Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,073,659	T→C	R707R (CGT→CGC)	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	2,073,659	0	T	C	100.0%	153.3 / NA	44	R707R (CGT→CGC)	flu	CP4‑44 prophage; self recognizing antigen 43 (Ag43) autotransporter
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (20/24);  total (20/24)

GTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGACCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCA  >  NC_000913/2073522‑2073793                                                                                                                                          |                                                                                                                                       gtggAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCgcgc                                                                                                                                      >  1:381974/1‑140 (MQ=255)   ggAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGCGCAg                                                                                                                                    <  1:450624/140‑1 (MQ=255)     aaGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGCGCAGaa                                                                                                                                  <  2:225361/140‑1 (MQ=255)      aGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGCGCAGAAg                                                                                                                                 <  2:667844/140‑1 (MQ=255)      aGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGCGCAGAAg                                                                                                                                 <  2:724711/140‑1 (MQ=255)      aGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGCGCAGAAg                                                                                                                                 <  1:213894/140‑1 (MQ=255)         cATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGCGCAGAAGTcc                                                                                                                              <  1:256798/140‑1 (MQ=255)                  tGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGCGCAGAAGTCCCCCTGTATg                                                                                                                     >  1:705583/1‑140 (MQ=255)                   gCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTTCTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGCGCAGAAGTcccc                                                                                                                            <  1:800063/132‑1 (MQ=255)                   gCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGCGCAGAAGTcccc                                                                                                                            >  2:800063/1‑132 (MQ=255)                   gCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATAAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGCGCAGAAGTCCCCCTGTATGc                                                                                                                    >  1:551726/1‑140 (MQ=255)                      accacGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGCGCAGAAGTCCCCCTGTATGCCTc                                                                                                                 <  2:705583/140‑1 (MQ=255)                              ggaAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGCGCAGAAGTCCCCCTGTATGCCt                                                                                                                  <  1:367465/131‑1 (MQ=255)                              ggaAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGCGCAGAAGTCCCCCTGTATGCCt                                                                                                                  >  2:367465/1‑131 (MQ=255)                              ggaAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGCGCAGAAGT‑CCCCTGTATGCCTCCATGCTGac                                                                                                        <  1:362813/140‑1 (MQ=255)                                 aGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGCGCAGAAGTCCCCCTGTATGCCTCCATGCTGacac                                                                                                      >  1:551936/1‑140 (MQ=255)                                 aGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGCGCAGAAGTCCCCCTGTATGCCTCCATGCTGacac                                                                                                      <  2:381974/140‑1 (MQ=255)                                       cTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGCGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCaa                                                                                                >  2:464961/1‑140 (MQ=255)                                       cTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGCGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCaa                                                                                                <  2:640726/140‑1 (MQ=255)                                           gTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGCGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGa                                                                                            <  2:551936/140‑1 (MQ=255)                                                      cAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGCGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTa                                                                                         >  2:91464/1‑132 (MQ=255)                                                      cAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGCGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTa                                                                                         <  1:91464/132‑1 (MQ=255)                                                                     tGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGCGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTccc                                                                  >  2:12883/1‑140 (MQ=255)                                                                     tGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGCGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTccc                                                                  >  2:49030/1‑140 (MQ=255)                                                                       ccTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGCGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGc                                                                >  1:413929/1‑140 (MQ=255)                                                                          ttAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGCGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAgg                                                                       <  2:21892/130‑1 (MQ=255)                                                                          ttAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGCGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAgg                                                                       >  1:21892/1‑130 (MQ=255)                                                                                 ctCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGCGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCa                                                               <  2:62493/131‑1 (MQ=255)                                                                                 ctCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGCGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCa                                                               >  1:62493/1‑131 (MQ=255)                                                                                 ctCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGCGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGa                                                      <  1:49030/140‑1 (MQ=255)                                                                                 ctCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGCGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGa                                                      <  1:464961/140‑1 (MQ=255)                                                                                 ctCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGCGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGa                                                      >  2:745649/1‑140 (MQ=255)                                                                                   cccTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGCGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGAcc                                                    <  1:745649/140‑1 (MQ=255)                                                                                     cTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGCGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGACCgg                                                  >  2:401635/1‑140 (MQ=255)                                                                                             ggACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGCGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGACCGGTGTAAATg                                          <  2:112705/140‑1 (MQ=255)                                                                                             ggACAGTGATAAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGCGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGACCGGTGTAAATg                                          <  2:551726/140‑1 (MQ=255)                                                                                              gACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGCGCAGAAGTCGCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGACCGGTGTAAATgg                                         >  2:4980/1‑140 (MQ=255)                                                                                                   tgatgaGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGCGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGACCGGTGTAAATGGTGaaa                                    >  2:548659/1‑140 (MQ=255)                                                                                                   tgatgaGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGCGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGACCAGTGTAAATGGTGaaa                                    <  2:394564/140‑1 (MQ=255)                                                                                                        agagCTGGTATCTGCGCAGTGAAAATGCTTATCGCGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGACCGGTGTAAATGGTGAAaacaac                               >  2:102090/1‑140 (MQ=255)                                                                                                             tGGTATCTGCGCAGTGAAAATGCTTATCGCGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGACCGGTGTAAATGGTGAAAACAACAGcgt                          >  2:83587/1‑140 (MQ=255)                                                                                                              ggTATCTGCGCAGTGAAAATGCTTATCGCGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGACCGGTGTAAATGGTGAAAACAACAGcgtc                         <  1:548659/140‑1 (MQ=255)                                                                                                              ggTATCTGCGCAGTGAAAATGCTTATCGCGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGACCGGTGTAAATGGTGAAAACAACAGcgtc                         >  1:137319/1‑140 (MQ=255)                                                                                                                           tGAAAATGCTTATCGCGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGACCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCAtt             >  1:237892/1‑139 (MQ=255)                                                                                                                           tGAAAATGCTTATCGCGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGACCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCAtt             <  2:237892/139‑1 (MQ=255)                                                                                                                                     tATCGCGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGACCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCa  >  2:802737/1‑140 (MQ=255)                                                                                                                                          |                                                                                                                                       GTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGACCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCA  >  NC_000913/2073522‑2073793

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑