Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,073,463	T→A	L642Q (CTG→CAG)	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	2,073,463	0	T	A	100.0%	185.7 / NA	49	L642Q (CTG→CAG)	flu	CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base A (20/29);  total (20/29)

TCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCTGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCT  >  NC_000913/2073319‑2073607                                                                                                                                                 |                                                                                                                                                 tCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGa                                                                                                                                             >  2:784548/1‑150 (MQ=255)         gCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGc                                                                                                                                     >  1:621102/1‑150 (MQ=255)           aaCCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAAc                                                                                                                                  >  2:875361/1‑151 (MQ=255)                 gAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCg                                                                                                                            <  2:846972/151‑1 (MQ=255)                   aaGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTc                                                                                                                          >  2:318555/1‑151 (MQ=255)                    aGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGCGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGCGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCg                                                                                                                         >  1:234554/1‑151 (MQ=255)                     gTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCgg                                                                                                                        <  1:790540/151‑1 (MQ=255)                       gAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCgggg                                                                                                                      >  2:371431/1‑151 (MQ=255)                                gAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGa                                                                                                               <  2:439006/149‑1 (MQ=255)                                gAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGAc                                                                                                              <  2:108264/150‑1 (MQ=255)                                       cAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAAACAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCgg                                                                                                        >  1:589779/1‑149 (MQ=255)                                          aaTGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAgg                                                                                                   <  2:11117/151‑1 (MQ=255)                                             ggCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGt                                                                                                 <  2:550851/150‑1 (MQ=255)                                               catcATCAGCCTGCGTGTACGCCCGGATATGGGACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGATGAACGCCGGCAACAGTGCGTCGGGGATGGCGACCAGCGGTAAGGGTAtt                                                                                              <  1:485804/148‑1 (MQ=255)                                               cACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGGGCGTCGGGGCTGGCGACCAGCGGTAAGGGGAtt                                                                                              >  1:96767/1‑151 (MQ=255)                                                aCCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTc                                                                                             <  1:836100/151‑1 (MQ=255)                                                 ccATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCa                                                                                            <  2:120676/151‑1 (MQ=255)                                                   aTCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAgg                                                                                          >  2:647517/1‑151 (MQ=255)                                                            cGTGTACGCCCGGATATGGCACAGAACAATGCTGACCGACTGGTCATTGACGTCGGCAGCGCAACCGGAAAAACCATCCTGAACCAGGGGAACGCCGGCAACAGTGCGTCTGGGCTTGCGACCAGCGGTAAGGGTATTCACGTGGTGGaa                                                                                  <  1:528285/150‑1 (MQ=255)                                                             gtgtACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGc                                                                                <  2:735046/151‑1 (MQ=255)                                                                  cGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCAtt                                                                            <  2:556130/150‑1 (MQ=255)                                                                   gCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTaa                                                                          <  2:357054/151‑1 (MQ=255)                                                                   gCCCGGAGAGGGCACAGGACAATGCTGACAGACTGGTCCTTGACGGCGGCAGGGCAACCGAAAAATCCATCCGGACCCAGGTGAACGCCGTCAACAGTCCATCGGGGCTGGCTACCAGCGGTAAGGGTATGCAGGTGGTGGAAGCCATTaa                                                                          <  1:573666/151‑1 (MQ=255)                                                                    cccGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAAc                                                                         >  2:867691/1‑151 (MQ=255)                                                                      cGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACgg                                                                       >  2:606779/1‑151 (MQ=255)                                                                       ggATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGt                                                                      <  1:508628/151‑1 (MQ=255)                                                                                  aGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACgg                                                            >  2:405954/1‑150 (MQ=255)                                                                                          gCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAgggg                                                   <  1:715597/151‑1 (MQ=255)                                                                                                 gACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGt                                            <  1:735684/151‑1 (MQ=255)                                                                                                 gACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGt                                            <  2:734065/151‑1 (MQ=255)                                                                                                    tGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGccagccccg                                          >  2:517817/1‑143 (MQ=255)                                                                                                         aTTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAgggg                                     >  1:100338/1‑150 (MQ=255)                                                                                                                gcggcAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCt                             <  1:19480/151‑1 (MQ=255)                                                                                                                gcggcAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCt                             <  1:251705/151‑1 (MQ=255)                                                                                                                 cggcAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCTCCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTg                            <  1:64316/151‑1 (MQ=255)                                                                                                                 cggcAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTg                            <  2:139986/151‑1 (MQ=255)                                                                                                                  ggcAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGc                           >  2:617072/1‑151 (MQ=255)                                                                                                                   gcAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCa                          <  1:776299/151‑1 (MQ=255)                                                                                                                    cAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGc                           >  2:732766/1‑149 (MQ=255)                                                                                                                     aGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGCATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAgg                        >  1:181160/1‑151 (MQ=255)                                                                                                                          aaCCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGt                   <  2:633963/151‑1 (MQ=255)                                                                                                                               gcaaaaACATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGCAGCCATTAACGGTGCCCCCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCtt              <  1:183685/149‑1 (MQ=255)                                                                                                                               gAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCgg                    <  1:209393/145‑1 (MQ=255)                                                                                                                               gAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCgg                    >  2:209426/1‑145 (MQ=255)                                                                                                                               gAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCtt              >  2:28558/1‑151 (MQ=255)                                                                                                                               gAAAAACCACCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGCGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGTTGGAAGCTATTAACGGTGCCTCCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCATTCCGCTGCCtt              <  1:422692/151‑1 (MQ=255)                                                                                                                                         ccTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTc     <  1:501081/150‑1 (MQ=255)                                                                                                                                          cTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTccc   >  2:100086/1‑151 (MQ=255)                                                                                                                                            gAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCt  <  2:312829/150‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                 TCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCTGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCT  >  NC_000913/2073319‑2073607

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑