Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,072,464	A→G	K309R (AAG→AGG)	flu →	CP4‑44 prophage; self recognizing antigen 43 (Ag43) autotransporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,072,464	0	A	G	100.0%	119.0 / NA	34	K309R (AAG→AGG)	flu	CP4‑44 prophage; self recognizing antigen 43 (Ag43) autotransporter
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (14/20);  total (14/20)

TCTGACACTGTTGTGAACAGTGACGGCTGGCAGATTGTCAAAAACGGGGGTGTGGCCGGGAATACCACCGTTAATCAGAAGGGCAGACTGCAGGTGGACGCCGGTGGTACAGCCACGAATGTCA‑CCCTGAAGCAGGGCGGCGCACTGGTTACCAGTACGGCTGCAACCGTTACCGGCATAAACCGCCTGGGAGCATTCTCTGTTGTGGAGGGTAAAGCTGATAATGTCGTACTGGAAAATGGCGGACGCCTGGATGTGCTGA  >  NC_000913/2072334‑2072595                                                                                                                                    |                                                                                                                                    tCTGACACTGTTGTGAACAGTGACGGCTGGCAGATTGTCAAAAACGGGGGTGTGGCCGGGAATACCACCGTTAATCAGAAGGGCAGACTGCAGGTGGACGCCGGTGGTACAGCCACGAATGTCA‑CCCTGAGGCAGggcgg                                                                                                                            >  1:636843/1‑140 (MQ=255) tCTGACACTGTTGTGAACAGTGACGGCTGGCAGATTGTCAAAAACGGGGGTGTGGCCGGGAATACCACCGTTAATCAGAAGGGCAGACTGCAGGTGGACGCCGGTGGTACAGCCACGAATGTCA‑CCCTGAGGCAGggcgg                                                                                                                            >  2:571099/1‑140 (MQ=255)     gcacTGTTGTGAACAGTGACGGCTGGCAGATTGTCAAAAACGGGGGTGTGGCTGGGAATCCCACCGTTAATCAGAAGGGCAGACTGCAGGTGGACGCCGGTGGTACAGCCACGAATGTCA‑CCCTGAGGCAGGGCGGCGCa                                                                                                                        <  2:533334/139‑1 (MQ=255)     acacTGTTGTGAACAGTGACGGCTGGCAGATTGTCAAAAACGGGGGTGTGGCCGGGAATACCACCGTTAATCAGAAGGGCAGACTGCAGGTGGACGCCGGTGGTACAGCCACGAATGTCA‑CCCTGAGGCATGGCGGCGCa                                                                                                                        <  2:659422/140‑1 (MQ=255)     acacTGTTGTGAACAGTGACGGCTGGCAGATTGTCAAAAACGGGGGTGTGGCCGGGAATACCACCGTTAATCAGAAGGGCAGACTGCAGGTGGACGCCGGTGGTACAGCCACGAATGTCA‑CCCTGAGGCAGGGCGGCGCa                                                                                                                        <  1:504933/140‑1 (MQ=255)     acacTGTTGTGAACAGTCACGGCTGGCAGATCGTCCAAATCGGGGGTGCGGCCGGGAATACCACCGTTAATCAGAAGGGCAGACTGCAGGTGGACGCCGGTGGTACAGCCACGAATGTCA‑CCCTGAGGCAGGGCGGCGCa                                                                                                                        <  2:193096/140‑1 (MQ=255)      cacTGTTGTGAACAGTGGCGGCTGGCAGATTTTCAAAAATGGGGGTGTAGCCGGGAATACCACCGTTAATCAGAAGGGCAGACTGCAGGTGGACGCCGGTGGTACAGCCACGAATGTCA‑CCCTGAGGCAGGGCGGCGCAc                                                                                                                       <  2:229205/140‑1 (MQ=255)          gttgtGAACAGTGACGACTGGGTGGTTGTCACAGACGGGAGTGAGGCCGGGAATACCACCGTTAATGAGAAGGGCAGACTGCAGGTGGAGGCAGGTGGTACAGCCACGGATGTCA‑CCCTGAGGCATGGCGGCGCACTGGt                                                                                                                   <  2:330370/140‑1 (MQ=255)           ttgtGAACAGTGACGGCTGGCAGATTGTCAAAAACGGGGGTGTGGCCGGGAATACCACCGTTAATCAGAAGGGCAGACTGCAGGTGGACGCCGGTGGTACAGCCACGAATGTCA‑CCCTGAGGCAGGGCGGCGCACTg                                                                                                                     >  1:40801/1‑137 (MQ=255)           ttgtGAACAGTGACGGCTGGCAGATTGTCAAAAACGGGGGTGTGGCCGGGAATACCACCGTTAATCAGAAGGGCAGACTGCAGGTGGACGCCGGTGGTACAGCCACGAATGTCA‑CCCTGAGGCAGGGCGGCGCACTg                                                                                                                     <  2:40801/137‑1 (MQ=255)               gAACAGTGACGGCTGGCAGATTGTCAAAAACGGGGGTGTGGCCGGGAATACCACCGTTAATCAGAAGGGCAGACTGCAGGTGGACGCCGGTGGTACAGCCACGAATGTCA‑CCCTGAGGCAGGGCGGCGCAc                                                                                                                       <  2:501468/131‑1 (MQ=255)               gAACAGTGACGGCTGGCAGATTGTCAAAAACGGGGGTGTGGCCGGGAATACCACCGTTAATCAGAAGGGCAGACTGCAGGTGGACGCCGGTGGTACAGCCACGAATGTCA‑CCCTGAGGCAGGGCGGCGCAc                                                                                                                       >  1:501468/1‑131 (MQ=255)               gAACAGTGACGGCTGGCAGATTGTCAAAAACGGGGGTGTGGCCGGGAATACCACCGTTAATCAGAAGGGCAGACTGCAGGTGGACGCCGGTGGTACAGCCACGAATGTCA‑CCCTAAGTCAGGGCGGCGCACTGGTTACCa                                                                                                              >  1:229205/1‑140 (MQ=255)                     tGACGGCTGGCAGATTGTCAAAAACGGGGGTGTGGCCGGGAATACCACCGTTAATCAGAAGGGCAGACTGCAGGTGGACGCCGGTGGTACAGCCACGAATGTCA‑CCCTGAGGCAGGGCGGCGCACTGGTTACCAGTACgg                                                                                                        >  2:42241/1‑140 (MQ=255)                     tGACGGCTGGCAGATTGTCAAAAACGGGGGTGTGGCCGGGAATACCACCGTTAATCAGAAGGGCAGACTGCAGGTGGACGCCGGTGGTACAGCCACGAATGTCA‑CCCTGAGGCAGGGCGGCGCACTGGTTACCAGTACgg                                                                                                        >  2:386754/1‑140 (MQ=255)                               cAGATTGTCAAAAACGGGGGTGTGGCCGGGAATACCACCGTTAATCAGAAGGGCAGACTGCAGGTGGACGCCGGTGGTACAGCCACGAATGTCA‑CCCTGAGGCAGGGCGGCGCACTGGTTACCAGTACGGCTGCAACCGt                                                                                              >  2:447875/1‑140 (MQ=255)                                           aaCGGGGGTGTGGCCGGGAATACCACCGTTAATCAGAAGGGCAGACTGCAGGTGGACGCCGGTGGTACAGCCACGAATGTCA‑CCCTGAGGCAGGGCGGCGCACTGGTTACCAGTACGGCTGCAACCGTTACCGGCATaaa                                                                                  <  2:57412/140‑1 (MQ=255)                                                   tgtgGCCGGGAATACCACCGTTAATCAGAAGGGCAGACTGCAGGTGGACGCCGGTGGTACAGCCACGAATGTCA‑CCCTGAGGCAGGGCGGCGCACTGGTTACCAGTACGGCTGCAACCGTTACCGGCATAAACCGCCTgg                                                                          <  1:571099/140‑1 (MQ=255)                                                       gCCGGGAATACCACCGTTAATCAGAAGGGCAGACTGCAGGTGGACGCCGGTGGTACAGCCACGAATGTCA‑CCCTGAGGCAGGGCGGCGCACTGGTTACCAGTACGGCTGCAACCGTTACCGGCATAAACCGCCTGGGAGc                                                                      <  1:19610/140‑1 (MQ=255)                                                        ccGGGAATACCACCGTTAATCAGAAGGGCAGACTGCAGGTGGACGCCGGTGGTACAGCCACGAATGTCA‑CCCTGAGGCAGGGCGGCGCACTGGTTACCAGTACGGCTGCAACCGTTACCGGCATAAACCGCCTGGGAGCa                                                                     <  1:738421/140‑1 (MQ=255)                                                            gAATACCACCGTTAATCAGAAGGGCAGACTGCAGGTGGACGCCGGTGGTACAGCCACGAATGTCA‑CCCTGAGGCAGGGCGGCGCACTGGTTACCAGTACGGCTGCAACCGTTACCGGCATAAACCGCCTGGGAGCATtct                                                                 >  2:159697/1‑140 (MQ=255)                                                            gAATACCACCGTTAATCAGAAGGGCAGACTGCAGGTGGACGCCGGTGGTACAGCCACGAATGTCA‑CCCTGAGGCAGGGCGGCGCACTGGTTACCAGTACGGCTGCAACCGTTACCGGCATAAACCGCCTGGGAGCATtct                                                                 <  2:636843/140‑1 (MQ=255)                                                            gAATACCACCGTTAATCAGAAGGGCAGACTGCAGGTGGACGCCGGTGGTACAGCCACGAATGTCA‑CCCTGAGGCAGGGCGGCGCACTGGTTACCAGTACGGCTGCAACCGTTACCGGCATAAACCGCCTGGGAGCATtct                                                                 <  1:390253/140‑1 (MQ=255)                                                            gAATACCACCGTTAATCAGAAGGGCAGACTGCAGGTGGACGCCGGTGGTACAGCCACGAATGTCA‑CCCTGAGGCAGGGCGGCGCACTGGTTACCAGTACGGCTGCAACCGTTACCGGCATAAACCGCCTGGGAGCATtct                                                                 <  1:386754/140‑1 (MQ=255)                                                             aaTACCACCGTTAATCAGAAGGGCAGACTGCAGGTGGACGCCGGTGGTACAGCCACGAATGTCA‑CCCTGAGGCAGGGCGGCGCACTGGTTACCAGTACGGCTGCAACCGTTACCGGCATAAACCGCCTGGGAGCATtctc                                                                <  1:409997/140‑1 (MQ=255)                                                               tACCACCGTTAATCAGAAGGGCAGACTGCAGGTGGACGCCGGTGGTACAGCCACGAATGTCA‑CCCTGAGGCAGGGCGGCGCACTGGTTACCAGTACGGCTGCAACCGTTACCGGCATAAACCGCCTGGGAGCATTCTCtg                                                              <  1:159697/140‑1 (MQ=255)                                                                       ttAATCAGAAGGGCAGACTGCAGGTGGACGCCGGTGGTACAGCCACGAATGTCACCCCTGAGGCAGGGCGGCGCACTGGTTACCAGTACGGCTGCAACCGTTACCGGCATAAACCGCCTGGGAGCATTCTCTGTTGTGGa                                                       >  2:406699/1‑140 (MQ=255)                                                                           tCAGAAGGGCAGACTGCAGGTGGACGCCGGTGGTACAGCCACGAATGTCA‑CCCTGAGGCAGGGCGGCGCACTGGTTACCAGTACGGCTGCAACCGTTACCGGCATAAACCGCCTGGGAGCATTCTCTGTTGTGGAGGGTa                                                  <  1:35186/140‑1 (MQ=255)                                                                             aGAAGGGCAGACTGCAGGTGGACGCCGGTGGTACAGCCACGAATGTCA‑CCCTGAGGCAGGGCGGCGCACTGGTTACCAGTACGGCTGCAACCGTTACCGGCATAAACCGCCTGGGAGCATTCTCTGTTGTGGAGGGTaaa                                                <  2:120070/140‑1 (MQ=255)                                                                                 gggCAGACTGCAGGTGGACGCCGGTGGTACAGCCACGAATGTCA‑CCCTGAGGCAGGGCGGCGCACTGGTTACCAGTACGGCTGCAACCGTTACCGGCATAAACCGCCTGGGAGCATTCTCTGTTGTGGAGGGTAAAGCTg                                            >  2:104611/1‑140 (MQ=255)                                                                                         tGCAGGTGGACGCCGGTGGTACAGCCACGAATGTCA‑CCCTGAGGCAGGGCGGCGCACTGGTTACCAGTACGGCTGCAACCGTTACCGGCATTAACCGCCTGGGAGCATGCTCTGTTGGGGAGAGGAAAGCTGATAAAGTc                                    >  2:217124/1‑140 (MQ=255)                                                                                            aGGTGGACGCCGGTGGTACAGCCACGAATGTCA‑CCCTGAGGCAGGGCGGCGCACTGGTTACCAGTACGGCTGCAACCGTTACCGGCATAAACCGCCTGGGAGCATTCTCTGTTGTGGAGGGTAAAGCTGATAATGTCGTa                                 >  2:164263/1‑140 (MQ=255)                                                                                            aGGTGGACGCCGGTGGTACAGCCACGAATGTCA‑CCCTGAGGCAGGGCGGCGCACTGGTTACCAGTACGGCTGCAACCGTTACCGGCATAAACCGCCTGGGAGCATTCTCTGTTGTGGAGGGTAAAGCTGATAATGTCGTa                                 <  1:447875/140‑1 (MQ=255)                                                                                                               aGCCACGAATGTCA‑CCCTGAGGCAGGGCGGCGCACTGGTTACCAGTACGGCTGCAACCGTTACCGGCATAAACCGCCTGGGAGCATTCTCTGTTGTGGAGGGTAAAGCTGATAATGTCGTACTGGAAAATGGCGGACGcc              <  1:122442/140‑1 (MQ=255)                                                                                                                           cA‑CCCTGAGGCAGGGCGGCGCACTGGTTACCAGTACGGCTGCAACCGTTACCGGCATAAACCGCCTGGGAGCATTCTCTGTTGTGGAGGGGGAAGCTGATGATGGCGTCTTGGAAAAAGGCGGACCGCCGGGTGTGCTGa  >  2:360067/1‑140 (MQ=255)                                                                                                                                    |                                                                                                                                    TCTGACACTGTTGTGAACAGTGACGGCTGGCAGATTGTCAAAAACGGGGGTGTGGCCGGGAATACCACCGTTAATCAGAAGGGCAGACTGCAGGTGGACGCCGGTGGTACAGCCACGAATGTCA‑CCCTGAAGCAGGGCGGCGCACTGGTTACCAGTACGGCTGCAACCGTTACCGGCATAAACCGCCTGGGAGCATTCTCTGTTGTGGAGGGTAAAGCTGATAATGTCGTACTGGAAAATGGCGGACGCCTGGATGTGCTGA  >  NC_000913/2072334‑2072595

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑