Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913_3_pae_tpiA	1,544,022	C→A	100%	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%	94.7 / NA	32	L13F (TTG→TTT)	narU	nitrate/nitrite transporter
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (16/16);  total (16/16)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTC‑GCG‑C‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAG  >  NC_000913_3_pae_tpiA/1543879‑1544158                                                                                                                                                  |                                                                                                                                           ttGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAAGCAAGAAGGAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATTTTTTCCTTTATTTTCCCACAAGGCCGGATTTTCTGGTTTCCAGTC‑CCG‑A‑aaa‑aa                                                                                                                                     >  2:557105/1‑148 (MQ=255)                  tGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTC‑GCGAA‑AAA‑AGATAACGACTATTTTtc                                                                                                                     >  1:506092/1‑149 (MQ=255)                     gcTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTC‑GCG‑A‑AAACAGATAACGACTATTTTTCTCa                                                                                                                  >  1:666407/1‑149 (MQ=255)                           tAGCATCAAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGCTGACTTCGAGCAAGAAGTTTTCCTTTATTTTCCCATAAGGCCGGATTTTCTGGTTTCCATTG‑GCGTA‑AAA‑AGATAACGACTATTTTTCTCATCTTGc                                                                                                            >  2:708838/1‑149 (MQ=255)                             gtgtCCAGACGCAGATGTCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTACTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTC‑GCGAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAg                                                                                                          <  2:281470/146‑1 (MQ=255)                                tCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTC‑GCGAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGc                                                                                                       >  2:603081/1‑149 (MQ=255)                                  cAGACACAGAGGGGAAGAAGGAGACAACGGACGGATCTCCAGAGATTTCAGCGAGCAATATGTTTTCCTTTATTTTACCAGAAGGCCGGATTTTCTGGATTCCAATC‑GCGAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCa                                                                                                     <  2:282663/149‑1 (MQ=255)                                   aGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCATTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTACAGTC‑GCGAA‑AAA‑AGATAACCACTATTCTTCTATTTTTGCAGTGCCat                                                                                                    >  2:426551/1‑149 (MQ=255)                                        caGAAGGCAAGAAGGAGACAACTGACGGATAACCAGAGATTTCTTCGAGCAATATGTTTGCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTC‑GCGAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGt                                                                                               <  1:113996/149‑1 (MQ=255)                                                aagaagTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTC‑GCGAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTcaca                                                                                       <  1:133968/149‑1 (MQ=255)                                                                  tgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGCTTTTCTGGTTTCCAGTC‑TCG‑AAAAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGACATATTGTTCCTCACATGCACACTATGGTAATGa                                                                     >  2:162538/1‑149 (MQ=255)                                                                         cAGAGATTTCTTCGAGCAATATGTTTTCCTTTCTTTTCCCGGAAGGCAGGATTTTCTGGTTTCCAGTC‑GCGAA‑AAA‑AGATAACGTATATTTTTCTCATTTTGCAGTGCACTATTGTTACTCTCATGCACACATATGTGATAaaaataat                                                              >  2:551858/1‑148 (MQ=255)                                                                         aagagATTTCTCCAAGCAACATGCCTTCCCTTCTTTACCCAGAAGACCCCATTATCTAGTTACCACAC‑AAGAA‑AAA‑AGAGAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACCTGCACACATTGGTAATGAAAAAAAg                                                              <  2:528636/148‑1 (MQ=255)                                                                          agagCTTTCCTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTC‑GCGAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCATATGCACACATTGGTAATGAAAAAAAGa                                                             <  1:87248/149‑1 (MQ=255)                                                                           gagaTTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTC‑GCGAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGAc                                                            >  1:135646/1‑149 (MQ=255)                                                                                    tcGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTC‑GCGAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGa                                                   <  1:494769/149‑1 (MQ=255)                                                                                      gAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTC‑GCGAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAgg                                                 >  1:129884/1‑149 (MQ=255)                                                                                      gAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTC‑GCGAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAgg                                                 >  1:130389/1‑149 (MQ=255)                                                                                         cAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTC‑GCGAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTaa                                              >  2:662880/1‑149 (MQ=255)                                                                                            tatGTTTGCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTC‑GCG‑AAAAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGgc                                           <  1:169927/149‑1 (MQ=255)                                                                                                 tttCCTTTATTTTCTCGGAGGGCCGGATTTTCTGGTTTCCAGTC‑GCGAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTGCCTCACATGCACACAGTGGTAATGAAAAAAAGACAAAACACGGGGTAAGGCGCAAt                                      <  2:512371/149‑1 (MQ=255)                                                                                                      tttATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTC‑GCG‑AAAAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGccg                                 >  1:55246/1‑148 (MQ=255)                                                                                                         aTTGTCCGAGAAGGACGGTTTTTCTGGTTTCGAGTC‑GGGAA‑AAA‑AGATAACGACGATTGTTCTGATTTTGCAGTGCCATATGGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGtt                              <  2:116081/149‑1 (MQ=255)                                                                                                                      gCCGGGTTTTCTGGTTTCCAGTCGGTA‑A‑AAA‑AGATAACGACTATTTTTCTCATTTTGTAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAgg                 <  2:61135/149‑1 (MQ=255)                                                                                                                       taggttttcCTGTTTTCCAGTCTACA‑A‑AAA‑AGACAACGACTATGTTTCGAAATTTGCAGTGCCATTTTGTTCCTCACATGCACACATTGGTAAGGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGa                <  2:291915/144‑1 (MQ=255)                                                                                                                         ggATTTTCTGGTTTCCAGTC‑GCGAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTaaaaaag              >  1:145301/1‑144 (MQ=255)                                                                                                                         ggATTTTCCGGTTTCCAGTC‑GCGAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTCGAATTAAGGagg              >  1:91114/1‑147 (MQ=255)                                                                                                                              ttCTGGTTTCCAGTC‑GCGAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTg         <  1:588047/149‑1 (MQ=255)                                                                                                                                cTGGTTTCCAGTC‑GCGAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTggg       <  1:475788/149‑1 (MQ=255)                                                                                                                                cTGGTTTCCAGTC‑GCGAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGAAGAATTggg       >  2:293888/1‑149 (MQ=255)                                                                                                                                cTGGTTTCCAGTA‑GCGAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTggg       <  2:135646/149‑1 (MQ=255)                                                                                                                                     ttCCAGTC‑GCGAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGATATTAGAATTAAGGATGAATTGGGTGAAg  <  1:603081/149‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                           TTGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTC‑GCG‑C‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAG  >  NC_000913_3_pae_tpiA/1543879‑1544158

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑