Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,918,962	T→A	E299V (GAG→GTG)	atpA ←	ATP synthase F1 complex subunit alpha

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,918,962	0	T	A	100.0%	162.8 / NA	45	E299V (GAG→GTG)	atpA	ATP synthase F1 complex subunit alpha
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base A (25/20);  total (25/20)

CAGAGAACCGGTTTTCCCTTTCACTTCACCTTTGGTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCTCCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACGTCCTGGCGGACGACGGAGCAGCAGGG  >  NC_000913/3918886‑3919037                                                                             |                                                                            cAGAGAACCGGTTTTCCCTTTCACTTCACCTTTGGTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACcag                                                                         >  2:712104/1‑81 (MQ=255)  agagAACCGGTTTTCCCTTTCACTTCACCTTTGGTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACcag                                                                         >  2:712108/1‑80 (MQ=255)  agagAACCGGTTTGCACGTTAACTTCACATTTGGTGAAGGCTTCAACGTATGGGGAGGTAAGAAGTGCAGCACGAACcag                                                                         <  2:893666/80‑1 (MQ=255)   gagaACCGGTTTTCCCTTTCACTTCACCTTTGGTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACcagca                                                                       <  2:712030/81‑1 (MQ=255)   gagaACCGGTTTTCCCTTTCACTTCACCTTTGGTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACcag                                                                         >  2:712093/1‑79 (MQ=255)     gaACCGGTTTTCCCTTTCACTTCACCTTTGGTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGa                                                                     >  1:712103/1‑81 (MQ=255)      aaCCGGTTTTCCCTTTCACTTCACCTTTGGTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGAc                                                                    <  2:712031/81‑1 (MQ=255)       aCCGGTTTTCCCTTTCACTTCACCTTTGGTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACg                                                                   <  2:712032/81‑1 (MQ=255)          ggTTTTCCCTTTCACTTCACCTTTGGTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACgaga                                                                <  1:712034/81‑1 (MQ=255)           gTTTTCCCTTTCACTTCACCTTTGGTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGagag                                                               >  1:712088/1‑81 (MQ=255)               tCCCTTTCACTTCACCTTTGGTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTg                                                             >  2:712096/1‑79 (MQ=255)                      cacttcacCTTTGGTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGa                                                     >  2:712121/1‑80 (MQ=255)                      cacttcacCTTTGGTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGa                                                     >  1:712075/1‑80 (MQ=255)                            acCTTTGGTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGt                                               <  1:712035/80‑1 (MQ=255)                            acCTTTGGTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTc                                              >  1:712120/1‑81 (MQ=255)                               tttGGTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGcc                                           >  1:712101/1‑81 (MQ=255)                                 tGGTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCg                                         >  2:712107/1‑81 (MQ=255)                                 tGGTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCg                                         >  2:712106/1‑81 (MQ=255)                                  ggTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCgg                                        >  2:712115/1‑81 (MQ=255)                                   gTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCggg                                       <  2:712036/81‑1 (MQ=255)                                   gTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCgg                                        <  2:712035/80‑1 (MQ=255)                                    tGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGa                                      <  1:712038/81‑1 (MQ=255)                                      aaGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAAt                                    <  2:712038/81‑1 (MQ=255)                                        ggCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGc                                  >  2:712111/1‑81 (MQ=255)                                         gCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCt                                 >  2:712090/1‑81 (MQ=255)                                               aCGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACGt                           >  2:712112/1‑81 (MQ=255)                                                      cGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACGTCCTGGc                     <  1:712040/80‑1 (MQ=255)                                                      cGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACGTCCTGGCg                    >  1:712110/1‑81 (MQ=255)                                                       ggCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACGTCCTGGCg                    <  2:712040/80‑1 (MQ=255)                                                       ggCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACGTCCTGGCg                    >  2:712110/1‑80 (MQ=255)                                                        gCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACGTCCTGGCGga                  <  2:712041/81‑1 (MQ=255)                                                         cGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACGTCCTGGCGgac                 >  2:712099/1‑81 (MQ=255)                                                             aaCACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACGTCCTGGCGgacgac              <  1:712043/80‑1 (MQ=255)                                                             aaCACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACGTCCTGGCGGacgacg             >  2:712116/1‑81 (MQ=255)                                                             aaCACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACGTCCTGGCGGacgacg             >  1:712136/1‑81 (MQ=255)                                                                acGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACGTCCTGGCGGACGACGGag          <  2:712043/81‑1 (MQ=255)                                                                 cGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACGTCCTGGCGGACGACGGagc         <  2:712045/81‑1 (MQ=255)                                                                 cGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACGTCCTGGCGGACGACGGagc         <  1:712045/81‑1 (MQ=255)                                                                 cGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACGTCCTGGCGGACGACGGag          >  2:712122/1‑80 (MQ=255)                                                                 cGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACGTCCTGGCGGACGACGGag          >  1:712127/1‑80 (MQ=255)                                                                  gTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACGTCCTGGCGGACGACGGagca        <  1:712047/81‑1 (MQ=255)                                                                  gTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACGTCCTGGCGGACGACGGag          >  1:712121/1‑79 (MQ=255)                                                                     cagcaCGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACGTCCTGGCGGACGACGGagcagc      <  2:712047/80‑1 (MQ=255)                                                                       gcacgcacCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACGTCCTGGTGGACGACGGAGCAGCAgg   <  2:712048/81‑1 (MQ=255)                                                                        caCGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACGTCCTGGCGGACGACGGAGCAGCAggg  <  1:712050/81‑1 (MQ=255)                                                                         aCGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACGTCCTGGCGGACGACGGAGCAGCAgg   >  2:712137/1‑79 (MQ=255)                                                                             |                                                                            CAGAGAACCGGTTTTCCCTTTCACTTCACCTTTGGTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCTCCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACGTCCTGGCGGACGACGGAGCAGCAGGG  >  NC_000913/3918886‑3919037

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑