Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,073,463 T→A L642Q (CTG→CAG)  flu → CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,073,4630TA100.0% 149.6 / NA 39L642Q (CTG→CAG) fluCP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base A (24/15);  total (24/15)

AGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCTGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAA  >  NC_000913/2073316‑2073610
                                                                                                                                                   |                                                                                                                                                   
aGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGt                                                                                                                                                  <  2:266237/151‑1 (MQ=255)
 gTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTg                                                                                                                                                 >  2:357238/1‑151 (MQ=255)
     gTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAAc                                                                                                                                              >  1:752733/1‑150 (MQ=255)
     gTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACg                                                                                                                                             >  1:750588/1‑151 (MQ=255)
          ggCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGc                                                                                                                                        >  1:667735/1‑151 (MQ=255)
           gCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCa                                                                                                                                       <  1:689832/151‑1 (MQ=255)
             aaCCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAAc                                                                                                                                     >  2:179242/1‑151 (MQ=255)
              aCCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACa                                                                                                                                    <  2:410891/151‑1 (MQ=255)
              aCCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACa                                                                                                                                    <  1:719137/151‑1 (MQ=255)
                      aGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCg                                                                                                                            >  1:169148/1‑151 (MQ=255)
                         gAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCgggg                                                                                                                         <  2:133923/151‑1 (MQ=255)
                         gAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCgggg                                                                                                                         >  1:129428/1‑151 (MQ=255)
                         gAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCggg                                                                                                                          <  2:169180/150‑1 (MQ=255)
                            aaaCCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTg                                                                                                                      <  1:109740/151‑1 (MQ=255)
                              aCCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGt                                                                                                                                  >  2:116299/1‑137 (MQ=255)
                              aCCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGt                                                                                                                                  <  1:116272/137‑1 (MQ=255)
                               ccTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCg                                                                                                                   >  1:445791/1‑151 (MQ=255)
                                 tGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGa                                                                                                                  >  2:553355/1‑150 (MQ=255)
                                        aCAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGt                                                                                                          >  2:320668/1‑151 (MQ=255)
                                           gAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTa                                                                                                         >  2:484569/1‑149 (MQ=255)
                                                gCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTAt                                                                                                  >  2:199633/1‑151 (MQ=255)
                                                gCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGGGCGTCGGGGCTGGCGACCAGCGGTCAGGGTa                                                                                                   >  1:585068/1‑150 (MQ=255)
                                                 cACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGGAAGGGTAtt                                                                                                 >  1:608222/1‑151 (MQ=255)
                                                   ccATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCa                                                                                               <  1:300781/151‑1 (MQ=255)
                                                    cATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAg                                                                                              <  2:754188/151‑1 (MQ=255)
                                                                        cGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACgg                                                                          >  2:36331/1‑151 (MQ=255)
                                                                                    aGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACgga                                                              <  2:78563/151‑1 (MQ=255)
                                                                                    aGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACgg                                                               <  1:233880/150‑1 (MQ=255)
                                                                                     gAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACgg                                                               >  2:552023/1‑149 (MQ=255)
                                                                                             cTGACAGACTGGTCATTGAAGTCGGCAGGGCAACAGGAAAAACCATCCTGAACCAGGTGAATGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGGAAGGGTATACAGGTGGGGGAAGCCATTAAGGGTGCCACCAAGGCGGAAgg                                                        >  1:267167/1‑148 (MQ=255)
                                                                                                     cTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTcc                                             >  1:376721/1‑151 (MQ=255)
                                                                                                          cATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAgggg                                        >  2:194023/1‑151 (MQ=255)
                                                                                                            ttGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGa                                       >  1:322895/1‑150 (MQ=255)
                                                                                                              gACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAAc                                     >  2:327693/1‑150 (MQ=255)
                                                                                                               aCGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAAc                                     >  1:112650/1‑149 (MQ=255)
                                                                                                                                      aCCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAact            <  2:490016/151‑1 (MQ=255)
                                                                                                                                           ccTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTc        <  1:547210/150‑1 (MQ=255)
                                                                                                                                               aaCCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTc    >  1:247244/1‑150 (MQ=255)
                                                                                                                                                aCCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTATCGGTGCCGCCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCaa  <  1:379977/151‑1 (MQ=255)
                                                                                                                                                   |                                                                                                                                                   
AGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCTGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAA  >  NC_000913/2073316‑2073610

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: