Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,073,282	G→A	G582R (GGA→AGA)	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	2,073,282	0	G	A	100.0%	102.4 / NA	30	G582R (GGA→AGA)	flu	CP4‑44 prophage, antigen 43 (Ag43) phase‑variable biofilm formation autotransporter
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (13/17);  total (13/17)

CTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGA  >  NC_000913/2073150‑2073412                                                                                                                                     |                                                                                                                                   cTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCcagacaga                                                                                                                              <  2:570157/139‑1 (MQ=255)    aaGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTc                                                                                                                           >  1:488353/1‑139 (MQ=255)    aaGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTc                                                                                                                           >  1:959559/1‑139 (MQ=255)      gCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTCAt                                                                                                                         <  1:517890/139‑1 (MQ=255)       cTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTCAtt                                                                                                                        <  1:534626/139‑1 (MQ=255)            cGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTCATTTCAcc                                                                                                                   <  2:839160/139‑1 (MQ=255)                     tgtgCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGc                                                                                                          >  1:198283/1‑139 (MQ=255)                                           cccACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCaa                                                                                    >  1:111328/1‑139 (MQ=255)                                                  aTGTCACTCTCGCCTCCGGTGCCGCCTGGAATATCCCCGATAACGCCACGGTGCAGTGGGTGGTGGATGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCCCCCGCACAGGGAAGTTCGTACCGGGAACCCTGaa                                                                             <  2:323846/139‑1 (MQ=255)                                                       aCTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGa                                                                        <  2:509588/139‑1 (MQ=255)                                                             gCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAAcc                                                                  >  2:944981/1‑139 (MQ=255)                                                                         aCCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGa                                                      <  2:198283/139‑1 (MQ=255)                                                                                         aTAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCt                                      >  2:1057499/1‑139 (MQ=255)                                                                                         aTAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCt                                      <  1:944981/139‑1 (MQ=255)                                                                                              gCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCgtg                                 <  1:503632/139‑1 (MQ=255)                                                                                              gCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCgtg                                 <  1:1057499/139‑1 (MQ=255)                                                                                                   ggTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGc                            >  1:971534/1‑139 (MQ=255)                                                                                                          tCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGata                     <  2:959559/139‑1 (MQ=255)                                                                                                               ggtggATGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGca                >  2:139289/1‑139 (MQ=255)                                                                                                               ggtggATGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGca                <  2:188892/139‑1 (MQ=255)                                                                                                                    aTGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCAc                                                                                                              <  1:595387/40‑1 (MQ=255)                                                                                                                    aTGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCAc                                                                                                              >  2:595387/1‑40 (MQ=255)                                                                                                                    aTGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGa                                                               <  2:199918/87‑1 (MQ=255)                                                                                                                    aTGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGa                                                               >  1:199918/1‑87 (MQ=255)                                                                                                                    aTGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGaa           <  1:1068188/139‑1 (MQ=255)                                                                                                                      gACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGata                     <  2:1055111/127‑1 (MQ=255)                                                                                                                      gACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGata                     >  1:1055111/1‑127 (MQ=255)                                                                                                                        ccTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGa                                                               <  2:1035949/83‑1 (MQ=255)                                                                                                                        ccTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGa                                                               >  1:1035949/1‑83 (MQ=255)                                                                                                                           cAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCt    >  2:748485/1‑139 (MQ=255)                                                                                                                             gCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGa  <  2:971534/139‑1 (MQ=255)                                                                                                                                     |                                                                                                                                   CTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGA  >  NC_000913/2073150‑2073412

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑