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

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: ‑