaatactgcatttgcaaactgttgcacttttaggtataacagaattaactacatttaaggagattgatgaacc  >  1:520679‑M1/1‑2 (MQ=255)                                                                                                                                          ttagacacactttattcacatttaacgtgattagggtgtgtctttttaaattaattttatgtaatataaatactgcatttgcaaactgttgcacttttaggtataacagaattaactacatttaaggagattgatgaacc  >  1:39071‑M1/1‑2 (MQ=255)                                                                                                                                           |                                                                                                                                           CGATAAAATTTAAGTCATGGGTACATTTAATGTTTTTTGATTCAAACTTCCATTTTGGTCAATTTGCTTTTTTTATAACATAGTTGAATATCAATAAAAGATTAGCAAGTTAGTTCAAAATGGCTATGTATTGTTTTTTGAAATACATAGGTTTGAAATCTATATTAATTATGCACCAAATAATTTAATTAGACTCTATCGAAAATTTCCAAATTTTGCTTACTATCTTTCTAATTTTACTTTTATATTGTTCGCAATGCATAAAAACAAGCGTTTT  >  CP000730/2501049‑2501325

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: ‑