Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,777,004 G→A 5.6% A61V (GCA→GTA)  clfB ← Clumping factor B

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,777,0040GA 5.6% 217.2 / 2.0 79A61V (GCA→GTA) clfBClumping factor B
Reads supporting (aligned to +/- strand):  ref base G (26/47);  new base A (3/2);  total (29/50)
Fisher's exact test for biased strand distribution p-value = 3.55e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-01

TGGTATTGCTCGTTTGTGTAGACATTGGTTTTGTTGTGCTATCTACATTCGCACTGTTTGTGTTTGCAC‑TAATATCAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGATTGCCTATCCCAAATAGTATAGTTGCCCCTACTATTACTGATGTGGTACCTACTGTAAAACGTCTAATCGAATAC  >  USA300TCH1516_ALE/2776864‑2777144
                                                                                                                                             |                                                                                                                                            
tGGTATTGCTCGTTTGTGTAGACATTGGTTTTGTTGTGCTATCTACATTCGCACTGTTTGTGTTTGCAC‑TAATATCAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTg                                                                                                                                              <  1:612567/141‑1 (MQ=255)
tGGTATTGCTCGTGTGTGTAGACATTGGTTTTGTTGTGCTATCTACATTCGCACTGTTTGTGTTTGCAC‑TAATATCATATGTATCATTAGCCGTTGTATTTAATTTAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTg                                                                                                                                              <  2:699752/141‑1 (MQ=255)
   tATTGCTCGTTTGTGTAGACATTGGTTTTGTTGTGCTATCTACATTCGCACTGTTTGTGTTTGCAC‑TAATATCAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCAc                                                                                                                                           <  2:32172/141‑1 (MQ=255)
     ttGCTCGTTTGTGTAGACATTGGTTTTGTTGTGCTATCTACATTCGCACTGTTTGTGTTTGCAC‑TAATATCAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACtt                                                                                                                                         >  2:167299/1‑141 (MQ=255)
      tGCTCGTTTGTGTAGACATTGGTTTTGTTGTGCTATCTACATTCGCACTGTTTGTGTTTGCAC‑TAATATCAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTg                                                                                                                                        <  1:44734/141‑1 (MQ=255)
       gCTCGTTTGTGTAGACATTGGTTTTGTTGTGCTATCTACATTCGCACTGTTTGTGTTTGCAC‑TAATATCAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGc                                                                                                                                       <  1:726952/141‑1 (MQ=255)
        cTCGTTTGTGTAGACATTGGTTTTGTTGTGCCATCCCCGTGCGCACTGTTTGTGTTTGCAC‑TAATATCAGCTGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTCTCATCTTGTTTTTTTCGGAATCTGCACTTGCa                                                                                                                                      >  2:243141/1‑141 (MQ=255)
         tCGTTTGTGTAGACATTGGTTTTGTTGTGCTATCTACATTCGCACTGTTTGTGTTTGCAC‑TAATATCAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCat                                                                                                                                     >  1:667636/1‑141 (MQ=255)
              tgtgTAGACATTGTTTTTGTTGTGCTATCTATATTCGCACTGTTTGTGTTTGCAC‑TAATATCAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTAttt                                                                                                                                <  2:217202/141‑1 (MQ=255)
              tgtgTAGACATTGGTTTTGTTGTGCTATCTACATTCGCACTGTTTGTGTTTGCAC‑TAATATCAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTAttt                                                                                                                                <  1:75853/141‑1 (MQ=255)
                tgtAGACATTGGTTTTGTTGTGCTATCTACATTCGCACTGTTTGTGTTTGCAC‑TAATATCAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTAttttt                                                                                                                              >  2:293955/1‑141 (MQ=255)
                tgtAGACATTGGTTTTGTTGTGCTATCTACATTCGCACTGTTTGTGTTTGCAC‑TAATATCAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTAttttt                                                                                                                              >  1:456806/1‑141 (MQ=255)
                 gtAGACATTGGTTTTGTTGTGCTATCTACATTCGCACTGTTTGTGTTTGCAC‑TAATATCAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTc                                                                                                                             >  1:7856/1‑141 (MQ=255)
                  tAGACATTGGTTTTGTTGTGCTATCTACATTCGCACTGTTTGTGTTTGCAC‑TAATATCAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCg                                                                                                                            <  1:268024/141‑1 (MQ=255)
                       tttggtttggtTGTGCTATCTACATTCGCACTGTTTGTGTTTGCAC‑TAATATCAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGAt                                                                                                                       <  2:123465/140‑1 (MQ=255)
                          ggTTTTGTTGTGCTATCTACATTCGCACTGTTTGTGTTTGCAC‑TAATATCAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGACGATTGc                                                                                                                    >  1:315146/1‑141 (MQ=255)
                                gttgtGCTATCTACATTCGCACTGTTTGTGTTTGCAC‑TAATATCAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTa                                                                                                              >  2:516536/1‑141 (MQ=255)
                                gttgtGCTATCTACATTCGCACTGTTTGTG‑TTACACAGAGCAGTTGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCAATTGCATTATTTTTCGCACATTTCTTTGtt                                                                                                              >  2:357884/1‑140 (MQ=255)
                                 ttgtGCTATCTACATTCGCACTGTTTGTGTTTGCAC‑TAATATCAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTAt                                                                                                             <  1:249942/141‑1 (MQ=255)
                                 ttgtGCTATCTACATTCGCACTGTTTGTGTTTGCAC‑TAATATCAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTAt                                                                                                             <  2:241993/141‑1 (MQ=255)
                                  tgtgCTATCTACATTCGCACTGTTTGTGTTTGCAC‑TAATATCAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCTCAATATATAGGTGCATTCTTTCTCGTAGTTTGCGTTGTATc                                                                                                            >  2:274985/1‑141 (MQ=255)
                                     gCTATCTACATTCGCACTGTTTGTGTTTGCAC‑TAATATCAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGtt                                                                                                         >  1:209721/1‑141 (MQ=255)
                                     gCTATCTACATTCGCACTGTTTGTGTTTGCAC‑TAATATCAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCAAACAGCTTCGTGTAGGGTCTGCACTTTCATTATTTTTCGAATATTACGTTGTATCGtt                                                                                                         >  2:554495/1‑141 (MQ=255)
                                       tATCTACCTTTGGTCTGTTTGTGTGTGCAC‑TAATATCAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCg                                                                                                       <  1:398877/141‑1 (MQ=255)
                                          cTACATTCGCACTGTTTGTGTTTGCAC‑TAATATCAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGAtt                                                                                                    >  1:439652/1‑141 (MQ=255)
                                          cTACATTCGCACTGTTTGTGTTTGCAC‑TAATATCAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGAtt                                                                                                    >  2:547152/1‑141 (MQ=255)
                                           tACATTCGCACTGTTTGTGTTTGCAC‑TAATATCAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTg                                                                                                   <  1:121712/141‑1 (MQ=255)
                                                 ctctcTGCTTTTGTTTGCAG‑TAATATCATATGTATCATTTGCCGTTGTATTTAATTGAGGTTTTTCTATCATATTGTTTTTTTCGGAATCTGCTCTTGCATTATTTTTCGAAGATTGTGTTGTATCGTTCGATTGTTCTGa                                                                                             <  2:267802/137‑1 (MQ=255)
                                                 cGCTCTGTTTGTGTTTGCAC‑TAATATCAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTTTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGa                                                                                             <  2:116029/141‑1 (MQ=255)
                                                  gCACTGTTTGTGTTTGCAC‑TAATATCAGATGTATCATTAGCTGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGaa                                                                                            <  2:367331/141‑1 (MQ=255)
                                                     ttgtttgtgtttgCAC‑TAATATCAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCt                                                                                         <  2:573843/140‑1 (MQ=255)
                                                          tgtgtttgCAC‑TAATATCAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGATCTTTTGGTGATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTTTTCTGAAGCTtgttc                                                                                    >  2:280197/1‑139 (MQ=255)
                                                              tttgCTC‑TAATATCGGATGTTGGATTAGCCATTGTATTTGATTGAGGTGTGTCTATCATATTCTTGTTTTCGGAATCTGCACTTTCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTtga                                                                                <  1:274882/141‑1 (MQ=255)
                                                              tttgCAC‑TAATATCAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTtga                                                                                <  1:262854/141‑1 (MQ=255)
                                                              tttgCAC‑TAATATCAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTtga                                                                                >  2:398281/1‑141 (MQ=255)
                                                                agcgc‑TAATATCAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGTAGATTGCGTTGTATCGTTTTATTGTTCTTATGCTTGTGCTtgatg                                                                              >  2:325677/5‑141 (MQ=255)
                                                                  gaC‑TAATTTCTGATGTATCATTAGCCGTTGTATTTAATTGTTTTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTgatgat                                                                            <  2:551964/140‑1 (MQ=255)
                                                                  cAC‑TAATATCAGATGTATCATTAGCTGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTgatgat                                                                            <  2:735604/141‑1 (MQ=255)
                                                                   aC‑TAATATCAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCGATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGAtt                                                                           <  1:745208/141‑1 (MQ=255)
                                                                   aC‑TAATATCAGATGTATCAGTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGAtt                                                                           <  2:775872/141‑1 (MQ=255)
                                                                       aaTATCAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCGTTCCTCATCAAAGATGGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGATTGcc                                                                        >  1:149631/1‑141 (MQ=255)
                                                                       aaTATCAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGATTGcc                                                                        <  1:293955/141‑1 (MQ=255)
                                                                       aaTATCAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGATTGcc                                                                        <  1:376047/141‑1 (MQ=255)
                                                                       aaTATCAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGATTGcc                                                                        <  1:597797/141‑1 (MQ=255)
                                                                        atatCAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTTGAAGATTTCGTTGTATCGTTCGATTTTTTTGAATCTTGTGATTGTTAATTGctt                                                                       >  2:751302/1‑139 (MQ=255)
                                                                          atCAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGATTGCCTAt                                                                     <  1:334649/141‑1 (MQ=255)
                                                                           tCAGATGTATCATTAGCCGTTGTATTTAATTGATGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGATTGCCTATc                                                                    <  2:499878/141‑1 (MQ=255)
                                                                           tCAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTGCGTGATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGATTGCCTATc                                                                    <  1:536369/141‑1 (MQ=255)
                                                                            tataTGTATTATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGATTGCCTATcc                                                                   <  2:708753/138‑1 (MQ=255)
                                                                            cAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGATTGCCTATcc                                                                   <  1:617157/141‑1 (MQ=255)
                                                                            cAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGATTGCCTATcc                                                                   <  2:587136/141‑1 (MQ=255)
                                                                            cAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGATTGCCTATcc                                                                   <  1:460332/141‑1 (MQ=255)
                                                                             aGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGATTGCCTATccc                                                                  >  1:680499/1‑141 (MQ=255)
                                                                                tGTATAATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGATTGCCTATCCCaaa                                                               <  2:646784/141‑1 (MQ=255)
                                                                                   aTCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGTAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGTTTGTTCTTAATCTTGTGCTTGATGATTGCCTATCCCCAatag                                                            >  2:492642/1‑141 (MQ=255)
                                                                                    tCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGAATTCTTTTTTGCAGGTTGGGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGATTGCCTATCCCAAatagt                                                           >  1:369704/1‑141 (MQ=255)
                                                                                    tCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTACACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGTTTGTTCTGAAGCTTGTGCTTGATGATTTCCTTTCCCaatttgt                                                           >  2:68709/1‑136 (MQ=255)
                                                                                    tCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTACACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGATTGCCTATCCCAAatagt                                                           >  2:66616/1‑141 (MQ=255)
                                                                                    tCACTAGCCTTAGTCTTTAATTGAGGTCTTTCTATCATATTGGTTTTTTCTTAATCTGCACTTGCATTTTTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGATTGCCTATCCCAAatagt                                                           <  1:475017/141‑1 (MQ=255)
                                                                                          gCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTGTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGATTGCCTATCCCAAATAGTATAGtt                                                     <  2:429904/141‑1 (MQ=255)
                                                                                               tctgtttATTTGAGTTGTTTCTATCATATTGTTTTTTTCGGAATCTTCACTTGCATTATTTATCTAAGATTGCGTTGTATCGTTCGCTTGTTCTGAAGCTTGTTCTTGATTATTGCCTATCCCAAATAGTATAGTTGcccc                                                <  2:778559/137‑1 (MQ=255)
                                                                                               tGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGATTGCCTATCCCAAATAGTATAGTTGcccc                                                <  2:74340/141‑1 (MQ=255)
                                                                                                ttttttAATTGAGGTTTTTCTGTCTTATTGTTTTTTTCGGACTCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGATGTTTGTGCTTGATGATTGCCTATCCCAAATAGTATAGTTGCCCct                                               <  2:151358/138‑1 (MQ=255)
                                                                                                  aTTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTTCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGATTGCCTATCCCAAATAGTATAGTTGCCCctac                                             <  1:641307/141‑1 (MQ=255)
                                                                                                    ttAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGATTGCCTATCCCAAATAGTATAGTTGCCCctacta                                           <  1:547152/141‑1 (MQ=255)
                                                                                                           aGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGATTGCCTATCCCAAATAGTATAGTTGCCCCTACTATTACTGa                                    <  1:393136/141‑1 (MQ=255)
                                                                                                             gtgtTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGATTGCCTATCCCAAATAGTATAGTTGCCCCTACTATTACTGAtg                                  <  1:192787/141‑1 (MQ=255)
                                                                                                                tttCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGATTGCCTATCCCAAATAGTATAGTTGCCCCTACTATTACTGATGTgg                               <  1:401817/141‑1 (MQ=255)
                                                                                                                tttCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGATTGCCTATCCCAAATAGTATAGTTGCCCCTACTATTACTGATGTgg                               <  1:530625/141‑1 (MQ=255)
                                                                                                                   cTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGATTGCCTATCGCAAATAGTTTATTTGACCCTCTTATTACTGTTGTGTTat                            >  2:85030/1‑140 (MQ=255)
                                                                                                                    tATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGATTGCCTATCCCAAATAGTATAGTTGCCCCTACTATTACTGATGTGGTAcc                           >  1:618897/1‑141 (MQ=255)
                                                                                                                     aTCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGATTGCCTATCCCAAATAGTATAGTTGCCCCTACTATTACTGATGTGCTACCt                          >  2:49894/1‑141 (MQ=255)
                                                                                                                      tCATATTGTTTTTTTCGGAATCTACACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGATTGCCTATCCCAAATAGTATAGTTGCCCCTACTATTACTGATGTGGTACCTa                         <  1:68709/141‑1 (MQ=255)
                                                                                                                      tCATATTGTTTTTTTCGGAATCTACACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGATTGCCTATCCCAAATAGTATAGTTGCCCCTACTATTACTGATGTGGTACCTa                         <  1:66616/141‑1 (MQ=255)
                                                                                                                      tCATATTGTTTTTGTCGGAATCTGCATTTGCATTATTTTTCGAAGAGTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGATTGCCTATCCCAAATAGTATAGTTGCCCCTACTATTACTGATGTGGTACCTa                         <  2:302814/141‑1 (MQ=255)
                                                                                                                       cATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGATTGCCTATCCCAAATAGTATAGTTGCCCCTACTATTACTGATGTGGTACCTAc                        <  1:54795/141‑1 (MQ=255)
                                                                                                                         tatTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGATTGCCTATCCCAAATAGTATAGTTGCCCCTACTATTACTGATGTGGTACCTACTg                      <  1:99455/141‑1 (MQ=255)
                                                                                                                             gTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGATTGCCTATCCCAAATAGTATAGTTGCCCCTACTATTACTGATGTGGTACCTACTGTaaa                  <  1:277934/141‑1 (MQ=255)
                                                                                                                             gTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGATTGCCTATCCCAAATAGTATAGTTGCCCCTACTATTACTGATGTGGTACCTACTGTaaa                  >  1:241277/1‑141 (MQ=255)
                                                                                                                                    tCGGAATCTGCACTTGCATTATTTTTCGAAGATTTCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGATTGCCTATCCTAAATAGTCTAGTTGCCCCTACTATTACTTATCTGTTACGTACTGTAAAATGTCTa           >  2:346253/1‑141 (MQ=255)
                                                                                                                                        aaTCTGCACTTGCATTATTTTTCGAATATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGATTGCCTATCCCAAATAGTATAGTTGCCCCTACTATTACTGATGTGGTACCTACTGTAAAACGTCTAATCg       <  1:654372/141‑1 (MQ=255)
                                                                                                                                             gCATTTGCTGTATTTGTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGATTGCCTATCCCAAATAGTATAGTTGCCCCTACTATTACTGATGTGGTACCTACTGTAAAACGTCTAATCGAATAc  <  2:326303/141‑1 (MQ=255)
                                                                                                                                             gCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGATTGCCTATCCCAAATAGTATAGTTGCACCTACTATTACTGATGTGGTACCTACTGTAAATCGTCTAATCGCATAc  <  2:174131/141‑1 (MQ=255)
                                                                                                                                             |                                                                                                                                            
TGGTATTGCTCGTTTGTGTAGACATTGGTTTTGTTGTGCTATCTACATTCGCACTGTTTGTGTTTGCAC‑TAATATCAGATGTATCATTAGCCGTTGTATTTAATTGAGGTGTTTCTATCATATTGTTTTTTTCGGAATCTGCACTTGCATTATTTTTCGAAGATTGCGTTGTATCGTTCGATTGTTCTGAAGCTTGTGCTTGATGATTGCCTATCCCAAATAGTATAGTTGCCCCTACTATTACTGATGTGGTACCTACTGTAAAACGTCTAATCGAATAC  >  USA300TCH1516_ALE/2776864‑2777144

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: ‑