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	81.1%	104.9 / 19.5	37	coding (40/1389 nt)	narU	nitrate/nitrite transporter
Reads supporting (aligned to +/- strand):  ref base . (6/1);  new base A (15/15);  total (21/16)
Fisher's exact test for biased strand distribution p-value = 1.13e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.87e-01
*	NC_000913_3_pae_tpiA	1,544,022	0	C	A	97.3%	121.4 / NA	37	L13F (TTG→TTT)	narU	nitrate/nitrite transporter
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base A (21/15);  total (21/16)
Fisher's exact test for biased strand distribution p-value = 4.32e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

TTGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑C‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGAAA  >  NC_000913_3_pae_tpiA/1543879‑1544170                                                                                                                                                 |||                                                                                                                                                     ttGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑A‑a‑aaaa                                                                                                                                                 >  1:55937/1‑148 (MQ=255)                        aaaaAGCATCCAGACAAAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTGCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTACCAGACAAGAA‑A‑AAAGATAACGACTATTTTTCTCAttt                                                                                                                           <  2:307399/149‑1 (MQ=255)                                tacAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGc                                                                                                                   <  1:268161/147‑1 (MQ=255)                                          gAAGGCAAGAAGTAGATCACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTc                                                                                                         <  2:478445/149‑1 (MQ=255)                                           aaGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTcc                                                                                                        >  2:900905/1‑149 (MQ=255)                                           aaGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTcc                                                                                                        >  2:509344/1‑149 (MQ=255)                                                      tAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCTTCACATGcaac                                                                                             >  1:355870/1‑147 (MQ=255)                                                           aaCTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTg                                                                                        >  1:756622/1‑149 (MQ=255)                                                            accgaaggaTAGCCAGAGATCTCTTGGAGCAATATATTTCCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTAAAAAAAAAAAAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTgg                                                                                       <  2:815609/142‑1 (MQ=255)                                                                        ccAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGCTAACGACTATTTTTGCCACGTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGaaaaaaa                                                                           >  1:411815/1‑149 (MQ=255)                                                                        ccAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGaaaaaaa                                                                           <  2:55937/149‑1 (MQ=255)                                                                           gagaTTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑AAA‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGAc                                                                        >  1:69946/1‑149 (MQ=255)                                                                              aTTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTcaca                                                                                                   <  1:615928/119‑1 (MQ=255)                                                                              aTTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTAGCG‑A‑ACAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTcaca                                                                                                   >  2:615928/1‑119 (MQ=255)                                                                               tttCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACaaaa                                                                    >  2:276689/1‑149 (MQ=255)                                                                                   ttcGAGCAATATGTTTTCCTTTATTTTGCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAACAAAGACAAACCACg                                                                >  2:911679/1‑149 (MQ=255)                                                                                      gAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCAAACATTGGTAATGAAAAAAAGACAAAACACGAgg                                                             >  1:501257/1‑149 (MQ=255)                                                                                      gAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑AAA‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAgg                                                             >  1:327065/1‑149 (MQ=255)                                                                                             atGTTTTCCTTTATTTTCCCAGAAGACCGGATTTTCTGGTTTCCCGTCGCGAA‑A‑AAAGATAACGCCATCTGCCCGCATTCTGCAGCCTGAGATGGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGgcg                                                      <  1:911679/149‑1 (MQ=255)                                                                                             atGTTTTCCTTTACTGACCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGCAATGAAAAAAAGACAAAACACGAGGTAAGgcg                                                      <  2:779055/149‑1 (MQ=255)                                                                                                ttttCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCaa                                                   >  1:341852/1‑149 (MQ=255)                                                                                                ttttCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCaa                                                   >  1:121775/1‑149 (MQ=255)                                                                                                  ttCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGCAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATa                                                 <  2:756622/149‑1 (MQ=255)                                                                                                      tttATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCa                                             >  1:465283/1‑149 (MQ=255)                                                                                                        tATTTTACCAGAAGGACGAATTTGCTAGTTTTCAGCCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTCCAGTGCCATATTGTTCCTCACATGCACACATTGTTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGt                                           <  2:603342/149‑1 (MQ=255)                                                                                                          ttttCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGtta                                         <  2:327065/149‑1 (MQ=255)                                                                                                              cccAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAg                                     >  1:535863/1‑149 (MQ=255)                                                                                                              cccAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAg                                     >  2:910565/1‑149 (MQ=255)                                                                                                               ccgatctgCCGGATCTGCGGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGCGGTAAGGCGCAATAGCCAGTTATTAGa                                    <  2:909830/142‑1 (MQ=255)                                                                                                                       ccGGGTTTTCTGGGGTCCAAGCGCG‑CAA‑AAAGATAACGAGTAGTTTTCTCATTTTGCAGTTCCATATTGTGCTTCACATGCACACATTGGTAATGAAAAAAATACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGa                            <  2:731749/149‑1 (MQ=255)                                                                                                                       ccGGATTTTCTGGTTTCCAGTCGCG‑AAA‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCGATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGaaagatcgg                            >  1:909830/1‑142 (MQ=255)                                                                                                                        cGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGAt                           >  2:748350/1‑149 (MQ=255)                                                                                                                           tttttCTGGTTTCCATTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACAGGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGaa                        <  2:411815/148‑1 (MQ=255)                                                                                                                            ttttCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAAt                       <  1:335129/149‑1 (MQ=255)                                                                                                                                     ttCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCGGTTATTAGAATTAAGGATGAGTTGGGTGAAg              >  1:532116/1‑149 (MQ=255)                                                                                                                                     ttCCAGTCGCG‑AAA‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAg              >  1:532159/1‑149 (MQ=255)                                                                                                                                       ccAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTg            <  2:818663/149‑1 (MQ=255)                                                                                                                                            tcgcgaaa‑aaaGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGa        <  1:748350/142‑1 (MQ=255)                                                                                                                                            tcgcgaaa‑aaaGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGa        >  2:744167/8‑149 (MQ=255)                                                                                                                                             cgcgaaa‑aaaGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGAt       <  1:744167/143‑1 (MQ=255)                                                                                                                                                  aa‑aaaGATAACGATTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGaaa  <  2:69946/148‑1 (MQ=255)                                                                                                                                                 |||                                                                                                                                                     TTGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑C‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGAAA  >  NC_000913_3_pae_tpiA/1543879‑1544170

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑