Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,073,151	T→C	L538P (CTG→CCG)	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	2,073,151	0	T	C	100.0%	220.2 / NA	61	L538P (CTG→CCG)	flu	CP4‑44 prophage, antigen 43 (Ag43) phase‑variable biofilm formation autotransporter
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (31/30);  total (31/30)

GGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGAC  >  NC_000913/2073030‑2073285                                                                                                                          |                                                                                                                                       ggCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGgcagca                                                                                                                       <  2:177638/139‑1 (MQ=255) ggCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGgcagca                                                                                                                       <  2:841303/139‑1 (MQ=255)       ctcactGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCCGCACTGTGc                                                                                                                 >  2:743197/1‑139 (MQ=255)          actGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGa                                                                                                              >  1:564572/1‑139 (MQ=255)           ctGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGaa                                                                                                             <  2:564572/139‑1 (MQ=255)                     caccacACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCAtt                                                                                                   <  2:720671/139‑1 (MQ=255)                          cacTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGAc                                                                                                                               >  1:1044536/1‑106 (MQ=255)                          cacTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGAc                                                                                                                               <  2:1044536/106‑1 (MQ=255)                          cacTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACt                                                                                                                     <  1:1431582/116‑1 (MQ=255)                          cacTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACt                                                                                                                     >  2:1431582/1‑116 (MQ=255)                           acTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGAcccc                                                                                             <  2:523315/139‑1 (MQ=255)                               aCCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACg                                                                                                           >  1:1432335/1‑121 (MQ=255)                               aCCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACg                                                                                                           <  2:1432335/121‑1 (MQ=255)                                  cAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCAtt                                                                                                   <  1:739103/126‑1 (MQ=255)                                  cAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCAtt                                                                                                   >  2:739103/1‑126 (MQ=255)                                    gAAAGCCGTCAACCTGAATGAAGGCACTCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGgcagca                                                                                                                       <  2:1096137/104‑1 (MQ=255)                                    gAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGgcagca                                                                                                                       >  1:1096137/1‑104 (MQ=255)                                         ccGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCActct                                                                               >  2:21703/1‑139 (MQ=255)                                          cGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACtctc                                                                              <  1:21703/139‑1 (MQ=255)                                           gTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCg                                                                             >  1:50010/1‑139 (MQ=255)                                            tCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGgcagca                                                                                                                       >  1:110143/1‑96 (MQ=255)                                            tCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGgcagca                                                                                                                       <  2:110143/96‑1 (MQ=255)                                                   gaatgaaGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGt                                                                     >  2:44590/1‑139 (MQ=255)                                                      tgaaGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTg                                                                                                                                 >  2:1196892/1‑76 (MQ=255)                                                      tgaaGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTg                                                                                                                                 <  1:1196892/76‑1 (MQ=255)                                                          ggCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGgcagca                                                                                                                       <  2:782029/82‑1 (MQ=255)                                                          ggCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGgcagca                                                                                                                       >  1:1100626/1‑82 (MQ=255)                                                          ggCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGgcagca                                                                                                                       <  2:1100626/82‑1 (MQ=255)                                                          ggCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGgcagca                                                                                                                       >  1:782029/1‑82 (MQ=255)                                                          ggCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTG‑‑CGGCAGCACTGTGCTGAACGGTGCCATTGAcccc                                                                                             <  2:806518/106‑1 (MQ=255)                                                          ggCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTG‑‑CGGCAGCACTGTGCTGAACGGTGCCATTGAcccc                                                                                             >  1:806518/1‑106 (MQ=255)                                                             acgctgacgctgAACGACAGTACCGTCACCACGGATGTCCTTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTACGGTGCCACCTGGa                                                           <  1:931592/139‑1 (MQ=255)                                                              cgctgacgctgaACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGAc                                                                                                                               <  2:1389756/70‑1 (MQ=255)                                                              cgctgacgctgaACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGAc                                                                                                                               >  1:1389756/1‑70 (MQ=255)                                                              cgctgacgctgaACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGaa                                                          >  1:1207192/1‑139 (MQ=255)                                                                  gacgctgaACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATc                                                      >  1:1263404/1‑139 (MQ=255)                                                                             aCAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCa                                                                                   >  2:1339372/1‑99 (MQ=255)                                                                             aCAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCa                                                                                   <  1:1339372/99‑1 (MQ=255)                                                                                      tCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCa                                  >  1:670351/1‑139 (MQ=255)                                                                                        accacGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGAcccc                                                                                             <  2:571124/78‑1 (MQ=255)                                                                                        accacGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGAcccc                                                                                             >  1:300392/1‑78 (MQ=255)                                                                                        accacGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGAcccc                                                                                             >  1:571124/1‑78 (MQ=255)                                                                                        accacGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGAcccc                                                                                             <  2:300392/78‑1 (MQ=255)                                                                                        accacGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGt                                <  1:132095/139‑1 (MQ=255)                                                                                           aaggATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTGGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCgg                             >  2:922352/3‑139 (MQ=255)                                                                                                  tCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCTACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGa                      <  2:1084238/139‑1 (MQ=255)                                                                                                    aTTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACt                                                                                                                     <  2:720117/42‑1 (MQ=255)                                                                                                    aTTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACt                                                                                                                     >  1:720117/1‑42 (MQ=255)                                                                                                         tCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCa                                                                                                     >  1:662890/1‑53 (MQ=255)                                                                                                         tCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCa                                                                                                     <  2:662890/53‑1 (MQ=255)                                                                                                           aGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGaa                                                                                                             <  2:750838/43‑1 (MQ=255)                                                                                                           aGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGaa                                                                                                             >  1:750838/1‑43 (MQ=255)                                                                                                           aGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACg                                                                                          <  2:32962/62‑1 (MQ=255)                                                                                                           aGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACg                                                                                          >  1:32962/1‑62 (MQ=255)                                                                                                           aGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTg                                                                    >  2:268325/1‑84 (MQ=255)                                                                                                           aGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTg                                                                    <  1:268325/84‑1 (MQ=255)                                                                                                           aGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAg             <  1:608763/139‑1 (MQ=255)                                                                                                             cgcgGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGAGCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTAGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTTGATGACCTCAAcc           >  1:595102/1‑139 (MQ=255)                                                                                                               cgGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCAt         >  2:852307/1‑139 (MQ=255)                                                                                                                     aGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGa   >  2:1394209/1‑139 (MQ=255)                                                                                                                      gCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGAc  <  2:1207192/139‑1 (MQ=255)                                                                                                                       ccccGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATg                    <  1:1151458/120‑1 (MQ=255)                                                                                                                          |                                                                                                                                       GGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGAC  >  NC_000913/2073030‑2073285

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑