Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_vch_tpiA	1,544,021	1	.	A	69.0%	89.4 / 39.7	42	coding (40/1389 nt)	narU	nitrate/nitrite transporter
Reads supporting (aligned to +/- strand):  ref base . (11/2);  new base A (16/13);  total (27/15)
Fisher's exact test for biased strand distribution p-value = 8.88e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

TTGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑C‑A‑AAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGC  >  NC_000913_3_vch_tpiA/1543879‑1544161                                                                                                                                                |                                                                                                                                                ttGAGATTAACGGTAACTGCGCTACATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTGTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑A‑a‑aaaa                                                                                                                                         <  1:337399/149‑2 (MQ=255)  tGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑A‑a‑aaaag                                                                                                                                        >  1:242931/1‑147 (MQ=255)   gagaTTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTTTGGTTTCCAGTCTCG‑A‑a‑aaaaga                                                                                                                                       >  2:577956/1‑146 (MQ=255)    agaTTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGCCTGCTATCCAGAGATTTCTTCGAGCAATATGATTTCCTTTATTTTGGCTGTAGCCCGGCTTTTCTGGTTTCCAGTCGCGAC‑A‑AAA‑GAt                                                                                                                                      >  2:505904/1‑149 (MQ=255)     gaTTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCTATTCGCG‑T‑a‑aaaagata                                                                                                                                     >  2:815038/1‑144 (MQ=255)     gaTTAACGGTAACTGCGCTAAATAGCATCAAGACACAGAAGGCAGGAAGTAGACGACAGACAGATATCCAAAGATTTCTTCGAGCACTATGTTTTCCTTTATTGTCCAAGAAGGCCGGATTTTCTCGTTTCCAGTCGCG‑A‑A‑AAA‑ggata                                                                                                                                    >  1:703587/1‑145 (MQ=255)       ttAACGGTAACTGCGCTAATTAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGTAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAA‑GATAAc                                                                                                                                   <  2:606348/149‑1 (MQ=255)       ttAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATACCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAA‑GATAAc                                                                                                                                   <  1:546495/149‑1 (MQ=255)        tAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑AAA‑AAA‑GATAACg                                                                                                                                  >  1:212362/1‑149 (MQ=255)                   gcgcTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTTCGGTTGTG‑T‑ATAAA‑GATAACGACTAttttttt                                                                                                                       >  1:361043/1‑147 (MQ=255)                   gcgcTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAA‑GATAACGACTATTTTtct                                                                                                                       >  1:362141/1‑149 (MQ=255)                   gcgcTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTAGTTTCCAGTCGCGAA‑A‑AAA‑GATAACGAATATTTTtct                                                                                                                       >  1:572998/1‑149 (MQ=255)                            aGCATCCAGACACAGAAGGAAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAA‑GATAACGACTATTTTTCTCATTTTGCa                                                                                                              <  1:226629/149‑1 (MQ=255)                              cATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCATTCGCGAA‑A‑AAA‑GATAACGACTATTTTTCTCATTTTGCAGt                                                                                                            <  1:121951/149‑1 (MQ=255)                               aTCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAAAAGGCCGGATTTTCTGGTTTCCAATCGCGAA‑A‑AAA‑GATAACGACTCTTTTTCTCATTTTGCatag                                                                                                           >  2:21903/1‑146 (MQ=255)                                       acaGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTg                                                                                                   >  1:746485/1‑149 (MQ=255)                                         aGAAGGCAAGAAGTAGACAACTGGCTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑AAA‑AAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGtt                                                                                                 >  1:331872/1‑149 (MQ=255)                                         aGAACGCAAGAAGTAGACAACTGACTTATCACCAGAGCTGTCTTCGATCAATATGTTTTCCTTTATTTTCCCAGACGGCCGCTTTTTCTGGTTTCCAGTCGCGAA‑A‑AAA‑GATCACGACTATTTTTCTCATTTTGCAGTGCCATATTGtt                                                                                                 <  2:507421/149‑1 (MQ=255)                                            tcgCAAAAAGTACACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGACGCGAA‑A‑AAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCt                                                                                              <  2:534670/147‑1 (MQ=255)                                                 agaagTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAA‑GATAACGACTATTTTTATCATTTTGCAGTGCCATATTGTTCCTCACAt                                                                                         >  1:646326/1‑149 (MQ=255)                                                       aGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAA‑GATAACGACTATTTTTATCATTTTGCAGTGCCATATTGTTCCTCACATGcaaac                                                                                   >  2:515730/1‑149 (MQ=255)                                                           aaCTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTg                                                                               <  1:566520/149‑1 (MQ=255)                                                           aaCTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTg                                                                               >  1:284324/1‑149 (MQ=255)                                                                  tgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTGTGGTTTCCAGTCGCG‑AAA‑AAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCCTATTGTTCCTCACATTCAAACATTGGTAATGa                                                                        >  1:729594/1‑149 (MQ=255)                                                                  tgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTTTTCCTCACATGCACACATTGTTAATGa                                                                        >  1:450815/1‑149 (MQ=255)                                                                         cAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAg                                                                 >  1:462564/1‑149 (MQ=255)                                                                          agagATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATCCACACATTGTTAATGAAAAAAAGa                                                                >  2:278984/1‑149 (MQ=255)                                                                                   ttcGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAA‑GATAACGCCTATTTTTCTCCTTTTGCAGTGCCATATTGTTCGTCCCATGCACTCTTTGGTAATGAAAAAAAGACACAACACg                                                       >  2:444463/1‑149 (MQ=255)                                                                                    tcGAGAAATATGTTTCCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTGCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGa                                                      <  1:680287/149‑1 (MQ=255)                                                                                      gAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑AAA‑AAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATGGGTAATGACACAAAGACAAAACACGAgg                                                    >  1:68033/1‑149 (MQ=255)                                                                                          aaTATGTTTTCCTTTATTCTCCCAGAAGGCGGGATTTTCTAGTTTCCAGTCGCGAA‑A‑AAA‑GATAACGACTCTTTTTCTCATTTTGCAGAGCCACATTGTTCCCCACATGCACCCATAGGTAATCAAAAAAAGACAAAACACGAGCTAAg                                                >  2:580146/1‑149 (MQ=255)                                                                                            tatGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTGTGGTTTCCAGTCGCG‑A‑A‑AAATGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCGCACATGCACACATTGGTAATGAAAAAAAACCAAAACACGAGGTAAGgc                                              >  1:489221/1‑149 (MQ=255)                                                                                                           tttCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCaa                                          <  2:323833/138‑1 (MQ=255)                                                                                                           tttCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCaa                                          >  1:323833/1‑138 (MQ=255)                                                                                                            ttCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑AAA‑AAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGttatt                              <  1:624271/149‑1 (MQ=255)                                                                                                                cAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACaa                                                             >  2:207875/1‑114 (MQ=255)                                                                                                                cAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACaa                                                             <  1:207875/114‑1 (MQ=255)                                                                                                                  gAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAA‑GATAACGACTATTTTTTTTTTTTTTTAGTGCCATATTGTTCCTTACATGTACACATTGGTAATGAAAAAAAAACAAAATAGGTTGTACGTCGCAATAAGAAGTTATTAGAAtt                        >  2:324366/1‑149 (MQ=255)                                                                                                                    cggCCGGAGTTTCTCGATTCAAGACGAGAA‑A‑AAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATGGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTaa                      <  2:451608/148‑1 (MQ=255)                                                                                                                     ggCGGGATTTTCGGGTTGCAAGTCGCGAA‑A‑AAA‑GATAACAACTATTTTTCTCATTTTGAAGTGCCATATTGTTCCTCACATGCAAACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAg                     <  2:203282/149‑1 (MQ=255)                                                                                                                       ccGGATTTTCGGGTTTCCAGTCGCGAA‑A‑AAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGa                   <  1:50586/149‑1 (MQ=255)                                                                                                                                        cAGTCGCG‑AAA‑AAA‑GATAACGACTATTTTTTTTATTTTTCTTTGCCATATTGTTCCTCACATGAACACCTTGGTAATGAAAAAAAGACAAAACACGACGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATAAATTGAGTGAAATGc  >  2:233588/1‑149 (MQ=255)                                                                                                                                                |                                                                                                                                                TTGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑C‑A‑AAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGC  >  NC_000913_3_vch_tpiA/1543879‑1544161

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: ‑