Predicted mutation
evidence seq id position mutation annotation gene description
RA USA300TCH1516_ALE 1,440,007 Δ1 bp coding (34/201 nt) cspA_2 ← Cold shock protein CspA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,440,0070C.97.3% 324.8 / 0.8 74coding (34/201 nt)cspA_2Cold shock protein CspA
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base . (23/49);  minor base T (0/2);  total (23/51)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCGCGGTCGCCTTCAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAAT  >  USA300TCH1516_ALE/1439871‑1440143
                                                                                                                                        |                                                                                                                                        
ccGCGGTCGCCTTCAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGt                                                                                                                                     <  2:852297/141‑1 (MQ=255)
   cgGTCGCCTTCAACTACTTCAAACTCAATAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCACTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTaa                                                                                                                                  <  1:680756/141‑1 (MQ=255)
   ccgTCGCCTTCAACTACTTCAAACTCATCAGCTTGACCTTCGGCTAATGCTTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAAGACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTaa                                                                                                                                  <  2:1641/139‑1 (MQ=255)
    ggTCGCCTTCAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAACACTTTTT‑TGCGTTaaa                                                                                                                                 >  2:387611/1‑141 (MQ=255)
          cTTCAACTACTTCAAACCCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGATAATAAAAAAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCAttt                                                                                                                           <  2:858840/141‑1 (MQ=255)
              cactactTCAAACTCAACATCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACt                                                                                                                       <  1:1121966/140‑1 (MQ=255)
              aaCTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTGCCCGAGCTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACt                                                                                                                       <  1:993077/141‑1 (MQ=255)
                ctactTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTCAAACCATTTAACTGt                                                                                                                     <  1:895070/141‑1 (MQ=255)
                  actTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTAc                                                                                                                   <  1:522986/141‑1 (MQ=255)
                  actTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTAc                                                                                                                   <  1:569064/141‑1 (MQ=255)
                   ctTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTAcc                                                                                                                  <  2:972583/141‑1 (MQ=255)
                    ttCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCt                                                                                                                 <  1:166435/141‑1 (MQ=255)
                    ttCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCt                                                                                                                 >  2:523499/1‑141 (MQ=255)
                                cgCTTTACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATc                                                                                                     <  2:1084565/140‑1 (MQ=255)
                                cgCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATc                                                                                                     <  2:167000/140‑1 (MQ=255)
                                atcTTGATCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCTATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATc                                                                                                     <  1:1007006/139‑1 (MQ=255)
                                 gCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCt                                                                                                    <  1:1185678/141‑1 (MQ=255)
                                   ttGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGa                                                                                                  <  2:69345/141‑1 (MQ=255)
                                   ttGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGGCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGa                                                                                                  <  1:38609/141‑1 (MQ=255)
                                       ccTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAAcc                                                                                              <  1:712569/141‑1 (MQ=255)
                                         ttcttcTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTc                                                                                            <  2:176118/141‑1 (MQ=255)
                                          tcttctAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTcc                                                                                           <  2:453352/141‑1 (MQ=255)
                                           cttctAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCa                                                                                          <  1:956566/141‑1 (MQ=255)
                                           cttctAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCa                                                                                          <  1:956372/141‑1 (MQ=255)
                                            ttcgAATGATTTGTAACCCTCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCaa                                                                                         <  2:721099/141‑1 (MQ=255)
                                              ctAATGATTTGTCACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGa                                                                                       <  1:906482/141‑1 (MQ=255)
                                                  tGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTaa                                                                                   <  2:800665/141‑1 (MQ=255)
                                                  tGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTaa                                                                                   <  1:988434/141‑1 (MQ=255)
                                                  tGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTaa                                                                                   <  1:988387/141‑1 (MQ=255)
                                                    aTTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTAATAATCTGAAACCTCCAAGACTaaaa                                                                                 >  2:173333/1‑141 (MQ=255)
                                                     tttGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAat                                                                                <  1:646448/141‑1 (MQ=255)
                                                         tAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAattcat                                                                            <  2:20438/141‑1 (MQ=255)
                                                          aaCCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAattcatt                                                                           <  2:693351/141‑1 (MQ=255)
                                                               tCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCCACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAata                                                                      >  2:991712/1‑141 (MQ=255)
                                                                 ttGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATg                                                                    >  1:94381/1‑141 (MQ=255)
                                                                 ttGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTAAatatt                                                                    >  1:617191/1‑140 (MQ=255)
                                                                  tGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGc                                                                   >  2:501446/1‑141 (MQ=255)
                                                                   ggTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCt                                                                  >  1:955716/1‑141 (MQ=255)
                                                                        aTTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTc                                                             <  1:1151695/141‑1 (MQ=255)
                                                                              gAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AAAGTTAAACCATTTATCTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCatat                                                       <  1:947454/141‑1 (MQ=255)
                                                                                 aaaTGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTAc                                                    <  1:636816/141‑1 (MQ=255)
                                                                                   aTGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACaa                                                  >  2:773341/1‑141 (MQ=255)
                                                                                    tGTACGAATACGTCATTTTCTCCTTCAGCTTCGATAAGGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAAGCTCCAGGACTAAAATTCATTCAATATGCGTATTCGCATATTACaaa                                                 >  1:166315/1‑141 (MQ=255)
                                                                                    tGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAGTCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACaaa                                                 >  2:467316/1‑141 (MQ=255)
                                                                                    tGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGCCTAAAATTCATTCAATATACTTATTCGCATATTACaaa                                                 >  2:1128616/1‑141 (MQ=255)
                                                                                      tACTAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACaaaaa                                               <  2:497565/141‑1 (MQ=255)
                                                                                        cggaTACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCAGTTAAATGTACCTTGTTTCATAAGCTGAAACCTCCAAGACTAAAATTCATTCAATATGCGTATTCGCATATTACAAAAAAt                                             <  2:1033845/138‑1 (MQ=255)
                                                                                         gAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATa                                            <  2:879528/141‑1 (MQ=255)
                                                                                           aTACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATaaa                                          >  2:1101232/1‑139 (MQ=255)
                                                                                             aCGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATg                                        <  1:936969/141‑1 (MQ=255)
                                                                                                    tttCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTCTTGGCCTATTTGAAAAAATAAATACAAAttt                                 >  1:23083/1‑141 (MQ=255)
                                                                                                         ccTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTc                            >  2:616265/1‑141 (MQ=255)
                                                                                                            tCAGCTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCaaa                         <  2:417966/141‑1 (MQ=255)
                                                                                                            tCAACTTGGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACGACAATTCATTCAATATGCTTATTCGCAGATTACAAAAAATACATGCAAATTTCACTCaaa                         <  1:201925/141‑1 (MQ=255)
                                                                                                              aaCTTCGAAAAAGTCGAATCCTTCTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTTAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAata                       <  2:291274/141‑1 (MQ=255)
                                                                                                               aCTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAatat                      <  2:210186/141‑1 (MQ=255)
                                                                                                                 ttCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTc                    >  1:854354/1‑141 (MQ=255)
                                                                                                                 ttCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTc                    >  1:908997/1‑141 (MQ=255)
                                                                                                                  tCGATAAGGCCTAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTTTAAGATTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCt                   <  1:173333/141‑1 (MQ=255)
                                                                                                                    gATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCGAATTTAACTCAAATATTAttt                 >  1:299334/1‑141 (MQ=255)
                                                                                                                    gATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCttt                 >  1:1059919/1‑141 (MQ=255)
                                                                                                                    gATAAAGCCGAATCACTTTT‑ATCGTTAAACCATTAAACTGTACCTTGCTTCATAATCTGACTCCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCttt                 <  2:483339/141‑1 (MQ=255)
                                                                                                                      aaaaGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGc               <  2:398773/140‑1 (MQ=255)
                                                                                                                       aaaGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCa              >  1:303626/1‑141 (MQ=255)
                                                                                                                        aaGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTCTTCGCATATTACAAAAAATACATACAAATTTCGCTCACATTTTCTTTGCaa             >  1:879645/1‑141 (MQ=255)
                                                                                                                        aaGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCaa             >  1:879743/1‑141 (MQ=255)
                                                                                                                        aaGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCaa             <  1:990579/141‑1 (MQ=255)
                                                                                                                        aaGACGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCaa             <  2:1024215/141‑1 (MQ=255)
                                                                                                                             gAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATgg        <  2:955716/141‑1 (MQ=255)
                                                                                                                               aTCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATCTGGaa      >  1:86041/1‑141 (MQ=255)
                                                                                                                                tCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGaat     <  2:819217/141‑1 (MQ=255)
                                                                                                                                tCCTTTTT‑AGCGTGAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAAGATTCTTTGCAATATGGaat     <  2:668567/141‑1 (MQ=255)
                                                                                                                                  cccttttAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGaata    <  1:137862/138‑1 (MQ=255)
                                                                                                                                   cttttTAGCGTTACACCATTTACCTGTACCTTATTTCATAATCTGACACCCCCAAGACTAAAATTCATTCAATATGCTGATTCGCATATTACAAAAAATACATGCAAATTTCACTCAACTATTCTTTGCAATATGGaataa   <  2:14436/140‑1 (MQ=255)
                                                                                                                                    ttttTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGaataat  <  2:340921/141‑1 (MQ=255)
                                                                                                                                        |                                                                                                                                        
CCGCGGTCGCCTTCAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAAT  >  USA300TCH1516_ALE/1439871‑1440143

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: ‑