Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,346,060	A→G	E448E (GAA→GAG)	rpoN →	RNA polymerase, sigma 54 (sigma N) factor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,346,060	0	A	G	100.0%	131.5 / NA	36	E448E (GAA→GAG)	rpoN	RNA polymerase, sigma 54 (sigma N) factor
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (17/19);  total (17/19)

TTTCCAGTCACGTCAATACCGAGGGCGGCGGCGAAGCTTCCTCCACGGCGATTCGTGCGCTGGTGAAGAAATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAACAAGGTATCATGGTGGCACGCCGCACTGTTGCGAAGTACCGAGAGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGAAGACACTATG  >  NC_000913/3345924‑3346175                                                                                                                                         |                                                                                                                    tttCCAGTCACGTCAATACCGAGGGCGGCGGCGAAGCTTCCTCCACGGCGATTCGTGCGCTGGTGAAGAAATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCa                                                                                                                   >  2:615106/1‑139 (MQ=255) tttCCAGTCACGTCAATACCGAGGGCGGCGGCGAAGCTTCCTCCACGGCGATTCGTGCGCTGGTGAAGAAATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCa                                                                                                                   <  2:351534/139‑1 (MQ=255)       gTCACGTCAATACCGAGGGCGGCGGCGAAGCTTCCTCCACGGCGATTCGTGCGCTGGTGAAGAAATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTAt                                                                                                             >  1:426552/1‑139 (MQ=255)                 tACCGAGGGCGGCGGCGAAGCTTCCTCCACGGCGATTCGTGCGCTGGTGAAGAAATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCa                                                                                                   >  1:144833/1‑139 (MQ=255)                 tACCGAGGGCGGCGGCGAAGCTTCCTCCACGGCGATTCGTGCGCTGGTGAAGAAATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCa                                                                                                   <  2:677138/139‑1 (MQ=255)                      aGGGCGGCGGCGAAGCTTCCTCCACGGCGATTCGTGCGCTGGTGAAGAAATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCAcgccg                                                                                              >  1:36122/1‑139 (MQ=255)                        ggcggcggcGAAGCTTCCTCCACGGCGATTCGTGCGCTGGTGAAGAAATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCa                                                                                            >  2:703627/1‑139 (MQ=255)                        ggcggcggcGAAGCTTCCTCCACGGCGATTCGTGCGCTGGTGAAGAAATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCa                                                                                            <  2:651993/139‑1 (MQ=255)                        ggcggcggcGAAGCTTCCTCCACGGCGATTCGTGCGCTGGTGAAGAAATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCa                                                                                            <  1:703627/139‑1 (MQ=255)                        ggcggcggcGAAGCTTCCTCCACGGCGATTCGTGCGCTGGTGAAGAAATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCa                                                                                            >  1:488356/1‑139 (MQ=255)                         gcggcggcgAAGCTTCCTCCACGGCGATTCGTGCGCTGGTGAAGAAATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCAc                                                                                           <  2:653268/139‑1 (MQ=255)                          cggcggcgAAGCTTCCTCCACGGCGATTCGTGCGCTGGTGAAGAAATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACt                                                                                          >  2:468587/1‑139 (MQ=255)                           ggcggcgAAGCTTCCTCCACGGCGATTCGTGCGCTGGTGAAGAAATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTg                                                                                         <  1:468587/139‑1 (MQ=255)                                cgAAGCTTCCTCCACGGCGATTCGTGCGCTGGTGAAGAAATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTGTTGCg                                                                                    <  1:615106/139‑1 (MQ=255)                                 gatgCTTCCTCCACGGCGATTCGTGCGCTGGTGAAGAAATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTACCCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTGTTGCGa                                                                                   <  2:268222/136‑1 (MQ=255)                                   aGCTTCCTCCACGGCGATTCGTGCGCTGGTGAAGAAATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTGTTGCGAAg                                                                                 <  2:426552/139‑1 (MQ=255)                                          tccACGGCGATTCGTGCGCTGGTGAAGAAATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTGTTGCGAAGTACCgag                                                                          <  2:144833/139‑1 (MQ=255)                                                          cgcTGGTGAAGAAATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTGTTGCGAAGTACCGAGAGTCTTTATCCATTct                                                          <  2:488356/139‑2 (MQ=255)                                                                    gaaATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTGTTGCGAAGTACCGAGAGTCTTTATCCATTCCGCCGTCAAAc                                                >  1:106331/1‑139 (MQ=255)                                                                    gaaATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTGTTGCGAAGTACCGAGAGTCTTTATCCATTCCGCCGTCAAAc                                                >  2:641167/1‑139 (MQ=255)                                                                         tAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTGTTGCGAAGTACCGAGAGTCTTTATCCATTCCGCCGTCaaa                                                 <  2:232357/133‑1 (MQ=255)                                                                         tAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTGTTGCGAAGTACCGAGAGTCTTTATCCATTCCGCCGTCaaa                                                 >  1:232357/1‑133 (MQ=255)                                                                           aTCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTGTTGCGAAGTACCGAGAGTCTTTATCCATTCCGCCGTCAAACCAGCGTa                                         <  2:249514/139‑1 (MQ=255)                                                                                     aaaaCCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTGTTGCg                                                                                    <  2:577449/86‑1 (MQ=255)                                                                                     aaaaCCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTGTTGCg                                                                                    >  1:577449/1‑86 (MQ=255)                                                                                            aGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTGTTGCGAAGTACCGAGAGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAACTCGTTTGAccc                        >  1:743583/1‑139 (MQ=255)                                                                                                           cGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTGTTGCGAAGTACCgag                                                                          <  2:23698/74‑1 (MQ=255)                                                                                                           cGACAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTGTTGCGAAGTACCgag                                                                          >  1:23698/1‑74 (MQ=255)                                                                                                             aCAGCAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTGTTGCGAAGTACCGAGAGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGAAGaca       >  2:426655/1‑139 (MQ=255)                                                                                                                 cAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTGTTGCGAAGt                                                                                >  1:206423/1‑62 (MQ=255)                                                                                                                 cAAGTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTGTTGCGAAGt                                                                                <  2:206423/62‑1 (MQ=255)                                                                                                                  aaGTTAACCTCTTTGCTGTCGGAGAAAGGTATCATGGTGGCACGCCGCACTGTTGCGAAGTACCGAGAGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGAAGACACTATg  <  2:587867/139‑1 (MQ=255)                                                                                                                    gTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCAc                                                                                           <  1:576386/48‑1 (MQ=255)                                                                                                                    gTTAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCAc                                                                                           >  2:576386/1‑48 (MQ=255)                                                                                                                     ttAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTGTTGCGAAGTACCGAGAGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAACTCGTTTGACCCAACCg                   >  1:338224/1‑119 (MQ=255)                                                                                                                     ttAACCTCTTTGCTGTCGGAGCAAGGTATCATGGTGGCACGCCGCACTGTTGCGAAGTACCGAGAGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAACTCGTTTGACCCAACCg                   <  2:338224/119‑1 (MQ=255)                                                                                                                                         |                                                                                                                    TTTCCAGTCACGTCAATACCGAGGGCGGCGGCGAAGCTTCCTCCACGGCGATTCGTGCGCTGGTGAAGAAATTAATCGCGGCGGAAAACCCAGCGAAACCGTTGAGCGACAGCAAGTTAACCTCTTTGCTGTCGGAACAAGGTATCATGGTGGCACGCCGCACTGTTGCGAAGTACCGAGAGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGAAGACACTATG  >  NC_000913/3345924‑3346175

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑