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%	106.0 / NA	29	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 (14/15);  total (14/15)

GTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCTGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCA  >  NC_000913/2073317‑2073609                                                                                                                                                   |                                                                                                                                                   gTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCACCCGGAAAAACCATCCTGAACCAGGTg                                                                                                                                                <  1:444352/151‑1 (MQ=255)     gTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACg                                                                                                                                            >  2:57076/1‑151 (MQ=255)                                   aaCGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGAcc                                                                                                               >  1:245041/1‑150 (MQ=255)                                     cGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGc                                                                                                            >  1:469231/1‑151 (MQ=255)                                           gAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTa                                                                                                        >  1:69734/1‑149 (MQ=255)                                             aTGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAggg                                                                                                    >  1:635304/1‑151 (MQ=255)                                              tGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAggg                                                                                                    >  2:426343/1‑150 (MQ=255)                                                       cAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAggtg                                                                                          >  1:556232/1‑151 (MQ=255)                                                       cAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAggt                                                                                           <  1:16145/150‑1 (MQ=255)                                                        aGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAggtgg                                                                                         <  1:341560/151‑1 (MQ=255)                                                        aGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAggtgg                                                                                         <  2:641246/151‑1 (MQ=255)                                                            tGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGtggtgg                                                                                      >  2:282108/1‑150 (MQ=255)                                                             gCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGtggtgg                                                                                      <  2:689736/149‑1 (MQ=255)                                                              cGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGa                                                                                     >  1:265564/1‑149 (MQ=255)                                                                      cccGGATATGGCACAGAACAGTGCTGACAGACTGGTCATTGACGGCGGCAGTGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAAc                                                                           <  1:49382/151‑1 (MQ=255)                                                                         ggATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGt                                                                        <  1:85017/151‑1 (MQ=255)                                                                                 cacaGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCcaccac                                                                <  2:100889/151‑1 (MQ=255)                                                                                         aaTGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGAGGTGGAAGCCATTAACGGTGCCACCACggagga                                                          >  1:172437/1‑149 (MQ=255)                                                                                           tGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGTAggg                                                      >  2:361093/1‑151 (MQ=255)                                                                                                          cATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAggg                                        <  2:9005/150‑1 (MQ=255)                                                                                                              gACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACa                                   <  2:439373/151‑1 (MQ=255)                                                                                                                  gcggcAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGc                                >  2:35745/1‑150 (MQ=255)                                                                                                                      cAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGc                             >  2:245173/1‑149 (MQ=255)                                                                                                                      cAGGGCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAg                           <  1:269911/151‑1 (MQ=255)                                                                                                                        gggCAACCGGAAAAACCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGc                         >  2:105442/1‑151 (MQ=255)                                                                                                                                  aaaaaCCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCttt               <  1:620790/151‑1 (MQ=255)                                                                                                                                   aaaaCCATCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTa              <  1:402029/151‑1 (MQ=255)                                                                                                                                         aTCCTGAACCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAactact        <  1:246990/151‑1 (MQ=255)                                                                                                                                               aaCCAGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCa  <  1:667401/151‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                                   GTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCTGGTGAACGCCGGCAACAGTGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCA  >  NC_000913/2073317‑2073609

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑