Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 740,322 G→C 6.7% intergenic (+549/+39) pitA_1 → / ← sle1_2 Low‑affinity inorganic phosphate transporter 1/N‑acetylmuramoyl‑L‑alanine amidase sle1

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE740,3220GC 6.7% 1126.5 / 56.9 322intergenic (+549/+39)pitA_1/sle1_2Low‑affinity inorganic phosphate transporter 1/N‑acetylmuramoyl‑L‑alanine amidase sle1
Reads supporting (aligned to +/- strand):  ref base G (117/183);  new base C (9/13);  total (126/196)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.57e-01

Only 100 of 354 total aligned reads displayed.

ATATAAATATGTATGATAGGGAAGGGTGAGATAATTTTTTGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCATAGCTAGAAACTTCTGAAGCTGGAATTGTACGGTAG  >  USA300TCH1516_ALE/740232‑740412
                                                                                           |                                                                                           
 tataaatatGTATGATAGGGAAGGGTTAGATAATTTTTTGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACatga                                                                                            <  2:455251/91‑1 (MQ=255)
 tataaatatGTATGATAGGGAAGGGTGAGATAATTTTTTGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACatga                                                                                            <  1:3680728/91‑1 (MQ=255)
  ataaatatGTATGATAGGGAAGGGTGAGATAATTTTTTGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACatgat                                                                                           <  1:2273116/91‑1 (MQ=255)
  ataaatatGTATGATAGGGAAGGGTGAGATAATTTTTTGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACGAGCAATCTCACatgat                                                                                           >  2:5388713/1‑91 (MQ=255)
   taaatatGTATGATAGGGAAGGGTGAGATAATTTTTTGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACatgatg                                                                                          <  1:1084483/91‑1 (MQ=255)
   taaatatGTATGATAGGGAAGGGTGAGATAATTTTTTGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACatgatg                                                                                          >  1:3259125/1‑91 (MQ=255)
    aaatatGTATGATAGGGAAGGGTGAGATAATTTTTTGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACATGAtgt                                                                                         >  2:3525177/1‑91 (MQ=255)
    aaatatGTATGATAGGGAAGGGTGAGATAATTTTTTGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACATGAtgt                                                                                         >  2:415763/1‑91 (MQ=255)
    aaatatGTATGATAGGGAAGGGTGAGATAATTTTTTGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACATGAtgt                                                                                         <  1:2553577/91‑1 (MQ=255)
    aaatatGTATGATAGGGAAGGGTGAGATAATTTTTTGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATTCACATCAtgtg                                                                                        <  1:3993126/91‑1 (MQ=255)
    aaatatGTATGATAGGGAAGGGTGAGATAATTTTTTGTACCAAAATGAAAATTTTAAAAAAAAAAAAAAAACTAGCAATCTCACATGAtgt                                                                                         <  2:1328927/91‑1 (MQ=255)
     aatatGTATGATAGGGAAGGGTGAGATAATTTTTTGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACATGAtgtg                                                                                        <  2:1523114/91‑1 (MQ=255)
     aaaatgtatgATAGGAAAGGGTGAGATAAGTTTTTGTACCAAGATGAAAATTCTATTCAAAAATAAAAAACTAGCAATTCACATCATGTGa                                                                                       <  2:1984743/88‑1 (MQ=255)
       tatgtatgATAGGGAAGGGTGAGATAATTTTTTGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATTCACATCATGTGaga                                                                                     <  1:2827243/91‑3 (MQ=39)
        atgtatgATAGGGAAGGGTGAGATAATTTTTTGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACATGATGTGAAt                                                                                    >  2:5201375/1‑91 (MQ=255)
        atgtatgATAGGGAAGGGTGAGATAATTTTTTGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACATGATGTGAAt                                                                                    <  2:2502566/91‑1 (MQ=255)
         tgtatgATAGGGAAGGGTGAGATAATTTTTTGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATTCACATCATGTGagatt                                                                                   <  1:1645307/91‑5 (MQ=38)
          gtatgATAGGGAAGGGTGAGATAATTTTTTGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTg                                                                                  <  1:2933168/91‑1 (MQ=255)
            atgATAGGGAAGGGTGAGATAATTTTTTGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCt                                                                                >  2:5347753/1‑91 (MQ=255)
            atgATAGGGAAGGGTGAGATAATTTTTTGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCt                                                                                <  2:4851827/91‑1 (MQ=255)
            atgATAGGGAAGGGTGAGATAATTTTTTGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATTCACATCATGTGAGATTGCt                                                                                <  2:4398960/91‑1 (MQ=38)
            atgATAGGGAAGGGTGAGATAATTTTTTGTACCAAAATGAAAATTTTTAAAAAAAAAAAAAAACTAGCAATCTCACATGATGTGAATTGCt                                                                                <  2:1940617/91‑1 (MQ=255)
             tgATAGGGAAGGGTGAGATAATTTTTTGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTa                                                                               <  2:3321931/91‑1 (MQ=255)
              gATAGGGAAGGGTGAGATAATTTTTTGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAg                                                                              <  1:1341332/91‑1 (MQ=255)
                 aGGGAAGGGTGAGATAATTTTTTGTACCAAAATGAAAATTTTTTTTAATTTTTAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGta                                                                            >  2:4275761/1‑91 (MQ=255)
                   ggAAGGGTGAGATAATTTTTTGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGtatat                                                                         >  1:2185493/1‑91 (MQ=255)
                     aaGGGTGAGATAATTTTTTGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTatatat                                                                       >  1:1554342/1‑91 (MQ=255)
                     aaGGGTGAGATAATTTTTTGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTatatat                                                                       <  1:4887406/91‑1 (MQ=255)
                      aGGGTGAGATAATTTTTTTTTTTTTTTTGAAAATTTTTTTCAAAAATATAAAACTAGCTATCTCACATGATGTGAATTGCTAGTATATATc                                                                      >  2:2915660/1‑91 (MQ=255)
                      aGGGTGAGATAATTTTTTGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTATATATc                                                                      >  1:645631/1‑91 (MQ=255)
                      aGGGTGAGATAATTTTTTGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTATATATc                                                                      <  1:2451417/91‑1 (MQ=255)
                       gggTGAGATAATTTTTTGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTATATATCa                                                                     >  1:1478899/1‑91 (MQ=255)
                        ggTGAGATAATTTTTTGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAg                                                                    <  1:4168710/91‑1 (MQ=255)
                            agaTAATTTTTTGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACa                                                                >  1:4573235/1‑91 (MQ=255)
                             aaTAATTTTTTGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACGAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACaa                                                               <  1:1928217/90‑1 (MQ=255)
                              aTAATTTTTTGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAat                                                              <  1:3555119/91‑1 (MQ=255)
                                aaTTTTTTGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAattt                                                            <  2:365792/91‑1 (MQ=255)
                                aaTTTTTTGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAattt                                                            >  2:1460225/1‑91 (MQ=255)
                                 aTTTTTTGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAattta                                                           >  2:2658247/1‑91 (MQ=255)
                                   tttttGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAatttatt                                                         >  1:386857/1‑91 (MQ=255)
                                   tttttGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAatttatt                                                         >  1:3179382/1‑91 (MQ=255)
                                    ttttGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAatttattt                                                        <  2:4001516/91‑1 (MQ=255)
                                     tttGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAAtttattta                                                       >  2:4575433/1‑91 (MQ=255)
                                      ttGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATttaa                                                      <  2:3236196/91‑1 (MQ=255)
                                       tGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATttaat                                                     >  2:82232/1‑91 (MQ=255)
                                       tGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATttaat                                                     >  2:2458370/1‑91 (MQ=255)
                                        gTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATttaatt                                                    <  2:1542700/91‑1 (MQ=255)
                                          aCCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATttaattaa                                                  <  1:583215/91‑1 (MQ=255)
                                           ccAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATTtaattaat                                                 >  1:5550137/1‑91 (MQ=255)
                                           ccAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATTtaattaat                                                 <  2:1609385/91‑1 (MQ=255)
                                            cAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATg                                                <  1:1049159/91‑1 (MQ=255)
                                              aaaTGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGa                                              <  1:889559/91‑1 (MQ=255)
                                                 tGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGa                                           <  1:2680711/91‑1 (MQ=255)
                                                    aaaTTTTTTTCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATg                                        <  2:5457738/91‑1 (MQ=255)
                                                    aaaTTTTTTTCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATg                                        <  1:3890861/91‑1 (MQ=255)
                                                     aaTTTTATTCAAAAATAAAAAGCTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGc                                       <  2:2133844/91‑1 (MQ=255)
                                                       tttttttCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCAt                                     <  2:1571278/91‑1 (MQ=255)
                                                       tttcttaCAAAAAAAAAAAGCTAGCAATCTCACATGATGTGAATTGCCAGTATATATCAGTACAATTTATTTTATTAATGGATGAATGCAt                                     <  2:2059058/91‑1 (MQ=255)
                                                          ttttCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCATAGc                                  <  1:3937248/91‑1 (MQ=255)
                                                          ttttCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCATAGc                                  <  2:1740528/91‑1 (MQ=255)
                                                           tttCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCATAGCt                                 <  1:3460766/91‑1 (MQ=255)
                                                           tttCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCATAGCt                                 <  1:5250502/91‑1 (MQ=255)
                                                           tttCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCATAGCt                                 <  2:2225920/91‑1 (MQ=255)
                                                           tttCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCATAGCt                                 <  2:1240973/91‑1 (MQ=255)
                                                            ttCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCATAGCTa                                >  2:3044826/1‑91 (MQ=255)
                                                            ttCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCATAGCTa                                >  1:3620740/1‑91 (MQ=255)
                                                             tCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCATAGCTAg                               >  1:3372155/1‑91 (MQ=255)
                                                              cAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCATAGCTAGa                              >  1:5023833/1‑91 (MQ=255)
                                                              cAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCATAGCTAGa                              <  1:1451763/91‑1 (MQ=255)
                                                              cAAAAATAAAAAACTAGCAATCTCACATGAGGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCATAGCTAGa                              <  1:4347283/91‑1 (MQ=255)
                                                                aaaaTAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCATAGCTAGaaa                            <  2:1690883/91‑1 (MQ=255)
                                                                    aTAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCATAGCTAGAAACtt                         <  1:3227797/91‑1 (MQ=255)
                                                                       aaaaaCTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTCATGGATGAATGCATAGCTAGAAACTTCTg                      >  1:4988203/1‑91 (MQ=255)
                                                                       aaaaaCTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCATAGCTAGAAACTTCTg                      <  1:1985034/91‑1 (MQ=255)
                                                                       aaaaaCTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCATAGCTAGAAACTTCTg                      >  2:595006/1‑91 (MQ=255)
                                                                         aaaCTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCATAGCTAGAAACTTCTGaa                    >  1:1262832/1‑91 (MQ=255)
                                                                         aaaCTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCATAGCTAGAAACTTCTGaa                    <  1:5388713/91‑1 (MQ=255)
                                                                          aaCTAGCCATCTCACATGATGTGAATTGCTAGTATATAGCAGTACAATTTATTTAATTAATGGATGAATGCATAGCTAGAAACTTCTGAAg                   >  1:5423362/1‑91 (MQ=255)
                                                                          aaCTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCATAGCTAGAAACTTCTGAAg                   >  2:1312621/1‑91 (MQ=255)
                                                                           aCTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCATAGCTAGACACTTCTGAAGc                  >  2:5631690/1‑91 (MQ=255)
                                                                           aCTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCATAGCTAGAAACTTCTGAAGc                  >  2:11366/1‑91 (MQ=255)
                                                                            cTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCATAGCTAGAAACTTCTGAAGCt                 <  2:1002913/91‑1 (MQ=255)
                                                                            cTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCATAGCTAGAAACTTCTGAAGCt                 <  2:4906652/91‑1 (MQ=255)
                                                                            cTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCATAGCTAGAAACTTCTGAAGCt                 <  1:5284506/91‑1 (MQ=255)
                                                                            cTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCATAGCTAGAAACTTCTGAAGCt                 >  1:2210270/1‑91 (MQ=255)
                                                                               gCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCATAGCTAGAAACTTCTGAAGCTGGa              >  1:3759469/1‑91 (MQ=255)
                                                                                 aaTCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCATAGCTAGAAACTTCTGAAGCTGGAAt            >  1:273404/1‑91 (MQ=255)
                                                                                   tctcACATGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCATAGCTAGAAACTTCTGAAGCTGGAATTg          <  1:3525177/91‑1 (MQ=255)
                                                                                    ctcACATGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCATAGCTAGAAACTTCTGAAGCTGGAATTGt         <  2:3446934/91‑1 (MQ=255)
                                                                                    ctcACATGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCATAGCTAGAAACTTCTGAAGCTGGAATTGt         <  1:5094995/91‑1 (MQ=255)
                                                                                      cacaTCATGTGAGATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCATAGCTAGAAACTTCTGAAGCTGGAATTGTa        >  1:4662247/1‑91 (MQ=255)
                                                                                       acaTGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCATAGCTAGAAACTTCTGAAGCTGGAATTGTACg      <  2:3710671/91‑1 (MQ=255)
                                                                                       acaTGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCATAGCTAGAAACTTCTGAAGCTGGAATTGTACg      >  2:2799622/1‑91 (MQ=255)
                                                                                       acaTCATGTGAGATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCATAGCTAGAAACTTCTGAAGCTGGAATTGTAc       >  2:3096351/1‑91 (MQ=255)
                                                                                       acaTCATGTGAGATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCATAGCTAGAAACTTCTGAAGCTGGAATTGTAc       >  1:2417885/1‑91 (MQ=255)
                                                                                        caTGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCATAGCTAGAAACTTCTGAAGCTGGCATTGTACgg     >  2:2393945/1‑91 (MQ=255)
                                                                                        caTGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCATAGCTAGAAACTTCTGAAGCTGGAATTGTACgg     <  1:2977286/91‑1 (MQ=255)
                                                                                        caTGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCATAGCTAGAAACTTCTGAAGCTGGAATTGTACgg     >  1:474321/1‑91 (MQ=255)
                                                                                        caTGATGTGAATTGCTAGTATATAACAGTACAATTTATTTAATTAATGGATGAATGCATAGCTAGAAACTTCTGAAGCTGGAATTGTACgg     >  1:4449235/1‑91 (MQ=255)
                                                                                          tgatgTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCATAGCTAGAAACTTCTGAAGCTGGAATTGTACGGTa   <  2:3832825/91‑1 (MQ=255)
                                                                                           |                                                                                           
ATATAAATATGTATGATAGGGAAGGGTGAGATAATTTTTTGTACCAAAATGAAAATTTTTTTCAAAAATAAAAAACTAGCAATCTCACATGATGTGAATTGCTAGTATATATCAGTACAATTTATTTAATTAATGGATGAATGCATAGCTAGAAACTTCTGAAGCTGGAATTGTACGGTAG  >  USA300TCH1516_ALE/740232‑740412

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: