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%	158.7 / NA	44	E299V (GAG→GTG)	atpA	ATP synthase F1 complex subunit alpha
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base A (19/25);  total (19/25)

AGAGAACCGGTTTTCCCTTTCACTTCACCTTTGGTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCTCCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACGTCCTGGCGGACGACGGAGCAGCAGGGA  >  NC_000913/3918887‑3919038                                                                            |                                                                             agagAACCGGTTTTCCCTTTCACTTCACCTTTGGTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACcag                                                                          >  2:779236/1‑80 (MQ=255)   agaACCGGTTTTCCCTTTCACTTCACCTTTGGTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACcagcag                                                                       <  2:779143/81‑1 (MQ=255)    gaACCGGTTTTCCCTTTCACTTCACCTTTGGTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGa                                                                      >  1:779231/1‑81 (MQ=255)     aaCCGGTTTTCCCTTTCACTTCACCTTTGGTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGAc                                                                     <  1:779144/81‑1 (MQ=255)     aaCCGGTTTTCCCTTTCACTTCACCTTTGGTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGAc                                                                     <  2:779145/81‑1 (MQ=255)       ccGGTTTTCCCTTTCACTTCACCTTTGGTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGAc                                                                     >  2:779222/1‑79 (MQ=255)        cGGTTTTCCCTTTCACTTCACCTTTGGTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACgag                                                                  <  2:779146/81‑1 (MQ=255)              tCCCTTTCACTTCACCTTTGGTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTg                                                              >  1:779224/1‑79 (MQ=255)               cccTTTCACTTCACCTTTGGTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAg                                                           >  2:779214/1‑81 (MQ=255)                ccTTTCACTTCACCTTTGGTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAgg                                                          >  1:779243/1‑81 (MQ=255)                 cTTTCACTTCACCTTTGGTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGt                                                         <  1:779147/81‑1 (MQ=255)                     cacttcacCTTTGGTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGa                                                      <  2:779148/80‑1 (MQ=255)                          cacCTTTGGTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACg                                                 <  1:779149/80‑1 (MQ=255)                           acCTTTGGTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTc                                               <  1:779150/81‑1 (MQ=255)                              tttGGTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGcc                                            >  1:779219/1‑81 (MQ=255)                               ttGGTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGccc                                           >  1:779230/1‑81 (MQ=255)                                  gTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCggg                                        <  2:779151/81‑1 (MQ=255)                                  gTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCggg                                        <  2:779152/81‑1 (MQ=255)                                   tGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGa                                       <  2:779153/81‑1 (MQ=255)                                    gAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGaa                                      >  1:779239/1‑81 (MQ=255)                                    gAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGaa                                      >  2:779238/1‑81 (MQ=255)                                     aaGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAAt                                     <  2:779156/81‑1 (MQ=255)                                     aaGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAAt                                     <  2:779154/81‑1 (MQ=255)                                     aaGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAAt                                     <  1:779155/81‑1 (MQ=255)                                        gCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCt                                  >  2:779218/1‑81 (MQ=255)                                            cAACGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCa                               <  2:779157/80‑1 (MQ=255)                                             aaCGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCAc                              <  2:779158/80‑1 (MQ=255)                                             aaCGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACg                             >  1:779227/1‑81 (MQ=255)                                             aaCGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACg                             >  2:779241/1‑81 (MQ=255)                                              aCGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACGt                            <  2:779159/81‑1 (MQ=255)                                              aCGTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACGt                            >  2:779228/1‑81 (MQ=255)                                                gTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACGTcc                          <  1:779160/81‑1 (MQ=255)                                                gTATTCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACGTcc                          <  1:779161/81‑1 (MQ=255)                                                   ttCGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACGTCCTgg                       >  1:779261/1‑81 (MQ=255)                                                     cGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACGTCCTGGc                      <  2:779162/80‑1 (MQ=255)                                                     cGGCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACGTCCTGGCg                     >  1:779254/1‑81 (MQ=255)                                                      ggCGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACGTCCTGGCg                     >  2:779233/1‑80 (MQ=255)                                                        cGTTAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACGTCCTGGCGgac                  <  2:779163/81‑1 (MQ=255)                                                           tAACACGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACGTCCTGGCGgacgac               >  2:779266/1‑81 (MQ=255)                                                                cGTGCAGCACGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACGTCCTGGCGGACGACGGagc          <  1:779164/81‑1 (MQ=255)                                                                   gcagcaCGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACGTCCTGGCGGACGACGGagcag        >  1:779235/1‑80 (MQ=255)                                                                       caCGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACGTCCTGGCGGACGACGGAGCAGCAggg   <  2:779165/81‑1 (MQ=255)                                                                       caCGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACGTCCTGGCGGACGACGGAGCAGCAggg   <  2:779166/81‑1 (MQ=255)                                                                        aCGCACCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACGTCCTGGCGGACGACGGAGCAGCAGGga  <  1:779167/81‑1 (MQ=255)                                                                            |                                                                             AGAGAACCGGTTTTCCCTTTCACTTCACCTTTGGTGAAGGCTTCAACGTATTCGGCGTTAACACGTGCAGCACGCTCCAGCAGACGAGAGTGGAGGTAGAAAACGTCGCCCGGGAATGCTTCACGTCCTGGCGGACGACGGAGCAGCAGGGA  >  NC_000913/3918887‑3919038

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑