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%	90.3 / NA	28	L13F (TTG→TTT)	narU	nitrate/nitrite transporter
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (15/13);  total (15/13)

TTGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑G‑C‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGT  >  NC_000913_3_pae_tpiA/1543879‑1544154                                                                                                                                                   |                                                                                                                                      ttGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑G‑A‑aaaaa                                                                                                                                 >  2:197787/1‑148 (MQ=255) ttGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑G‑A‑aaaaa                                                                                                                                 >  1:704595/1‑148 (MQ=255)      aTTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑GTA‑AAAAGATaa                                                                                                                             >  2:176556/1‑149 (MQ=255)                  tGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑G‑AAAAAAGATAACGACTATTTTtc                                                                                                                 >  1:254274/1‑149 (MQ=255)                              cATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑GAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGt                                                                                                     >  1:439636/1‑149 (MQ=255)                                         aGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑GAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGtt                                                                                          >  2:191742/1‑149 (MQ=255)                                          gAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑GAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTc                                                                                         <  1:294095/149‑1 (MQ=255)                                            aGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑GAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCt                                                                                       <  2:259120/149‑1 (MQ=255)                                                aagaagTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑GAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTcaca                                                                                   <  1:197787/149‑1 (MQ=255)                                                aagaagTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑G‑AAAAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTcaca                                                                                   >  2:228092/1‑149 (MQ=255)                                                               gactgaTATCCAGTGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑GAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCAAACATTGGTaa                                                                    <  1:701176/149‑1 (MQ=255)                                                               gactgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑GAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCGTTTTTGTTCCTCGCATGCACACATTGGTaa                                                                    <  2:341842/149‑1 (MQ=255)                                                                tctgaTATCCAGGCATTTCTTCTAGCAATATGTTTTCCTTTATTTTGCCAGAAGGCCGTATTTTCTGGTTTCCAGTCG‑C‑GAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAAt                                                                   <  2:584012/148‑1 (MQ=255)                                                                actgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑GAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAAt                                                                   >  1:617413/1‑149 (MQ=255)                                                                actgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑GAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAAt                                                                   >  1:495441/1‑149 (MQ=255)                                                                                    tggAGCAATATGCTTTCCTTTATTTTCGCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCC‑A‑A‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGa                                               <  2:367921/147‑1 (MQ=255)                                                                                     ctagaaaTATGGGTTCCTTTATTTTCGAAGAAGGCTGGATTTTAAGGGTTGTAGTTG‑G‑GAA‑AAAAGATAACGACTGTATTTCGTATTTTGCAGAGAAATAGTGGTCCGCACATGCATACATTGGTAATGAAAAAAAGACAAAACACGAg                                              <  2:287898/144‑1 (MQ=255)                                                                                          aaTATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑GAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAg                                         <  1:432095/149‑1 (MQ=255)                                                                                           atatGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CTA‑A‑AAAAGATCACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACAAGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGAAAgg                                        >  2:676247/1‑149 (MQ=255)                                                                                                ttttCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑GAA‑AAAAGATAACGACTATTTTTCTAATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAAGCGCat                                   >  1:315120/1‑148 (MQ=255)                                                                                                      tgtATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑G‑AAAAAAGATAACGATTATTTTTCTCACTTAGCACTGCCAACTTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCa                             <  2:620416/147‑1 (MQ=255)                                                                                                             tCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑GAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGttatta                      >  2:327639/1‑149 (MQ=255)                                                                                                                     ggCCGGATTTTCTGGTTTCCAGTCG‑C‑GAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAg              <  1:327639/149‑1 (MQ=255)                                                                                                                       ccGGATTTTCTGGTTTCCAGTCG‑C‑GAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATGTTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGACTTAAGGa            >  2:257637/1‑149 (MQ=255)                                                                                                                        cGGATTTTCTGGTTTCCAGTCG‑C‑GAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTACGGCGCAATCGCCAGTTATTAGACTTAAgggt           >  2:195287/1‑147 (MQ=255)                                                                                                                               tCTGGTTTCCAGTCG‑C‑GAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCAGATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTgg    <  2:439636/149‑1 (MQ=255)                                                                                                                                 tGGTTTCCAGTCG‑C‑GAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGt  >  1:663291/1‑149 (MQ=255)                                                                                                                                 tGGTTTCCAGTCG‑C‑GAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGt  <  2:495441/149‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                      TTGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑G‑C‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGT  >  NC_000913_3_pae_tpiA/1543879‑1544154

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: ‑