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_000913	2,073,463	0	T	A	100.0%	149.6 / NA	39	L642Q (CTG→CAG)	flu	CP4‑44 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: ‑