Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	41,171	T→C	intergenic (‑38/‑62)	pbp ← / → mecR1	Beta‑lactam‑inducible penicillin‑binding protein/Methicillin resistance mecR1 protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	41,171	0	T	C	100.0%	224.2 / NA	70	intergenic (‑38/‑62)	pbp/mecR1	Beta‑lactam‑inducible penicillin‑binding protein/Methicillin resistance mecR1 protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (39/31);  total (39/31)

GTATTATTAATTTCTTTATCTTTTGAAGCATAAAAATATATACCAAACCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGTTAAGTATAATCAGTTCATTGCTCACGATATGTGTAATTTTTTTAGTGAGAA  >  USA300TCH1516_ALE/41036‑41305                                                                                                                                        |                                                                                                                                       gttctattaATTTGTTTATCCTTTGAAGCATAAAAATATATACCAAACTCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACaa                                                                                                                                   <  2:160826/137‑1 (MQ=255)             tCTTTATCTTTTGAAGCATAAAAATATATACCAAACCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCATTATTCTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTa                                                                                                                       >  2:275058/1‑141 (MQ=255)              cTTTATCTTTTGAAGCATAAAAATAAATACCAAACCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTAt                                                                                                                      >  1:935881/1‑141 (MQ=255)               tttATCTTTTGAAGCATAAAAATATATACCAAACCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTAtt                                                                                                                     >  2:321614/1‑140 (MQ=255)               tttATCTTTTGAAGCATAAAAATATATACCAAACCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATg                                                                                                                     >  1:143911/1‑141 (MQ=255)               tttATCTTTTGAAGCATAAAAATATATACCAAACCCGACAACTACAACTATTAAAATAAACGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATACGACTATCTTTGAAGTATACTACAAATGTAGTATTTATg                                                                                                                     >  2:158400/1‑141 (MQ=255)                  ttCTTTTCAAACATAAACATATATACCAAACCCCACAACTCCAACCGCTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAACATCCTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCa                                                                                                                  <  2:120531/140‑1 (MQ=255)                  aTCTTTTGAAGCATAAAAATATATACCAAACCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCa                                                                                                                  <  1:870065/141‑1 (MQ=255)                       ttGAAGCATAAAAATATATACCAAACCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAaata                                                                                                             <  1:794170/141‑1 (MQ=255)                          aaGCATAAAAATATATACCCGCATCACGAACTACAACTATTAAAATAAGTGAAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATg                                                                                                          >  2:706020/1‑141 (MQ=255)                          aaGCATAAAAATATATACCAAACCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTATTATTTATGTCAAAATAATg                                                                                                          >  1:266195/1‑141 (MQ=255)                          aaGCATAAAAATATATACCAAACCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATg                                                                                                          >  2:741734/1‑141 (MQ=255)                          aaGCATAAAAATATATACCAAACCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATg                                                                                                          >  2:826111/1‑141 (MQ=255)                          aaGCATAAAAATATATACCAAACCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAAAAATg                                                                                                          >  1:459477/1‑141 (MQ=255)                          aaGCATAAAAATATATACCAAACCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTAAATTTGTAGTATACTACAAGTGTAGTATTTATGTCAAAATAATg                                                                                                          >  1:856670/1‑141 (MQ=255)                           aGCATAAAAATATATACCAAACCCGACAACTACAACTATTAAAATAAGTGGAACAAGTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTCTGTCAAAATAATGt                                                                                                         >  1:933883/1‑141 (MQ=255)                            gCATAAAGATATATACCAAACCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATTATGtt                                                                                                        >  1:302920/1‑141 (MQ=255)                            gCATAAAAATATATACCAAACCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGtt                                                                                                        >  1:824909/1‑141 (MQ=255)                            acATAAAAATATATACCAAACCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGtt                                                                                                        <  1:881853/140‑1 (MQ=255)                                      atataCCAAACCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTtg                                                                                              <  2:143911/141‑1 (MQ=255)                                      atataCCAAACCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACGCCTTATATAAGACTACATTTGCAGTATACTACAAATGTAGTATTTATGGCAAAATAATGTTATAATTTTtg                                                                                              <  1:455430/141‑1 (MQ=255)                                          aCCAAACCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGat                                                                                          >  2:288906/1‑141 (MQ=255)                                           ccAAACCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTTAAAATAATGTTATAATTTTTGTGata                                                                                         >  1:20529/1‑141 (MQ=255)                                            cAAACCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGatag                                                                                        >  1:244269/1‑140 (MQ=255)                                                cccGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAg                                                                                    >  1:199788/1‑141 (MQ=255)                                                cccGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTACTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAg                                                                                    >  1:135921/1‑141 (MQ=255)                                                 ccGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAgg                                                                                   <  1:695920/141‑1 (MQ=255)                                                 ccGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAgg                                                                                   <  2:19798/141‑1 (MQ=255)                                                  cGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGgt                                                                                  >  2:730300/1‑141 (MQ=255)                                                  cGAAAACTACAACAATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGgt                                                                                  <  1:158400/141‑1 (MQ=255)                                                   gACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAATATAATGTTATAATTTTTGTGATATGGAGgtg                                                                                 >  1:4005/1‑141 (MQ=255)                                                    acaactacaactATTAAAATAATTGGAACAAATTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGgtgt                                                                                <  1:19736/141‑1 (MQ=255)                                                    acaactacaacgAATAAACTAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGgtgt                                                                                <  1:224395/141‑1 (MQ=255)                                                     aaattcaaactaTTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTa                                                                               <  1:304255/134‑1 (MQ=255)                                                      aactacaactaTTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAg                                                                              <  2:180333/141‑1 (MQ=255)                                                      aactacaactaTTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAg                                                                              <  2:146034/141‑1 (MQ=255)                                                       actacaactaTTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGTTATTATTTTTGTGATATGGAGGTGTTGa                                                                             >  2:975910/1‑141 (MQ=255)                                                       actacaactaTTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGa                                                                             >  2:49437/1‑141 (MQ=255)                                                       actacaactaTTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGa                                                                             <  2:826697/141‑1 (MQ=255)                                                       actacaactaTTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGa                                                                             >  2:72841/1‑141 (MQ=255)                                                       actacaactaTTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGa                                                                             >  2:197383/1‑141 (MQ=255)                                                           catctaTTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGgt                                                                         <  2:760994/138‑1 (MQ=255)                                                           caactaTTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGgt                                                                         <  2:562042/141‑1 (MQ=255)                                                                   aaaaTAAGTTGAACAATTTTTATATTTTTCATCGATATACTCCATATATAAGACTACATTGGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTatcat                                                                 <  1:259044/141‑1 (MQ=255)                                                                   aaaaTAAGTGGAACAATTGTTATCTTTTTCATAAATCTGCTCCTTATATAAGACGACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGTTTTAATTTTTGTGATATGGAGGTCTAGAAGGTGTTatcat                                                                 <  1:555741/141‑1 (MQ=255)                                                                      aTAAGTGGAACCATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCtt                                                              <  1:283855/141‑1 (MQ=255)                                                                         aGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCttttt                                                           <  2:975449/141‑1 (MQ=255)                                                                                   tttttATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGTTAAg                                                 >  1:167110/1‑141 (MQ=255)                                                                                   tttttATCTTTTTCATCAATAGACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGTTAAg                                                 >  1:510022/1‑141 (MQ=255)                                                                                    ttttATCTTTTTCATCAATATATTCCTTATATTAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGTTAAGt                                                <  1:17724/141‑1 (MQ=255)                                                                                    ttttATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGTTAAGt                                                >  1:349742/1‑141 (MQ=255)                                                                                    ttttATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGAGTTATCATCTTTTTTAATGTTAAGt                                                >  1:128460/1‑141 (MQ=255)                                                                                          cTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGTTAAGTATAATc                                          >  1:698704/1‑141 (MQ=255)                                                                                            ttttCATCAATATACTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGTTAAGTATAATCAg                                        >  2:775560/1‑141 (MQ=255)                                                                                                        taCTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGGGGTGTAGAAGGTGTTATCATCTTTTTTAATGTTAAGTATAATCAGTTCATTGCTCAc                            <  1:955340/141‑1 (MQ=255)                                                                                                        taCTCCTTATATAAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGTTAAGTATAATCAGTTCATTGCTCAc                            <  1:994494/141‑1 (MQ=255)                                                                                                            ccTTATATAAGACTACATGTTTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGTTAAGTATAATCGGTTCATTGCTGACGata                        >  2:752090/1‑141 (MQ=255)                                                                                                                tgtataGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTTATGTTAAGTATAATCAGTTCATTGCTCACGATAtgtg                    <  2:652346/136‑1 (MQ=255)                                                                                                                aaataAGACTACATTTGTAGTATACTAAAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGTTAAGTATAATCAGTTCATTGCTCACGATAtgtg                    <  2:20529/139‑1 (MQ=255)                                                                                                                  ataAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGTTAAGTATAATCAGTTCATTGTTCACGATATGTGTa                  >  1:497179/1‑141 (MQ=255)                                                                                                                  ataAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGTTAAGTATAATCAGTTCATTGCTCACGATATGTGTa                  >  1:784930/1‑141 (MQ=255)                                                                                                                  ataAGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGTTAAGTATAATCAGTTAATTGCTCACGatacagata                  >  1:529299/1‑135 (MQ=255)                                                                                                                    aaGACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGTTAAGTATAATCAGTTCATTGCTCACGATATGTGTAAt                <  1:706905/141‑1 (MQ=255)                                                                                                                      gACTACATTTGTAGTATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGTTAAGTATAATCAGTTCATTGCTCACGATATGTGTAAttt              >  2:19542/1‑141 (MQ=255)                                                                                                                      gACTACATTTGTAGAATACCACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGTTAAGTATAATCAGTTCATTTCTCACGATAAGTGTAAttt              >  1:547827/1‑141 (MQ=255)                                                                                                                           cATTTGTAGTATACTACAAATGGAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGTTAAGTATAATCAGTTCATTGCTCACGATATGTGTAATTTTTTTa         <  1:452202/141‑1 (MQ=255)                                                                                                                                 tagtaTACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGTTAAGTATAATCAGTTCATTGCTCACGATATGTGTAATTTTTTTAGTgaga   <  2:167110/141‑1 (MQ=255)                                                                                                                                 tagtaTACTACAAATGTAGTATTTATGTCAAAATAATGTTATAACTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGTTAAGTATAATCAGTTCATTGCTCACGATATGTGTAATTTTTTTAGTgaga   <  2:510022/141‑1 (MQ=255)                                                                                                                                  agtaTACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGTTAAGTATAATCAGTTCATTGCTCACGATATGTGTAATTTTTTTAGTGAGaa  >  1:962411/1‑141 (MQ=255)                                                                                                                                  agtaTACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAAGGTTAAGGATAATCCGTTCATTACTCACGATATGTGTAGTTTTTTTAGTAAGaa  >  1:226486/1‑141 (MQ=255)                                                                                                                                        |                                                                                                                                       GTATTATTAATTTCTTTATCTTTTGAAGCATAAAAATATATACCAAACCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGTTAAGTATAATCAGTTCATTGCTCACGATATGTGTAATTTTTTTAGTGAGAA  >  USA300TCH1516_ALE/41036‑41305

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: ‑