Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 41,166 G→A 16.8% intergenic (‑33/‑67) 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_ALE41,1660GA16.8% 863.2 / 148.6 354intergenic (‑33/‑67)pbp/mecR1Beta‑lactam‑inducible penicillin‑binding protein/Methicillin resistance mecR1 protein
Reads supporting (aligned to +/- strand):  ref base G (168/124);  new base A (13/46);  total (182/172)
Fisher's exact test for biased strand distribution p-value = 6.57e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.75e-03

Only 100 of 373 total aligned reads displayed.

TACCAAACCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGTTA  >  USA300TCH1516_ALE/41076‑41256
                                                                                           |                                                                                          
taCCAAACCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTgtag                                                                                            <  2:3414985/91‑1 (MQ=255)
  ccAAACCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTgtagta                                                                                          <  1:3602199/91‑1 (MQ=255)
   cAAACCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGtat                                                                                         <  1:2804050/91‑1 (MQ=255)
    aaaCCCGACAACTACAACTATTAAAGTAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGtata                                                                                        <  1:3689920/91‑1 (MQ=255)
    aaaCCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAAtata                                                                                        <  1:1909851/91‑1 (MQ=255)
     aaCCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATGCTCCTTATATAAGACTACATTTGTAGTatat                                                                                       <  1:2647675/91‑1 (MQ=255)
     aaCCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTatat                                                                                       <  1:2216636/91‑1 (MQ=255)
      aCCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATAtt                                                                                      >  1:2833892/1‑91 (MQ=255)
      aCCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAAtatact                                                                                      <  2:1205889/91‑3 (MQ=255)
      aCCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAAtatact                                                                                      <  1:2336755/91‑3 (MQ=255)
      aCCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAAtatact                                                                                      <  2:2193053/91‑3 (MQ=255)
      aCCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAAtatact                                                                                      <  2:494716/91‑3 (MQ=255)
       cccGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAAtatacta                                                                                     <  1:3850049/91‑4 (MQ=255)
       cccGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAAtatacta                                                                                     <  1:2519789/91‑4 (MQ=255)
        ccGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTAc                                                                                    >  1:894902/1‑91 (MQ=255)
        ccGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAATAtactac                                                                                    <  1:2770270/91‑1 (MQ=255)
        ccGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAATAtactac                                                                                    <  2:3642166/91‑1 (MQ=255)
        ccGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTATCATCAATATACTCCTTATATAAGACTACATTTGTAATAtactac                                                                                    <  1:876067/91‑1 (MQ=255)
         cGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAATAtactac                                                                                    <  1:3043828/91‑1 (MQ=255)
         cGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACa                                                                                   >  1:1984079/1‑91 (MQ=255)
            caactacaactaTTAAAATAAGTGGAACCATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACaaaa                                                                                >  2:1391945/1‑90 (MQ=255)
            caactacaactaTTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAATATACTACAAAt                                                                                <  2:3142198/91‑1 (MQ=255)
              actacaactaTTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACCCCTTATATAAGACTACATTTGTAGTATATTACAAATgt                                                                              >  2:763508/1‑91 (MQ=255)
                 acaactaTTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATgtagt                                                                           >  1:468190/1‑91 (MQ=255)
                      taTTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTa                                                                      >  2:1186657/1‑91 (MQ=255)
                      taTTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTa                                                                      <  1:3233105/91‑1 (MQ=255)
                       aTTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTAt                                                                     >  1:1619673/1‑91 (MQ=255)
                        ttAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATg                                                                    >  2:2860388/1‑91 (MQ=255)
                        ttAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATg                                                                    >  2:3048069/1‑91 (MQ=255)
                         tAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGt                                                                   <  1:1339448/91‑1 (MQ=255)
                           aaaTAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCa                                                                 <  1:2118424/91‑1 (MQ=255)
                             aTAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCaaa                                                               >  2:1016979/1‑91 (MQ=255)
                               aaGTGGAACAATTTTTTTTTTTTTCTTCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAaat                                                             >  2:3797166/1‑91 (MQ=255)
                               aaGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAaat                                                             >  1:1739175/1‑91 (MQ=255)
                               aaGTGGAAATATTTTTATGTTTTTCATCAATATACGCCTTATATATAACTACATTTGTTGTATATTACAAATGTAGTATTTATGTCaaatt                                                             <  2:3717257/91‑3 (MQ=255)
                                 gTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAaataa                                                           >  2:2085621/1‑91 (MQ=255)
                                  tGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAaataat                                                          >  1:2727425/1‑91 (MQ=255)
                                  tGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAAGGTAGTATTTATGTCAAaataat                                                          <  2:1427106/91‑1 (MQ=255)
                                   ggAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATg                                                         >  1:1282943/1‑91 (MQ=255)
                                   ggAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATg                                                         >  2:411462/1‑91 (MQ=255)
                                    gAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGt                                                        <  1:3453174/91‑1 (MQ=255)
                                    gAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGt                                                        >  1:816602/1‑91 (MQ=255)
                                     aaCAATTTTTATCTTTTTCATCAATATGCTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCATAATAATGtt                                                       <  2:1547504/91‑1 (MQ=255)
                                     aaCAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGtt                                                       <  2:2798256/91‑1 (MQ=255)
                                     aaCAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGtt                                                       <  2:576144/91‑1 (MQ=255)
                                       cAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTtat                                                     <  2:2779881/91‑1 (MQ=255)
                                       cAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTtat                                                     >  2:654540/1‑91 (MQ=255)
                                       cAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTGGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTtat                                                     <  2:321614/91‑1 (MQ=255)
                                       cAATTTTTAGCTTTTGCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAGATGTAGTATTTATGTCAAAATAATGTtat                                                     <  2:1301731/91‑1 (MQ=255)
                                          tttttATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAAt                                                  <  2:1261851/91‑1 (MQ=255)
                                             ttATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAAtttt                                               <  2:3661688/91‑1 (MQ=255)
                                              tATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAAttttt                                              >  2:3110749/1‑91 (MQ=255)
                                                tCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTtgt                                            <  1:1409637/91‑1 (MQ=255)
                                                   tttttCATCGATATACTCCTTATATAAGACTACATTTGTTGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGa                                          <  2:1439916/91‑1 (MQ=255)
                                                   tttttCATCAATATACTCCTTATATAAGGCTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGa                                          <  2:2323584/91‑1 (MQ=255)
                                                    ttttCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTCTAATTTTTGAGat                                         >  2:1863247/1‑91 (MQ=255)
                                                       tcatcaATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATg                                      >  2:3544989/1‑91 (MQ=255)
                                                         atcaATATACTCCTTATATAAGACTACCTTTGTATTATATTACTAATGTTGTATTTATGTCAAAATTATGTTCTCATTTTTGTTATATGGa                                    >  2:1583698/1‑91 (MQ=255)
                                                         atcaATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGa                                    <  1:2256149/91‑1 (MQ=255)
                                                          tcaATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAg                                   >  1:3118016/1‑91 (MQ=255)
                                                          tcaATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAg                                   <  2:2452646/91‑1 (MQ=255)
                                                           caATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAgg                                  >  2:1135497/1‑91 (MQ=255)
                                                           caATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAgg                                  >  1:329698/1‑91 (MQ=255)
                                                            aaTATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGgt                                 >  2:1626156/1‑91 (MQ=255)
                                                            aaTATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGgt                                 >  2:3336010/1‑91 (MQ=255)
                                                            aaTATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGgt                                 >  2:2720485/1‑91 (MQ=255)
                                                             atatACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGgtg                                >  1:1818216/1‑91 (MQ=255)
                                                             atatACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGgtg                                <  1:1213878/91‑1 (MQ=255)
                                                              tataCTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGgtgt                               >  2:1871334/1‑91 (MQ=255)
                                                               ataCTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTa                              <  1:2690149/91‑1 (MQ=255)
                                                               ataCTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTa                              <  2:3907597/91‑1 (MQ=255)
                                                                taCTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAg                             >  2:3791128/1‑91 (MQ=255)
                                                                    ccTTATATAAGACTACATTTGTAGTATATTACAGATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAgcatg                         >  2:2519821/1‑87 (MQ=255)
                                                                    ccTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAgg                         <  1:540295/91‑1 (MQ=255)
                                                                    ccTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAgg                         >  2:2975537/1‑91 (MQ=255)
                                                                     cTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGgt                        >  1:2426146/1‑91 (MQ=255)
                                                                     cTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGgt                        >  1:144248/1‑91 (MQ=255)
                                                                       tatataAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGgtgt                      <  1:791792/91‑1 (MQ=255)
                                                                       aatataAAACTACATTTGTAGTATATTACAAATTTACTATTTATGTCAAAATAATTTTAGAATTTTTGTGAGATGGATGTGTAGAAGgtgt                      <  2:3573316/90‑1 (MQ=255)
                                                                         tataAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTa                    <  2:1642747/91‑1 (MQ=255)
                                                                         tataAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTa                    <  2:2597300/91‑1 (MQ=255)
                                                                          ataAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTat                   >  2:1844566/1‑91 (MQ=255)
                                                                          ataAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTat                   <  2:1499582/91‑1 (MQ=255)
                                                                          ataAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTat                   <  1:3003922/91‑1 (MQ=255)
                                                                             aGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTatcat                >  2:2992803/1‑91 (MQ=255)
                                                                                cTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCtt             >  2:212611/1‑91 (MQ=255)
                                                                                 tACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCttt            <  2:1820461/91‑1 (MQ=255)
                                                                                 tACATTTGTAGTATATTACAAATGTAGAATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCttt            >  2:2027637/1‑91 (MQ=255)
                                                                                  aCATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCtttt           <  1:1855412/91‑1 (MQ=255)
                                                                                   cATTTGTAGTATATTACAAATGTAGTCTTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCttttt          >  2:2239689/1‑91 (MQ=255)
                                                                                   cATTTGTAGTATATTACAAATGTAGTATTTATTTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCttttt          <  1:3371523/91‑1 (MQ=255)
                                                                                   cATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCttttt          >  1:1042040/1‑91 (MQ=255)
                                                                                    aTTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGCTATGGAGGTGTAGAAGGTGTTATCATCtttttt         >  2:932276/1‑91 (MQ=255)
                                                                                     tttGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTa        >  2:1087607/1‑91 (MQ=255)
                                                                                     tttGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTa        >  1:642662/1‑91 (MQ=255)
                                                                                     tttGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTa        <  1:1136271/91‑1 (MQ=255)
                                                                                      ttGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGGTATGGAGGTGTAGAAGGTGTTATCATCTTTTTTaa       <  2:228753/91‑1 (MQ=255)
                                                                                      ttGTAATATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTaa       >  2:586524/1‑91 (MQ=255)
                                                                                          agtaTATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGtt   >  1:1000001/1‑91 (MQ=255)
                                                                                           gtaTATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGTTa  <  1:3197510/91‑1 (MQ=255)
                                                                                           |                                                                                          
TACCAAACCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGTTA  >  USA300TCH1516_ALE/41076‑41256

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: