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	82.6%	121.2 / 22.8	46	coding (40/1389 nt)	narU	nitrate/nitrite transporter
Reads supporting (aligned to +/- strand):  ref base . (3/5);  new base A (20/18);  total (23/23)
Fisher's exact test for biased strand distribution p-value = 6.99e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01
*	NC_000913_3_pae_tpiA	1,544,022	0	C	A	100.0%	143.3 / NA	46	L13F (TTG→TTT)	narU	nitrate/nitrite transporter
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (23/23);  total (23/23)

TATTGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑C‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGAAA  >  NC_000913_3_pae_tpiA/1543877‑1544170                                                                                                                                                   |||                                                                                                                                                     tATTGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑a‑a‑aa                                                                                                                                                   >  2:941038/1‑149 (MQ=255)    tGAGATTAACGGTAACTGCTCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑A‑a‑aaaag                                                                                                                                                <  1:834925/149‑3 (MQ=255)           aaCGGTAACTGCGCTAAATAGCATCCAGACACAGTAACCAAAAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGa                                                                                                                                          <  1:720713/149‑1 (MQ=255)             cGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACt                                                                                                                                        >  1:563387/1‑149 (MQ=255)                    tGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGCCTCTTTTtc                                                                                                                                 >  1:205290/1‑149 (MQ=255)                     gcgcTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTtct                                                                                                                                <  2:563387/149‑1 (MQ=255)                      cgcTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTtctc                                                                                                                               >  2:583530/1‑149 (MQ=255)                       gcTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGAGTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTTTCa                                                                                                                              >  2:531338/1‑149 (MQ=255)                              aGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCa                                                                                                                       <  1:546696/149‑1 (MQ=255)                                 aTCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTg                                                                                                                    >  1:397458/1‑149 (MQ=255)                                  tCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGc                                                                                                                   >  2:957888/1‑149 (MQ=255)                                             aaGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑AAA‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTcc                                                                                                        >  1:855327/1‑149 (MQ=255)                                             aaGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑AAA‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTcc                                                                                                        <  1:99872/149‑1 (MQ=255)                                              aGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCt                                                                                                       <  1:707892/149‑1 (MQ=255)                                                    gaagTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATaa                                                                                                                                             >  1:1044482/1‑105 (MQ=255)                                                    gaagTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATaa                                                                                                                                             <  2:1044482/105‑1 (MQ=255)                                                      agTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGca                                                                                               <  1:54275/149‑1 (MQ=255)                                                       gTAGACAACTGACTGATAGCCAGAGATTTCTTCGCGCAATATGTTTTCCTTTATTCTCCCAGACGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGcac                                                                                              <  1:935598/149‑1 (MQ=255)                                                         aGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGcacac                                                                                            >  2:770629/1‑149 (MQ=255)                                                           aCAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACCTGcatcata                                                                                          >  2:258922/1‑144 (MQ=255)                                                              actgactgATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTgg                                                                                       <  1:367636/149‑1 (MQ=255)                                                               cttactgaTATCAAGAGTTTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGt                                                                                      <  2:365645/146‑1 (MQ=255)                                                                tgactgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCGCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGGCTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTa                                                                                     >  1:550887/1‑149 (MQ=255)                                                                  actgaTATCCAGCGTGTTCTTCGAGAAATATGTGTTCCTTTAGTTTCCCAGAAGGCCGGATTTTCTGCTTTCCAGTCGCG‑A‑ATAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAAt                                                                                   <  2:281836/149‑1 (MQ=255)                                                                    tgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGa                                                                                 >  1:155271/1‑149 (MQ=255)                                                                     gaTATACAGTAATTTCTTCGAGCAATATGTTTTCCCTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGAAATCTTCTATTTTCATCATTTTTCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGaa                                                                                <  1:248384/149‑1 (MQ=255)                                                                           cAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTTTCTTTTTTTTTTTCCATTTATTTCTTAACTTGCACACAATTGTATTGTAAAAAAg                                                                          >  2:483022/1‑149 (MQ=255)                                                                                    cttcGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAacac                                                                 <  1:698209/149‑1 (MQ=255)                                                                                    cttcGAGCAATATGTCTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑AAA‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAacac                                                                 <  2:765642/149‑1 (MQ=255)                                                                                     ttcGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTAGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAGAAAAGACAAAACACg                                                                >  2:83389/1‑149 (MQ=255)                                                                                      tcGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGa                                                               <  1:287803/149‑1 (MQ=255)                                                                                         aGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTTCCGTGCCATATTGTTCCTCACATGCACACATTGGTACTGAAAAAAAGACAAAACCCTAGGt                                                            >  2:757992/1‑149 (MQ=255)                                                                                                tGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTCTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTGGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAATAAAGACAAAACACGAGGTAAGgcgc                                                     <  1:799076/149‑1 (MQ=255)                                                                                                  ttttCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAAt                                                                                   >  2:132558/1‑117 (MQ=255)                                                                                                  ttttCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑AAA‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAAt                                                                                   <  1:132558/117‑1 (MQ=255)                                                                                                   tttCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAAt                                                  >  2:261604/1‑149 (MQ=255)                                                                                                    ttCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑AAA‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGAAAGGCGCAATa                                                 >  1:162401/1‑149 (MQ=255)                                                                                                         ttATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTTCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGAAAAACCACGAGGTAAGGCACAATATCCAg                                            >  2:222592/1‑149 (MQ=255)                                                                                                          tATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGt                                           <  1:68975/149‑1 (MQ=255)                                                                                                           aTTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGGTAACGACTATTTTTCTCATTTTGCAGTGCCATATTGt                                                                                                           >  1:951383/1‑84 (MQ=255)                                                                                                           aTTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGt                                                                                                           <  2:951383/84‑1 (MQ=255)                                                                                                                      aGGCCGGGTTTGCCGGTGTGCAGTCGCGAA‑A‑AAAGAAAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCCCAAGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTaa                               <  1:483022/149‑1 (MQ=255)                                                                                                                      aGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCAATCATTGGGAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTaa                               <  2:646378/149‑1 (MQ=255)                                                                                                                         ccGGATTTTCTGGTTTCCAGTCGCG‑AAA‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGGAAGGCGCAATAGCCAGTTATTCGAATTAAGGa                            >  1:608084/1‑149 (MQ=255)                                                                                                                          cGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGAt                           >  1:329270/1‑149 (MQ=255)                                                                                                                             aTTTTCTGGTTTCCAGTAGCGAA‑A‑AAAAATAACGACTATTTTTCTCATTTTGCAGTGACATATTGTTCCTCACATGCACAAATTAGAAAAGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGac                        <  2:448559/149‑2 (MQ=255)                                                                                                                                 tCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTgg                    >  2:977868/1‑149 (MQ=255)                                                                                                                                              tcgcgaaa‑aaaGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGACGGGCTTATTAGCCCGTTATTAAAATTAAGGAGGAATTGGGTGAAGTGCTGa        >  1:238805/8‑149 (MQ=255)                                                                                                                                                gcgaaa‑aaaGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAACAAAAGACAACACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGAtt      >  2:776511/6‑149 (MQ=255)                                                                                                                                                    aa‑aaaGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGaaa  <  1:938710/148‑1 (MQ=255)                                                                                                                                                   |||                                                                                                                                                     TATTGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑C‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGAAA  >  NC_000913_3_pae_tpiA/1543877‑1544170

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: ‑