Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_pae_tpiA	1,544,022	1 bp→AA	coding (39/1389 nt)	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	1,544,021	1	.	A	77.8%	95.6 / 23.4	36	coding (40/1389 nt)	narU	nitrate/nitrite transporter
Reads supporting (aligned to +/- strand):  ref base . (5/3);  new base A (13/15);  total (18/18)
Fisher's exact test for biased strand distribution p-value = 6.91e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.84e-01
*	NC_000913_3_pae_tpiA	1,544,022	0	C	A	100.0%	115.3 / NA	36	L13F (TTG→TTT)	narU	nitrate/nitrite transporter
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (18/18);  total (18/18)

TTGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑C‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGAAAG  >  NC_000913_3_pae_tpiA/1543879‑1544171                                                                                                                                                  |||                                                                                                                                                      ttGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑A‑aa‑aaa                                                                                                                                                  <  1:109523/149‑2 (MQ=255)    agaTTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑A‑aa‑aaagat                                                                                                                                               >  2:311063/1‑145 (MQ=255)       ttAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑AAAA‑AAGATAAc                                                                                                                                             >  1:214025/1‑149 (MQ=255)                  tGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTtc                                                                                                                                  >  1:124427/1‑149 (MQ=255)                     gcTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGAAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGGTTTTCTGGTTGCATGTCGC‑GAA‑AA‑AAGCTGAGGACTAtttttttta                                                                                                                               >  1:90739/1‑145 (MQ=255)                          aTAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTCTTCTCATTTTg                                                                                                                          <  1:311063/149‑1 (MQ=255)                                    gACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCata                                                                                                                <  1:398246/149‑1 (MQ=255)                                                      tAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGcaaa                                                                                              >  1:369792/1‑147 (MQ=255)                                                          cAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTAtt                                                                                                                                      >  2:59/1‑105 (MQ=255)                                                          cAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTAtt                                                                                                                                      <  1:59/105‑1 (MQ=255)                                                              tgactgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTa                                                                                      >  2:158848/1‑149 (MQ=255)                                                                    atatCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGaaa                                                                                >  1:249859/1‑149 (MQ=255)                                                                    atatCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑AAAA‑AAGATAACGACTATTTTTCTCATTTTGTAGTGCCATATTGTTCCTCACATGCTCCCATTGGTAATGaaa                                                                                >  1:44821/1‑149 (MQ=255)                                                                         cAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAg                                                                           <  1:308590/149‑1 (MQ=255)                                                                           gagaTTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGTCTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGAc                                                                         <  1:208806/149‑1 (MQ=255)                                                                              aTTTCTTCGAGCAATATGTTTGCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACaaa                                                                      <  1:57678/149‑1 (MQ=255)                                                                                       aGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCCCATGCACACATTGGTAATGAAAAAAAGAAAAAAAACGAGGt                                                             >  1:52296/1‑149 (MQ=255)                                                                                       aGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTATGGTTTCCAGTCGC‑G‑AAAA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGt                                                             >  2:199977/1‑149 (MQ=255)                                                                                            tttattttCCATTATGTGCCCAGAGGGCCGGAGTTTCTGGTGTACAGTAGA‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGGGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGgc                                                        <  2:171589/145‑1 (MQ=255)                                                                                                      tttATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTTTCATTTTGCTGTGCCATATTGTTCCTCACATGCACACATTGGTATTGAAACAAGGACAATCCACGAGGTAAGGCGCattcgacg                                              >  2:40219/1‑142 (MQ=255)                                                                                                      tttATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑AAAA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCa                                              >  1:286473/1‑149 (MQ=255)                                                                                                                taGAAGGCCGGATTTTCTGGTTTCCAGTGGC‑GAA‑AA‑AAGATAATGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACAGATTGGTAATGAAAAAAAGACAAAACACGAGGTACGGGACAATAGCCAGATATTAgga                                    >  1:478999/2‑147 (MQ=255)                                                                                                                cAGAAGGCCGGATTTTCAGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGaa                                    >  2:282689/1‑149 (MQ=255)                                                                                                                    aGGCCGGATTTTCTGGTTTCTAGTGGCAA‑A‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTaa                                <  2:259816/149‑1 (MQ=255)                                                                                                                    aGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTaa                                <  1:322188/149‑1 (MQ=255)                                                                                                                       ccGGATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGa                             <  2:124427/149‑1 (MQ=255)                                                                                                                        cGGATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGtta                                          <  1:379826/135‑1 (MQ=255)                                                                                                                        cGGATTTTCTGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGtta                                          >  2:379826/1‑135 (MQ=255)                                                                                                                               tCTGGTTGCCAGTCAC‑GAA‑AA‑AAGATAACGACTATTTATCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACAAAAAAAATAAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTgg                     <  2:421083/149‑1 (MQ=255)                                                                                                                               tCTGGGTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTgg                     <  2:421074/149‑1 (MQ=255)                                                                                                                                cgtgTTTTCGGTCGC‑G‑A‑AAGAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTggg                    <  2:251712/146‑1 (MQ=255)                                                                                                                                 tGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTTATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGt                   <  1:472076/149‑1 (MQ=255)                                                                                                                                 tGGTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGt                   >  1:394441/1‑149 (MQ=255)                                                                                                                                  ggTTTCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTg                  <  2:286473/149‑1 (MQ=255)                                                                                                                                    tttCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGTTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGaa                <  2:75925/149‑1 (MQ=255)                                                                                                                                    tttCCAGTCGC‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGaa                >  1:111157/1‑149 (MQ=255)                                                                                                                                               gcgaaaa‑aaGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAGACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGAtt       <  1:395289/144‑1 (MQ=255)                                                                                                                                                   aaa‑aaGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGaaa   <  2:279692/148‑1 (MQ=255)                                                                                                                                                    aa‑aaGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGAAAg  >  1:434964/1‑149 (MQ=255)                                                                                                                                                  |||                                                                                                                                                      TTGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑C‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGAAAG  >  NC_000913_3_pae_tpiA/1543879‑1544171

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: ‑