Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,072,994	C→A	L486I (CTC→ATC)	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	2,072,994	0	C	A	100.0%	136.2 / NA	40	L486I (CTC→ATC)	flu	CP4‑44 prophage; self recognizing antigen 43 (Ag43) autotransporter
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (26/14);  total (26/14)

TTCACCGCCAGGGGCGGCACACTGGCGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCA  >  NC_000913/2072859‑2073129                                                                                                                                        |                                                                                                                                        ttCACCGCCAGGGGCGGCACACTGGCGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTATCAc                                                                                                                                     >  2:590058/1‑140 (MQ=255)        ccAGGGGCGGCACACTGGCGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTATCACCGGTAAc                                                                                                                              >  2:686529/1‑140 (MQ=255)           ggggCGGCACACTGGCGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTATCACCGGTAACGGc                                                                                                                           >  1:240965/1‑140 (MQ=255)           ggggCGGCACACTGGCGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTATCACCGGTAACGGc                                                                                                                           >  2:896112/1‑140 (MQ=255)                        ggCGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTATCACCGGTAACGGCAGCGTGGAAAAAt                                                                                                              <  2:350636/140‑1 (MQ=255)                            ggCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTATCACCGGTAACGGCAGCGTGGAAAAATCAgg                                                                                                          <  2:82397/140‑1 (MQ=255)                                   ccacGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTATCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGc                                                                                                   >  2:607027/1‑140 (MQ=255)                                            aTAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTATCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCAcactcact                                                                                          <  1:686529/140‑1 (MQ=255)                                            aTAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTATCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCAcactcact                                                                                          <  2:697275/140‑1 (MQ=255)                                                cGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTATCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCAcact                                                                                              >  2:241965/1‑132 (MQ=255)                                                cGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTATCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCAcact                                                                                              <  1:241965/132‑1 (MQ=255)                                                cGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTATCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCa                                                                                      >  2:205091/1‑140 (MQ=255)                                                     ccATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTATCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAac                                                                                 >  2:7784/1‑140 (MQ=255)                                                     ccATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTATCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAac                                                                                 >  1:820388/1‑140 (MQ=255)                                                           ttACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTATCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACcaca                                                                           <  2:778947/140‑1 (MQ=255)                                                           ttACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTATCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACcaca                                                                           <  1:896112/140‑1 (MQ=255)                                                             aCCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTATCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACt                                                                         >  2:565302/1‑140 (MQ=255)                                                               ccTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTATCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCa                                                                       >  2:963669/1‑140 (MQ=255)                                                                   tCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTATCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAg                                                                                     <  2:131486/122‑1 (MQ=255)                                                                   tCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTATCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAg                                                                                     >  1:131486/1‑122 (MQ=255)                                                                                     aacGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTATCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCtgaa                                                 <  2:17611/140‑1 (MQ=255)                                                                                       cGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTATCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCtgaatg                                               <  1:7784/140‑1 (MQ=255)                                                                                       cGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTATCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCtgaatg                                               >  2:618760/1‑140 (MQ=255)                                                                                           aCCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTATCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCGCTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAgg                                           <  2:114165/140‑1 (MQ=255)                                                                                               tGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTATCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCacg                                       >  1:181263/1‑140 (MQ=255)                                                                                                 aCCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTATCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCacgct                                     >  2:811979/1‑140 (MQ=255)                                                                                                     tCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTATCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCacgctgacg                                 <  1:607027/140‑1 (MQ=255)                                                                                                      ccGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTATCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCacgctgacgc                                >  1:354609/1‑140 (MQ=255)                                                                                                       cGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTATCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCacgctgacgct                               >  1:547724/1‑140 (MQ=255)                                                                                                           aaGGCGATGCACTCCTGCAGGGAGGCTCTATCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGGACGCTGACGCTGAAc                           >  2:559706/1‑140 (MQ=255)                                                                                                               cGATGCACTCCTGCAGGGAGGCTCTATCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACa                       >  2:34145/1‑140 (MQ=255)                                                                                                               cGATGCACTCCTGCAGGGAGGCTCTATCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACa                       >  2:935583/1‑140 (MQ=255)                                                                                                               cGATGCACTCCTGCAGGGAGGCTCTATCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACa                       <  2:820388/140‑1 (MQ=255)                                                                                                                        ccTGCAGGGAGGCTCTATCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTca              >  2:840295/1‑140 (MQ=255)                                                                                                                            cAGGGAGGCTCTATCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTcaccac          >  2:1001673/1‑140 (MQ=255)                                                                                                                               ggAGGCTCTATCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGa       <  1:471670/140‑1 (MQ=255)                                                                                                                               ggAGGCTCTATCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGa       >  1:353905/1‑140 (MQ=255)                                                                                                                                 aGGCTCTATCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATg     >  1:972338/1‑140 (MQ=255)                                                                                                                                 aGGCTCTATCACCGGTAACAGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATg     >  1:599140/1‑140 (MQ=255)                                                                                                                                   gCTCTATCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTc   >  1:645418/1‑140 (MQ=255)                                                                                                                                    ctctatCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCa  <  1:618760/140‑1 (MQ=255)                                                                                                                                        |                                                                                                                                        TTCACCGCCAGGGGCGGCACACTGGCGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCA  >  NC_000913/2072859‑2073129

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑