Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,073,366	A→G	T610A (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	2,073,366	0	A	G	100.0%	97.1 / NA	28	T610A (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 (16/12);  total (16/12)

CCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCTGGTGAACGCCGGCAACAGTGCGTCGGGG  >  NC_000913/2073233‑2073491                                                                                                                                      |                                                                                                                              ccccGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCGCCATCa                                                                                                                         >  1:639082/1‑140 (MQ=255)  cccGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAGCGGACAGAATGGCGCCATCAg                                                                                                                        >  2:510585/1‑140 (MQ=255)   ccGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCGCCATCAGc                                                                                                                       <  1:418067/140‑1 (MQ=255)          cGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCGCCATCAGCCTGCgtg                                                                                                                >  1:589586/1‑140 (MQ=255)            ccACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAGCGGACAGAATGGCGCCATCAGCCTGCGTGTa                                                                                                              <  1:510585/140‑1 (MQ=255)                  tGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCGCCATCAGCCTGCGTGTACGCCCg                                                                                                        >  1:366761/1‑140 (MQ=255)                    cAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCGCCATCAGCCTGCGTGTACGCCCGGa                                                                                                      >  1:134637/1‑140 (MQ=255)                      gTCGGTGGTGGATGACCTCAGCCCTGCCGTACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCGCCATCAGCCTGCGTGTACGCCCGGata                                                                                                    <  1:354298/140‑1 (MQ=255)                      gTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCGCCATCAGCCTGCGTGTACGCCCGGata                                                                                                    <  2:176837/140‑1 (MQ=255)                      gTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCGCCATCAGCCTGCGTGTACGCCCGGata                                                                                                    <  2:86691/140‑1 (MQ=255)                      gTCGGTGGTGGATGACCCCAGCCATGCCGGATAGATTCACTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCGCCATCAGCCTGCGTGTACGCCCGGata                                                                                                    <  2:287733/140‑1 (MQ=255)                           tggtggATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCGCCATCAGCCTGCGTGTACGCCCGGATATGGca                                                                                               <  1:456111/140‑1 (MQ=255)                               ggATGACCTCAGCCATGCCGGATAGATTCATCTCACCTCTACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCGCCATCAGCCTGCGTGTACGCCCGGATATGGCACAGa                                                                                           <  2:253519/140‑1 (MQ=255)                                 aTGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCGCCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAAc                                                                                         >  2:667448/1‑140 (MQ=255)                                        cAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCGCCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTg                                                                                  <  1:667448/140‑1 (MQ=255)                                             aTGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCGCCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGa                                                                             <  2:44245/140‑1 (MQ=255)                                                        aTTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCGCCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGa                                                                  >  2:122206/1‑140 (MQ=255)                                                        aTTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCGCCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGa                                                                  >  1:376249/1‑140 (MQ=255)                                                          tCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCGCCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGAcg                                                                <  2:551200/140‑1 (MQ=255)                                                                            cacaGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCGCCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGaa                                              >  2:389118/1‑140 (MQ=255)                                                                             acaGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCGCCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTCGTCATTCACGGCGGCAGGGCAACCGGaaa                                             >  1:327516/1‑140 (MQ=255)                                                                                 ggAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCGCCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAAcc                                         >  1:470956/1‑140 (MQ=255)                                                                                        cGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCGCCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGa                                  >  2:625932/1‑140 (MQ=255)                                                                                         gTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCGCCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGGCATGGACGGCGGCAGGACAACGGGAAAAACCATCCTGaa                                 >  2:231445/1‑140 (MQ=255)                                                                                           aCCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCGCCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAAcc                               >  2:170224/1‑140 (MQ=255)                                                                                                              aaaaaCCTGAACGGACAGAATGGCGCCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCTGGTGAACGCCGGCAACAg            >  1:80506/1‑140 (MQ=255)                                                                                                               aaaaCCTGAACGGACAGAATGGCGCCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCTGGTGAACGCCGGCAACAGt           >  1:611524/1‑140 (MQ=255)                                                                                                                        aCGGACAGAATGGCGCCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCTGGTGAACGCCGGCAACAGTGCGTCgggg  <  1:625932/140‑1 (MQ=255)                                                                                                                                      |                                                                                                                              CCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGACTGGTCATTGACGGCGGCAGGGCAACCGGAAAAACCATCCTGAACCTGGTGAACGCCGGCAACAGTGCGTCGGGG  >  NC_000913/2073233‑2073491

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑