Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_pae_tpiA	1,544,022	C→A	L13F (TTG→TTT)	narU ←	nitrate/nitrite transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_pae_tpiA	1,544,022	0	C	A	100.0%	98.8 / NA	33	L13F (TTG→TTT)	narU	nitrate/nitrite transporter
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (17/16);  total (17/16)

AGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑C‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTG  >  NC_000913_3_pae_tpiA/1543882‑1544155                                                                                                                                               |                                                                                                                                        agaTTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTGGC‑G‑A‑aaaaagat                                                                                                                                >  1:641857/1‑145 (MQ=255)  gaTTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑A‑aaaaagata                                                                                                                               >  1:299288/1‑144 (MQ=255)   aTTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATaa                                                                                                                              <  1:570432/149‑1 (MQ=255)         ggTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTAGC‑GAA‑AAAA‑GATAACGACTa                                                                                                                        >  2:636177/1‑149 (MQ=255)                   cTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑A‑AAAACGATAACGACTATTTTTCTCAt                                                                                                              >  2:581250/1‑149 (MQ=255)                           cATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGt                                                                                                      <  1:235285/149‑1 (MQ=255)                             tCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTTCCGTGc                                                                                                    >  2:433071/1‑149 (MQ=255)                                aGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATGTGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATaa                                                                                                                              <  1:36157/120‑1 (MQ=255)                                aGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATaa                                                                                                                              >  2:36157/1‑120 (MQ=255)                                       taaGTCAATAAGTAGACAACTTACTGATTTCCAGTGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTc                                                                                          <  2:646090/148‑1 (MQ=255)                                          agcaaagagTAGAAAACTGACTGATATCCAGAGATTTCTTCGAGCCATAGGTTTTCCTTTATTTTCACAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑AAAAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTc                                                                                       <  2:116359/142‑1 (MQ=255)                                            cAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGATGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑AAAAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTcac                                                                                     <  1:67258/149‑1 (MQ=255)                                             aagaagTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTca                                                                                      >  1:473093/1‑147 (MQ=255)                                             aagaagTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTca                                                                                      <  2:473093/147‑1 (MQ=255)                                               gaagTAGACAACTGACTGATATCCATAGTTTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATg                                                                                  <  1:186735/149‑1 (MQ=255)                                                       cAACTGACTGATATCCAGAGATTTCTTCGAGCAATCTGTTTTCCTTTATTTTCACAGCAGCCAAGATATTCTGGTTTCTAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTGCTCTTTTTGCAGTACCATATTGTTCCTCACATGCACACAtt                                                                          >  2:504444/1‑149 (MQ=255)                                                        aaCTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTg                                                                         >  2:204300/1‑149 (MQ=255)                                                            gactgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTaa                                                                     >  2:289427/1‑149 (MQ=255)                                                                           aTTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGGCGCGG‑A‑AAAA‑GATAACGACTATTTTTCTCATTTTTCAGTGCCTTATTGTTCCTCACATGCACACATTGGTATTGGAAAAAAAACaaa                                                      >  1:197946/1‑149 (MQ=255)                                                                           aTTTCTTCGAGCAATATGTTTTCCATTATTTTCCCAGAATGCCGTATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATGTTATTCCTCACATGAACCCATTGGTAATAAAAAAAAGACaaa                                                      >  2:289844/1‑149 (MQ=255)                                                                            tttCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACaaaa                                                     >  1:277544/1‑149 (MQ=255)                                                                            tttCTTCGAGCAATATGTTTTCCTATATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACaaaa                                                     <  1:584662/149‑1 (MQ=255)                                                                             ttcttcGAGCAATATGTTTTCCTTTATTTTCCCAGACGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGCCTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAac                                                    <  1:285714/149‑1 (MQ=255)                                                                                    aGCAATATGTTTTCTTTTAATTAAACAGAAGGCCGGATTTTCTGGGTTCAAGTCGC‑G‑AAAAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACAAAAAAAAAAAAAAAAAAAGACAAAACACGAGGt                                             <  2:277544/149‑1 (MQ=255)                                                                                       aaTATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAg                                          <  1:289427/149‑1 (MQ=255)                                                                                           ggTTTTCCATTATTTGCCTGAAACGCCGGATTTTTTGGTTTCCAGTCCC‑G‑AAAAAA‑GATAACGACTATTTTACTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGgcgc                                      <  2:406647/148‑1 (MQ=255)                                                                                                tCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTGATGAAAAAAAGACAAAACACGAGGTAGGGCCCAATAg                                 >  2:17328/1‑149 (MQ=255)                                                                                                 cccttATTTCCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGc                                <  1:184275/146‑1 (MQ=255)                                                                                                                    ccGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTcc                                                                                         <  2:213475/73‑1 (MQ=255)                                                                                                                    ccGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTcc                                                                                         >  1:213475/1‑73 (MQ=255)                                                                                                                           ttCTGGTTTCCAGTCGC‑G‑AAAAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTg      >  2:450118/1‑149 (MQ=255)                                                                                                                              tGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGt   >  1:376684/1‑149 (MQ=255)                                                                                                                               ggTTGCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTg  <  1:5125/149‑1 (MQ=255)                                                                                                                                               |                                                                                                                                        AGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑C‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTG  >  NC_000913_3_pae_tpiA/1543882‑1544155

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑