Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,288,658	A→G	T299A (ACC→GCC)	nrfA →	cytochrome c552 nitrite reductase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,288,658	0	A	G	100.0%	103.2 / NA	29	T299A (ACC→GCC)	nrfA	cytochrome c552 nitrite reductase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (11/18);  total (11/18)

GCCAATGCTGAAAGCGCAGCACCCGGAATATGAAACCTGGACAGCGGGCATTCACGGTAAAAACAACGTGACCTGTATCGACTGCCATATGCCAAAAGTGCAGAACGCCGAAGGCAAACTCTACACCGACCATAAAATTGGTAATCCGTTTGATAACTTCGCCCAGACTTGTGCGAACTGCCATACCCAGGACAAAGCTGCCTTGCAAAAAGTGGTCGCGGAACGTAAGCAGTCGATTAACGACCTGAAAATCA  >  NC_000913/4288534‑4288787                                                                                                                             |                                                                                                                                  gCCAATGCTGAAAGCGCAGCACCCGGAATATGAAACCTGGACAGCGGGCATTCACGGTAAAAACAACGTGACCTGTATCGACTGCCATATGCCAAAAGTGCAGAACGCCGAAGGCAAACTCTACGCCGACCAt                                                                                                                           <  1:239949/133‑1 (MQ=255)   cAATGCTGAAAGCGCAGCACCCGGAATATGAAACCTGGACAGCGGGCATTCACGGTAAAAACAACGTGACCTGTATCGACTGCCATATGCCAAAAGTGCAGAACGCCGAAGGCAAACTCTACGCCGACCATaa                                                                                                                         <  2:138332/133‑1 (MQ=255)           aaaGCGCAGCACCCGGAATATGAAACCTGGACAGCGGGCATTCACGGTAAAAACAACGTGACCTGTATCGACTGCCATATGCCAAAAGTGCAGAACGCCGAAGGCAAACTCTACGCCGACCATAAAATTGGTa                                                                                                                 <  1:629030/133‑1 (MQ=255)              gcgcAGCACCCGGAATATGAAACCTGGACAGCGGGCATTCACGGTAAAAACAACGTGACCTGTATCGACTGCCATATGCCAAAAGTGCAGAACGCCGAAGGCAAACTCTACGCCGACCATAAAATTGGTAATc                                                                                                              <  1:64550/133‑1 (MQ=255)                         ggAATATGAAACCTGGACAGCGGGCATTCACGGTAAAAACAACGTGACCTGTATCGACTGCCATATGCCAAAAGTGCAGAACGCCGAAGGCAAACTCTACGCCGACCATAAAATTGGTAATCCGTTTGATAAc                                                                                                   <  1:97146/133‑1 (MQ=255)                          gAATATGACACCTGGACACCGGTCATTCACAGTAAAAACAACGTGACCTGTATCGACTGCCATATGCCAAAAGTGCAGAACGCCGAAGGCAAACTCTACGCCGACCATAAAATTGGTAATCCGTTTGATAACt                                                                                                  <  1:178370/133‑1 (MQ=255)                          gAATATGAAACCTGGACAGCGGGCATTCACGGTAAAAACAACGTGACCTGTATCGACTGCCATATGCCAAAAGTGCAGAACGCCGAAGGCAAACTCTACGCCGACCATAAAATTGGTAATCCGTTTGATAACt                                                                                                  <  1:3093/133‑1 (MQ=255)                              atGAAACCTGGACAGCGGGCATTCACGGTAAAAACAACGTGACCTGTATCGACTGCCATATGCCAAAAGTGCAGAACGCCGAAGGCAAACTCTACGCCGACCATAAAATTGGTAATCCGTTTGATAACTTCGc                                                                                              >  2:145101/1‑133 (MQ=255)                                     cTGGACAGCGGGCATTCACGGTAAAAACAACGTGACCTGTATCGACTGCCATATGCCAAAAGTGCAGAACGCCGAAGGCAAACTCTACGCCGACCATAAAATTGGTAATCCGTTTGATAACTTCGCCCAGACt                                                                                       >  2:78437/1‑133 (MQ=255)                                     cTGGACAGCGGGCATTCACGGTAAAAACAACGTGACCTGTATCGACTGCCATATGCCAAAAGTGCAGAACGCCGAAGGCAAACTCTACGCCGACCATAAAATTGGTAATCCGTTTGATAACTTCGCCCAGACt                                                                                       >  2:441670/1‑133 (MQ=255)                                       ggACAGCGGGCATTCACGGTAAAAACAACGTGACCTGTATCGACTGCCATATGCCAAAAGTGCAGAACGCCGAAGGCAAACTCTACGCCGAGCATAAAATGGGTGATCAGTTTGATAGCTTCGCCCAGACTtg                                                                                     >  2:176676/1‑133 (MQ=255)                                        gACAGCGGGCATTCACGGTAAAAACAACGTGACCTGTATCGACTGCCATATGCCAAAAGTGCAGAACGCCGAAGGCAAACTCTACGCCGACCATAAAATTGGTAATCCGTTTGATAACTTCGCCCAGACTtgt                                                                                    >  2:400492/1‑133 (MQ=255)                                         aCAGCGGGCATTCACGGTAAAAACAACGTGACCTGTATCGACTGCCATATGCCAAAAGTGCAGAACGCCGAAGGCAAACTCTACGCCGACCATAAAATTGGTAAACCGATTGATAACCTCGCCCAGACTtgtg                                                                                   >  2:216708/1‑133 (MQ=255)                                           aGCGGGCATTCACGGTAAAAACAACGTGACCTGTATCGACTGCCATATGCCAAAAGTGCAGAACGCCGAAGGCAAACTCTACGCCGACCATAAAATTGGTAATCCGTTTGATAACTTCGCCCAGACTTGTGCg                                                                                 <  2:425629/133‑1 (MQ=255)                                             cGGGCATTCACGGTAAAAACAACGTGACCTGTATCGACTGCCATATGCCAAAAGTGCAGAACGCCGAAGGCAAACTCTACGCCGACCATAAAATTGGTAATCCGTTTGATAACTTCGCCCAGACTTGTGCGaa                                                                               <  1:142172/133‑1 (MQ=255)                                                  aTTCACGGTAAAAACAACGTGACCTGTATCGACTGCCTTATGCCAAAAGTGCAGAACGCCGAAGGCAAACTCTACGCCGACCATAAAATTGGTAATCCGTTTGATAACTTCGCCCAGACTTGTGCGAACTGcc                                                                          <  1:400492/133‑1 (MQ=255)                                                  aTTCACGGTAAAAACAACGTGACCTGTATCGACTGCCATATGCCAAAAGTGCAGAACGCCGAAGGCAAACTCTACGCCGACCATAAAATTGGTAATCCGTTTGATAACTTCGCCCAGACTTGTGCGAACTGcc                                                                          <  1:35800/133‑1 (MQ=255)                                                       cGGTAAAATCAACGTCACCTGTCTCGACTGCCATATGCCAAAAGTGCAGAACGCCGAAGGCAAACTCTACGCCGACCATAAAATTGGTAATCCGTTTGATAACTTCGCCCAGACTTGTGCGAACTGCCATAcc                                                                     <  1:176676/133‑1 (MQ=255)                                                       cGGTAAAACCAACGTGACCTGTATCGACTGCCATATGCCAAAAGTGCAGAACGCCGAAGGCAAACTCTACGCCGACCATAAAATTGGTAATCCGTTTGATAACTTCGCCCAGACTTGTGCGAACTGCCATAcc                                                                     <  1:245741/133‑1 (MQ=255)                                                            aaaaCAACGTGACCTGTATCGACTGCCATATGCCAAAAGTGCAGAACGCCGAAGGCAAACTCTACGCCGACCATAAAATTGGTAATCCGTTTGATAACTTCGCCCAGACTTGTGCGAACTGCCATACCCAGGa                                                                <  1:408815/133‑1 (MQ=255)                                                                 aacGTGACCTGTATCGACTGCCATATGCCAAAAGTGCAGAACGCCGAAGGCAAACTCTACGCCGACCATAAAATTGGTAATCCGTTTGATAACTTCGCCCAGACTTGTGCGAACTGCCATACCCAGGACAAAg                                                           <  1:93825/133‑1 (MQ=255)                                                                  acGTGACCTGTATCGACTGCCATATGCCAAAAGTGCAGAACGCCGAAGGCAAACTCTACGCCGACCATAAAATTGGTAATCCGTTTGATAACTTCGCCCAGACTTGTGCGAACTGCCATACCCAGGACAAAGc                                                          >  1:428987/1‑133 (MQ=255)                                                                                      cATATGCCAAAAGTGCAGAACGCCGAAGGCAAACTCTACGCCGACCATAAAATTGGGAATCCGTTTGATAACTTCGCCCAGACTTGTGCGAACTGCCATACCCAGGACAAAGCTGCCTTGCAAAAAGTGGTcg                                      >  2:639530/1‑133 (MQ=255)                                                                                               aaaGTGCAGAACGCCGAAGGCAAACTCTACGCCGACCATAAAATTGGTAATCCGTTTGATAACTTCGCCCAGACTTGTGCGAACTGCCATACCCAGGACAAATCTGCCTTGCAAGAATTGGTCGGGGAACGTa                             >  1:253774/1‑133 (MQ=255)                                                                                                 aGTGCAGAACGCCGAAGGCAAACTCTACGCCGACCATAAAATTGGTAATCCGTTTGATAACTTCGCCCAGACTTGTGCGAACTGCCATACCCAGGACAAAGCTGCCTTGCAAAAAGTGGTCGCGGAACGTAAg                           <  1:526715/133‑1 (MQ=255)                                                                                                    gCAGAACGCCGAAGGCAAACTCTACGCCGACCATAAAATTGGTAATCCGTTTGATAACTTCGCCCAGACTTGTGCGAACTGCCATACCCAGGACAAAGCTGCCTTGCAAAAAGTGGTCGCGGAACGt                              >  1:567809/1‑127 (MQ=255)                                                                                                    gCAGAACGCCGAAGGCAAACTCTACGCCGACCATAAAATTGGTAATCCGTTTGATAACTTCGCCCAGACTTGTGCGAACTGCCATACCCAGGACAAAGCTGCCTTGCAAAAAGTGGTCGCGGAACGt                              <  2:567809/127‑1 (MQ=255)                                                                                                     cAGAACGCCGAAGGCAAACTCTACGCCGACCATAAAATTGGTAATCCGTTTGATAACTTCGCCCAGACTTGTGCGAACTGCCATACCCAGGACAAAGCTGCCTTGCAAAAAGTGGTCGCGGAACGTAAGCAGt                       >  2:32602/1‑133 (MQ=255)                                                                                                                          tACGCCGACCATAAAATTGGTAATCCGTTTGATAACTTCGCCCAGACTTGTGCGAACTGCCATACCCAGGACAAAGCTGCCTTGCAAAAAGTGGTCGCGGAACGTAAGCAGTCGATTAACGACCTGAAAATCa  <  1:145101/133‑1 (MQ=255)                                                                                                                             |                                                                                                                                  GCCAATGCTGAAAGCGCAGCACCCGGAATATGAAACCTGGACAGCGGGCATTCACGGTAAAAACAACGTGACCTGTATCGACTGCCATATGCCAAAAGTGCAGAACGCCGAAGGCAAACTCTACACCGACCATAAAATTGGTAATCCGTTTGATAACTTCGCCCAGACTTGTGCGAACTGCCATACCCAGGACAAAGCTGCCTTGCAAAAAGTGGTCGCGGAACGTAAGCAGTCGATTAACGACCTGAAAATCA  >  NC_000913/4288534‑4288787

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: ‑