Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,072,889	A→G	T451A (ACC→GCC)	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	2,072,889	0	A	G	100.0%	145.0 / NA	44	T451A (ACC→GCC)	flu	CP4‑44 prophage; self recognizing antigen 43 (Ag43) autotransporter
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (13/31);  total (13/31)

CAGTATCGGAGGCGGTCAGGCGGATGCCCTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCA  >  NC_000913/2072753‑2073023                                                                                                                                         |                                                                                                                                       cAGTATCGGAGGCGGTCAGGCGGATGCCCTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGTTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGcgcca                                                                                                                                     <  1:194901/140‑1 (MQ=255)    tATCGGAGGCGGTCAGGCGGATGCCCTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGcgccacca                                                                                                                                  <  2:328436/140‑1 (MQ=255)    tATCGGAGGCGGTCAGGCGGATGCCCTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGcgccacca                                                                                                                                  >  1:772717/1‑140 (MQ=255)      tCGGAGGCGGTCAGGCGGATGCCCTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACg                                                                                                                                <  1:268457/140‑1 (MQ=255)         gAGGCGGTCAGGCGGATGCCCTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCCCCACGccg                                                                                                                             >  1:531628/1‑138 (MQ=255)         gAGGCGGTCAGGCGGATGCCCTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTg                                                                                                                             >  1:814674/1‑140 (MQ=255)         gAGGCGGTCAGGCGGATGCCCTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTg                                                                                                                             >  1:469265/1‑140 (MQ=255)         gAGGCGGCCAGGCGGATGCCCTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTg                                                                                                                             >  1:798421/1‑140 (MQ=255)            gCGGTCAGGCGGATGCCCTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTGAAt                                                                                                                          >  2:443111/1‑140 (MQ=255)              ggTCAGGCGGATGCCCTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCCCCACGCCGAaaaa                                                                                                                        >  2:676268/1‑140 (MQ=255)              ggTCAGGCGGATGCCCTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTGAATaa                                                                                                                        >  2:141546/1‑140 (MQ=255)              ggTCAGGCGGATGCCCTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTGAATaa                                                                                                                        <  1:683601/140‑1 (MQ=255)              ggTCAGGCGGATGCCCTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTGAATaa                                                                                                                        <  1:443111/140‑1 (MQ=255)               gTCAGGCGGATGCCCTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTGAATAAc                                                                                                                       >  1:922616/1‑140 (MQ=255)                   ggCGGATGCCCTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTGAATAACGgcg                                                                                                                   <  2:531628/140‑1 (MQ=255)                   ggCGGATGCCCTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTGAATAACGgcg                                                                                                                   <  2:469265/140‑1 (MQ=255)                    gCGGATGCCCTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTGAATAACGgcgc                                                                                                                  <  1:549676/140‑1 (MQ=255)                          gtccTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTGAATAACGGCGCCATACt                                                                                                            >  1:281771/3‑140 (MQ=255)                            ccTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGGGCCACCACGCTGAATAAACGCGCCATACttt                                                                                                          >  2:71244/1‑139 (MQ=255)                            ccTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTGAATAACGGCGCCATACTTa                                                                                                          <  2:281771/140‑1 (MQ=255)                            ccTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTGAATAACGGCGCCATACTTa                                                                                                          <  1:676268/140‑1 (MQ=255)                              tGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTGAATAACGGCGCCATACTTAcc                                                                                                        <  2:235374/140‑1 (MQ=255)                              tGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTGAATAAAGGCGCCATACTTAcc                                                                                                        >  2:408053/1‑140 (MQ=255)                                aTGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTGAATAACGGCGCCATACTTACCCt                                                                                                      >  2:518998/1‑140 (MQ=255)                                  gCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTGAATAACGGCGCCATACTTACCCttt                                                                                                    >  2:911641/1‑140 (MQ=255)                                   cTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTGAATAACGGCGCCATACTTACCCTTTc                                                                                                   <  2:814674/140‑1 (MQ=255)                                      gAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCgg                                                                                                >  1:702148/1‑140 (MQ=255)                                         aaaGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGaa                                                                                             <  2:669094/140‑1 (MQ=255)                                             gCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACg                                                                                         <  1:949965/140‑1 (MQ=255)                                                gTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTg                                                                                      <  1:518998/140‑1 (MQ=255)                                                  tcattcaCGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGaa                                                                                    <  2:702148/140‑1 (MQ=255)                                                       caCGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACg                                                                               <  1:141546/140‑1 (MQ=255)                                                           cTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATAc                                                                           >  2:19791/1‑140 (MQ=255)                                                             gAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGaacaac                                                                                >  1:738846/1‑133 (MQ=255)                                                             gAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGaacaac                                                                                <  2:738846/133‑1 (MQ=255)                                                              aaCGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCt                                                                        >  2:69213/1‑140 (MQ=255)                                                              aaCGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTGAATAACGGCGCCATAATTACCCTTTCCCGGAAGACGGGGAACAACGATAcccc                                                                        >  2:786559/1‑139 (MQ=255)                                                                             gCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAgg                                                         >  1:744160/1‑140 (MQ=255)                                                                                aCGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTGAAAAACGGCGCCCTACTTACCCTTTCCCGGGAGACGGTGAACAACGAAACCCCGACCATCCGTGAAGGCgg                                                      >  2:433769/1‑139 (MQ=255)                                                                                  ggATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATg                                                    <  2:798421/140‑1 (MQ=255)                                                                                  ggATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATg                                                    <  1:433769/140‑1 (MQ=255)                                                                                    aTACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGATGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCa                                                  <  1:71244/140‑1 (MQ=255)                                                                                    aTACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGAAACCCTGACCATCCGTGAAGGCGATGCa                                                  <  1:806413/140‑1 (MQ=255)                                                                                     tACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCAc                                                 <  2:772717/140‑1 (MQ=255)                                                                                        cACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTcc                                              <  1:69213/140‑1 (MQ=255)                                                                                             tAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCg                                                       <  2:391963/126‑1 (MQ=255)                                                                                             tAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCg                                                       >  1:391963/1‑126 (MQ=255)                                                                                                   gCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGc                                   <  1:19791/140‑1 (MQ=255)                                                                                                    cGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGct                                  <  2:744160/140‑1 (MQ=255)                                                                                                       aCTGTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGctctc                               >  1:381016/1‑140 (MQ=255)                                                                                                          gTTCACCGCCAGGGGCGGCACACTGGCGGGCGCCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTCTCa                            <  1:911641/140‑1 (MQ=255)                                                                                                                    aGGGGCGGCACACTGGCGGGCGCCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTCTCACCGGTAACgg                  <  2:922616/140‑1 (MQ=255)                                                                                                                     ggggCGGCACACTGGCGGGCGCCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTCTCACCGGTAACgg                  <  2:521213/139‑1 (MQ=255)                                                                                                                     ggggCGGCACACTGGCGGGCGCCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTCTCACCGGTAACgg                  >  1:521213/1‑139 (MQ=255)                                                                                                                      gggCGGCACACTGGCGGGCGCCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTCTCACCGGTAACGGCa                <  2:381016/140‑1 (MQ=255)                                                                                                                                    cGGGCGCCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCa  <  2:51071/140‑1 (MQ=255)                                                                                                                                    cGGGCGCCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCa  <  2:197674/140‑1 (MQ=255)                                                                                                                                         |                                                                                                                                       CAGTATCGGAGGCGGTCAGGCGGATGCCCTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCA  >  NC_000913/2072753‑2073023

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑