Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,074,362	(C)6→7	coding (2824/3120 nt)	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	2,074,356	1	.	C	100.0%	207.1 / NA	56	A940P (GCC→CCC)	flu	CP4‑44 prophage; self recognizing antigen 43 (Ag43) autotransporter
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (27/29);  total (27/29)

GGACTTTCCCTGGATGACGGTAAGGACAACGCCGGTTATGTGAAGTTCGGGCATGGCAGTGCACAACATGTGCGTGCCGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTG‑‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGCCTTCTGTTATCCGCACCTTCAGCTCCCGGGGAGATATGCGTGTGGGGACTTCCACTGCAGGCAGCG  >  NC_000913/2074221‑2074485                                                                                                                                         |                                                                                                                                   ggACTTTCCCTGGATGACGGTAAGGACAACGCCGGTTATGTGAAGTTCGGGCATGGCAGTGCACAACATGTGCGTGCCGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTG‑‑cccc                                                                                                                               <  1:1036951/140‑1 (MQ=255)  gACTTTCCCTGGATGACGGTAAGGACAACGCCGGTTATGTGAAGTTCGGGCATGGCAGTGCACAACATGTGCGTGCCGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTG‑‑ccccc                                                                                                                              >  2:985527/1‑140 (MQ=255)   aCTTTCCCTGGATGACGGTAAGGACAACGCCGGTTATGTGAAGTTCGGGCATGGCAGTGCACAACATGTGCGTGCCGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTG‑‑cccccc                                                                                                                             >  1:172607/1‑140 (MQ=255)           tGGATGGCGGTAAGGACAACGCCGGTTATGTGAAGTTCGGGCATGGCAGTGCACAACATGTGCGTGCCGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGa                                                                                                                      <  2:744506/140‑1 (MQ=255)           tGGATGACGGTAAGGACAACGCCGGTTATGTGAAGTTCGGGCATGGCAGTGCACAACATGTGCGTGCCGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGa                                                                                                                      <  1:889701/140‑1 (MQ=255)           tGGATGACGGTAAGGACAACGCCGGTTATGTGAAGTTCGGGCATGGCAGTGCACAACATGTGCGTGCCGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGa                                                                                                                      <  1:794417/140‑1 (MQ=255)             gATGACGGTAAGGACAACGCCGGTTATGTGAAGTTCGGGCATGGCAGTGCACAACATGTGCGTGCCGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACa                                                                                                                    >  2:232520/1‑140 (MQ=255)             gATGACGGTAAGGACAACGCCGGTTATGTGAAGTTCGGGCATGGCAGTGCACAACATGTGCGTGCCGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACa                                                                                                                    <  1:919154/140‑1 (MQ=255)                 aCGGTAAGGACAACGCCGGTTATGTGAAGTTCGGGCATGGCAGTGCACAACATGTGCGTGCCGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGc                                                                                                                >  2:235925/1‑140 (MQ=255)                  cGGTAAGGACAACGCCGGTTATGTGAAGTTCGGGCATGGCAGTGCACAACATGTGCGTGCCGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCa                                                                                                               <  2:914567/140‑1 (MQ=255)                  cGGTAAGGACAACGCCGGTTATGTGAAGTTCGGGCATGGCAGTGCACAACATGTGCGTGCCGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCa                                                                                                               >  2:847711/1‑140 (MQ=255)                       aGGACAACGCCGGTTATGTGAAGTTCGGGCATGGCAGTGCACAACATGTGCGTGCCGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAaca                                                                                                          <  1:346630/140‑1 (MQ=255)                         gACAACGCCGGTTATGTGAAGTTCGGGCATGGCAGTGCACAACATGTGCGTGCCGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAAcaca                                                                                                        <  2:852739/140‑1 (MQ=255)                             aCGCCGGTTATGTGAAGTTCGGGCATGGCAGTGCACAACATGTGCGTGCCGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAgtgt                                                                                                    >  1:229495/1‑140 (MQ=255)                                            aGTTCGGGCATGGCAGTGCACAACATGTGCGTGCCGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGt                                                                                     <  2:356091/140‑1 (MQ=255)                                               tCGGGCATGGCAGTGCACAACATGTGCGTGCCGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGaa                                                                                  <  1:437184/140‑1 (MQ=255)                                                 gggCATGGCAGTGCACAACATGTGCGTGCCGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACt                                                                                >  2:616923/1‑140 (MQ=255)                                                  ggCATGGCAGTGCACAACATGTGCGTGCCGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACtg                                                                               >  1:231917/1‑140 (MQ=255)                                                         cAGTGCACAACATGTGCGTGCCGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACCCCGTGTGAGTGAATTACCGGTGAACTGGTGGGTa                                                                        <  1:135622/140‑1 (MQ=255)                                                         cAGTGCACAACATGTGCGTGCCGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTa                                                                        <  1:232520/140‑1 (MQ=255)                                                         cAGTGCACAACATGTGCGTGCCGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTa                                                                        <  1:894475/140‑1 (MQ=255)                                                            tGCACAACATGTGCGTGCCGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAg                                                                     >  2:4935/1‑140 (MQ=255)                                                                  acaTGTCCGTGCCGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGCCTTCt                                                               <  2:751640/140‑1 (MQ=255)                                                                      gtgcgtgcCGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGCCTTCTGTTa                                                           >  1:218973/1‑140 (MQ=255)                                                                      gtgcgtgcCGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGCCTTCTGTTa                                                           >  1:201553/1‑140 (MQ=255)                                                                      gtgcgtgcCGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGCCTTCTGTTa                                                           <  1:364034/140‑1 (MQ=255)                                                                          gtgcCGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGCCTTCTGTTATCCg                                                       <  1:225372/140‑1 (MQ=255)                                                                          gtgcCGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGCCTTCTGTTATCCg                                                       <  1:985527/140‑1 (MQ=255)                                                                           tgcCGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGCCTTCTGTTATCCGc                                                      >  1:433916/1‑140 (MQ=255)                                                                             ccGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGCCTTCTGTTATCCGCAc                                                    >  2:693302/1‑140 (MQ=255)                                                                             ccGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGCCTTCTGTTATCCGCAc                                                    >  1:590300/1‑140 (MQ=255)                                                                             ccGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGCCTTCTGTTATCCGCAc                                                    >  1:454967/1‑140 (MQ=255)                                                                             ccGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGCCTTCTGTTATCCGCAc                                                    >  1:906431/1‑140 (MQ=255)                                                                             ccGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGCCTTCTGTTATCCGCAc                                                    >  1:144719/1‑140 (MQ=255)                                                                             ccGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGCCTTCTGTTATCCGCAc                                                    >  2:246351/1‑140 (MQ=255)                                                                             ccGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGCCTTCTGTTATCCGCAc                                                    >  1:974148/1‑140 (MQ=255)                                                                             ccGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGCCTTCTGTTATCCGCAc                                                    >  1:998448/1‑140 (MQ=255)                                                                             ccGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGGGAGGGAATTACCGGGGAACTGGTGGGGACAGCCTTCTGGTATCCGCAc                                                    >  1:100060/1‑140 (MQ=255)                                                                               ggTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGCCTTCTGTTATCCGCACCt                                                  >  1:123973/1‑140 (MQ=255)                                                                                gTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGCCTTCTGTTATCCGCACCtt                                                 <  2:229495/140‑1 (MQ=255)                                                                                   tCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGCCTTCTGTTATCCGCACCTTCAg                                              <  1:116577/140‑1 (MQ=255)                                                                                   tCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGCCTTCTGTTATCCGCACCTTCAg                                              <  1:235925/140‑1 (MQ=255)                                                                                     cGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGCCTTCTGTTATCCGCACCTTCAGCt                                            <  2:199887/140‑1 (MQ=255)                                                                                       tCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGCCTTCTGTTATCCGCACCTTCAGCTcc                                          <  1:819216/140‑1 (MQ=255)                                                                                        cTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGCCTTCTGTTATCCGCACCTTCAGCTccc                                         <  1:616923/140‑1 (MQ=255)                                                                                          gggCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGCCTTCTGTTATCCGCACCTTCAGCTCCCgg                                       <  2:231917/140‑1 (MQ=255)                                                                                           ggCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGCCCCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGCCTTCTGTTATCCGCACCTTCAGCTCCCgg                                       >  1:553680/1‑140 (MQ=255)                                                                                           ggCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGCCTTCTGTTATCCGCACCTTCAGCTCCCggg                                      <  1:779739/140‑1 (MQ=255)                                                                                            gCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAGCTGGTGGGTACAGCCTTCTGTTATCCGCACCTTCAGCTCCCgggg                                     <  2:440315/140‑1 (MQ=255)                                                                                             cAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGATAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGCCTTCTGTTATCCGCACCTTCAGCTCCCGGGga                                    >  1:819800/1‑140 (MQ=255)                                                                                               gCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGCCTTCTGTTATCCGCACCTTCAGCTCCCGGGgaga                                  >  1:778771/1‑140 (MQ=255)                                                                                                           tGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGCCTTCTGTTATCCGCACCTTCAGCTCCCGGGGAGATATGCGTGTggg                      >  2:574368/1‑140 (MQ=255)                                                                                                           tGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGCCTTCTGTTATCCGCACCTTCAGCTCCCGGGGAGATATGCGTGTggg                      <  2:201553/140‑1 (MQ=255)                                                                                                           tGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGCCTTCTGTTATCCGCACCTTCAGCTCCCGGGGAGATATGCGTGTggg                      <  2:144719/140‑1 (MQ=255)                                                                                                           tGACCTTTGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGCCTTCTGTTATCCGCACCTTCAGCTCCCGGGGAGATATGCGTGTggg                      <  1:847711/140‑1 (MQ=255)                                                                                                                  tGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGCCTTCTGTTATCCGCACCTTCAGCTCCCGGGGAGATATGCGTGTGGGGACTTcc               >  2:275993/1‑140 (MQ=255)                                                                                                                  tGGCGAAGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGCCTTCTGTTATCCGCACCTTCAGCTCCCGGGGAGATATGCGTGTGGGGACTTcc               >  1:972537/1‑140 (MQ=255)                                                                                                                       aaGGCACCTCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGCCTTCTGTTATCCGCACCTTCAGCTCCCGGGGAGATATGCGTGTGGGGACTTCCACTgc          >  2:361590/1‑140 (MQ=255)                                                                                                                               tCATCCCGTGC‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGCCTTCTGTTATCCGCACCTTCAGCTCCCGGGGAGATATGCGTGTGGGGACTTCCACTGCAGGCAGCg  <  2:311976/140‑1 (MQ=255)                                                                                                                                         |                                                                                                                                   GGACTTTCCCTGGATGACGGTAAGGACAACGCCGGTTATGTGAAGTTCGGGCATGGCAGTGCACAACATGTGCGTGCCGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTG‑‑CCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGCCTTCTGTTATCCGCACCTTCAGCTCCCGGGGAGATATGCGTGTGGGGACTTCCACTGCAGGCAGCG  >  NC_000913/2074221‑2074485

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: ‑