Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,074,419	C→T	P961S (CCT→TCT)	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	2,074,419	0	C	T	100.0%	139.0 / NA	41	P961S (CCT→TCT)	flu	CP4‑44 prophage; self recognizing antigen 43 (Ag43) autotransporter
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (19/22);  total (19/22)

CATGTGCGTGCCGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGCCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGCCTTCTGTTATCCGCACCTTCAGCTCCCGGGGAGATATGCGTGTGGGGACTTCCACTGCAGGCAGCGGGATGACGTTCTCTCCCTCACAGAATGGCACATCACTGGACCTGCAGGCCGGACTGGAAG  >  NC_000913/2074287‑2074545                                                                                                                                     |                                                                                                                               caTGTGCGTGCCGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGCCCCCCTGCGTGACAGTGCAAAACACAGTGTGCGTGAATTCCCGCTGGACTGGTCGGTACAGTCTTCTGt                                                                                                                         >  1:256676/1‑140 (MQ=255)   tgtgCGTGCCGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGCCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGTCTTCTGTTa                                                                                                                       <  1:509093/140‑1 (MQ=255)    gtgcgtgcCGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGCCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTTAATTACCCGTGTACTGGTGGGCACAGTCTTCTGTTAt                                                                                                                      >  1:380165/1‑140 (MQ=255)    gtgcgtgcCGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGCCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGTCTTCTGTTAt                                                                                                                      >  1:457144/1‑140 (MQ=255)       cgtgcCGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGCCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGTCTTCTGTTATCCg                                                                                                                   >  2:471713/1‑140 (MQ=255)         tgcCGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGCCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGTCTTCTGTTATCCGCa                                                                                                                 >  2:105901/1‑140 (MQ=255)         tgcCGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGCCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGTCTTCTGTTATCCGCa                                                                                                                 >  1:505525/1‑140 (MQ=255)           ccGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGCCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGTCTTCTGTTATCCGCAcc                                                                                                               >  1:803625/1‑140 (MQ=255)           ccGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGCCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGTCTTCTGTTATCCGCAcc                                                                                                               >  1:192503/1‑140 (MQ=255)           ccGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGCCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGTCTTCTGTTATCCGCAcc                                                                                                               >  1:23093/1‑140 (MQ=255)           ccGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGCCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGTCTTCTGTTATCCGCAcc                                                                                                               >  1:511451/1‑140 (MQ=255)             ggTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGCCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGTCTTCTGTTATCCGCACCtt                                                                                                             >  2:25988/1‑140 (MQ=255)                   cGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGCCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGTCTTCTGTTATCCGCACCTTCAGCTc                                                                                                       <  1:471713/140‑1 (MQ=255)                       tGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGCCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGTCTTCTGTTATCCGCACCTTCAGCTCCCgg                                                                                                   <  2:803625/140‑1 (MQ=255)                         ggCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGCCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGTCTTCTGTTATCCGCACCTTCAGCTCCCgggg                                                                                                 <  1:30100/140‑1 (MQ=255)                            aGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGCCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGTCTTCTGTTATCCGCACCTTCAGCTCCCGGGgaga                                                                                              <  1:683597/140‑1 (MQ=255)                              ccACAACGATATGACTTTTGGCTAACGCACCTCATCCTGTGCCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGTCTTCTGTTATCCGCACCTTCAGCTCCCGGGGAGata                                                                                            <  1:318837/140‑1 (MQ=255)                               cacaACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGCCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGTCTTCTGTTATCCGCACCTTCAGCTCCCGGGGAGatat                                                                                           <  2:457144/140‑1 (MQ=255)                                        atGACCTTTGGCGAAGGCACCTCATCCCGTGCCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGTCTTCTGTTCTCCGCACCTTCGGCTCCCGGGAAGATATGCGTGTggg                                                                                  >  1:400157/1‑140 (MQ=255)                                        atGACCTTTGGCGAAGGCACCTCATCCCGTGCCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGTCTTCTGTTATCCGCACCTTCAGCTCCCGGGGAGATATGCGTGTggg                                                                                  <  2:96542/140‑1 (MQ=255)                                        atGACCTTTGGCGAAGGAACCTCATCCCGTGCCCCCCTGTGTGACAGTTCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGTCTTCTGTTATCCGCACCTTCAGCTCCCGGGGAGATATGCGTGTggg                                                                                  <  2:256676/140‑1 (MQ=255)                                             cTTTGGCGAAGGCACCTCATCCCGTGCCCCCGTGCCTGACAGTGCAAAACACAGCGTGAGTGAATTACCGGTGAACTGGTGGGTACAGTCTTCTGTTATCCGCACCTTCAGCTCCCGGGGAGATATGCGTGTGGGGACtt                                                                             <  2:245520/140‑1 (MQ=255)                                              tttGGCGAAGGCACCTCATCCCGTGCCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGTCTTCTGTTATCCGCACCTTCAGCTCCCGGGGAGATATGCGTGTGGGGACTTc                                                                            >  1:772418/1‑140 (MQ=255)                                              tttGGCGAAGGCACCTCATCCCGTGCCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGTCTTCTGTTATCCGCACCTTCAGCTCCCGGGGAGATATGCGTGTGGGGACTTc                                                                            <  1:105901/140‑1 (MQ=255)                                                 ggCGAAGGCACCTCATCCCGTGCCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGTCTTCTGTTATCCGCACCTTCAGCTCCCGGGGAGATATGCGTGTGGGGACTTCCAc                                                                         >  1:714608/1‑140 (MQ=255)                                                 ggCGAAGGCACCTCATCCCGTGCCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGTCTTCTGTTATCCGCACCTTCAGCTCCCGGGGAGATATGCGTGTGGGGACTTCCAc                                                                         >  1:5242/1‑140 (MQ=255)                                                     aaGGCACCCCATCCCGTGCCCCCCTGCGTGCGAATCCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGTCTTCTGTTATCCGCACCTTCAGCTCCCGGGGAGATATGCGTGTGGGGACTTCCACTgca                                                                     <  2:380165/140‑1 (MQ=255)                                                               aTCCCGTGCCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGTCTTCTGTTATCCGCACCTTCAGCTCCCGGGGAGATATGCGTGTGGGGACTTCCACTGCAGGCAGCGGGa                                                           <  2:714608/140‑1 (MQ=255)                                                                 cccGTGCCGCCCTGCGTGACAGTGCAAAACTGATTCTGATTGAATTACCGGTGAACTGGTGGGTACAGTCTTCTGTTATCCGCACCTTCAGCTCCCGGGGAGATATGCGTGTGGGGACTTCCACTGCAGGCAGCGGGATg                                                         <  2:400157/140‑1 (MQ=255)                                                                 cccGTGCCCCCCTGCGTGACAGGGCAAAACACAGTTTGACTGAATTACCGGTGAACTGGTGGGTACAGTCTTCTGTTATCCGCACCTTCAGCTCCCGGGGAGATATGCGTGTGGGGACTTCCACTGCAGGCAGCGGGATg                                                         <  2:223713/140‑1 (MQ=255)                                                                    gTGCCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGTCTTCTGTTATCCGCACCTTCAGCTCCCGGGGAGATATGCGTGTGGGGACTTCCACTGCAGGCAGCGGGATGACg                                                      <  2:772418/140‑1 (MQ=255)                                                                        cccccTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGTCTTCTGTTATCCGCACCTTCAGCTCCCGGGGAGATATGCGTGTGGGGACTTCCACTGCAGGCAGCGGGATGACGTtct                                                  <  2:23093/140‑1 (MQ=255)                                                                           ccTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGTCTTCTGTTATCCGCACCTTCAGCTCCCGGGGAGATATGCGTGTGGGGACTTCCACTGCAGGCAGCGGGATGACGTtctctc                                               <  2:192503/140‑1 (MQ=255)                                                                                    cAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGTCTTCTGTTATCCGCACCTTCAGCTCCCGGGGAGATATGCGTGTGGGGACTTCCACTGCAGGCAGCGGGATGACGTTCTCTCCCTCACAGa                                      >  1:182173/1‑140 (MQ=255)                                                                                    cAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGTCTTCTGTTATCCGCACCTTCAGCTCCCGGGGAGATATGCGTGTGGGGACTTCCACTGCAGGCAGCGGGATGACGTTCTCTCCCTCACAGa                                      >  1:699203/1‑140 (MQ=255)                                                                                     aGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGTCTTCTGTTATCCGCACCTTCAGCTCCCGGGGAGATATGCGTGTGGGGACTTCCACTGCAGGCAGCGGGATGACGTTCTCTCCCTCACAGaa                                     <  2:182173/140‑1 (MQ=255)                                                                                       tGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGTCTTCTGTTATCCGCACCTTCAGCTCCCGGGGAGATATGCGTGTGGGGACTTCCACTGCAGGCAGCGGGATGACGTTCTCTCCCTCACAGAATg                                   >  1:780128/1‑140 (MQ=255)                                                                                               acaGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGTCTTCTGTTATCCGCACCTTCAGCTCCCGGGGAGATATGCGTGTGGGGACTTCCACTGCAGGCAGCGGGATGACGTTCTCTCCCTCACAGAATGGCACATCa                           <  2:511451/140‑1 (MQ=255)                                                                                                            aTTACCGGTGAACTGGTGGGTACAGTCTTCTGTTATCCGCACCTTCAGCTCCCGGGGAGATATGCGTGTGGGGACTTCCACTGCAGGCAGCGGGATGACGTTCTCTCCCTCACAGAATGGCACATCACTGGACCTGCAgg              <  2:505525/140‑1 (MQ=255)                                                                                                               aCCGGTGAACTGGTGGGTACAGTCTTCTGTTATCCGCACCTTCAGCTCCCGGGGAGATATGCGTGTGGGGACTTCCACTGCAGGCAGCGGGATGACGTTCTCTCCCTCACAGAATGGCACATCACTGGACCTGCAGGCCg           <  2:778952/140‑1 (MQ=255)                                                                                                                      aaCTGGTGGGTACAGTCTTCTGTTATCCGCACCTTCAGCTCCCGGGGAGATATGCGTGTGGGGACTTCCACTGCAGGCAGCGGGATGACGTTCTCTCCCTCACAGAATGGCACATCACTGGACCTGCAGGCCGGACTGGa    >  1:319442/1‑140 (MQ=255)                                                                                                                        cTGGTGGGTACAGTCTTCTGTTATCCGCACCTTCAGCTCCCGGGGAGATATGCGTGTGGGGACTTCCACTGCAGGCAGCGGGATGACGTTCTCTCCCTCACAGAATGGCACATCACTGGACCTGCAGGCCGGACTGGAAg  >  1:44976/1‑140 (MQ=255)                                                                                                                                     |                                                                                                                               CATGTGCGTGCCGGTTTCCGTCTGGGCAGCCACAACGATATGACCTTTGGCGAAGGCACCTCATCCCGTGCCCCCCTGCGTGACAGTGCAAAACACAGTGTGAGTGAATTACCGGTGAACTGGTGGGTACAGCCTTCTGTTATCCGCACCTTCAGCTCCCGGGGAGATATGCGTGTGGGGACTTCCACTGCAGGCAGCGGGATGACGTTCTCTCCCTCACAGAATGGCACATCACTGGACCTGCAGGCCGGACTGGAAG  >  NC_000913/2074287‑2074545

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑