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	67.5%	88.9 / 43.6	40	coding (40/1389 nt)	narU	nitrate/nitrite transporter
Reads supporting (aligned to +/- strand):  ref base . (11/2);  new base A (15/12);  total (26/14)
Fisher's exact test for biased strand distribution p-value = 8.97e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.76e-01
Rejected as consensus: Frequency below/above cutoff threshold.

ATTTTATTGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAG‑TCGCG‑C‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGT  >  NC_000913_3_vch_tpiA/1543873‑1544154                                                                                                                                                       |                                                                                                                                        aTTTTATTGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAG‑Tcgcg                                                                                                                                          >  2:703113/1‑149 (MQ=255)          agaTTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGCACGGATTTTTTGTTTTCCAG‑TCGCG‑A‑aaa‑aagaa                                                                                                                              >  2:750587/1‑145 (MQ=255)           gaTTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAG‑TCGCG‑A‑aaa‑aagata                                                                                                                             >  1:483844/1‑144 (MQ=255)            aTTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAG‑TCGCGAA‑AAA‑AGATaa                                                                                                                             <  1:442864/149‑1 (MQ=255)             ttAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAG‑TCGCGAA‑AAA‑AGATAAc                                                                                                                            <  1:703113/149‑1 (MQ=255)                  ggTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAG‑TCGCGAA‑AAA‑AGATAACGACTa                                                                                                                       <  1:59443/149‑1 (MQ=255)                  ggTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAG‑TCGCG‑AAAAA‑AGATAACGACTa                                                                                                                       <  1:106574/149‑1 (MQ=255)                   gTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGAGTTCTTCTAGCAATATGTTTTCCTTTATTTTCCAAGAAGGCCGGATTTGCTGGATCCGAGCACCTA‑C‑AAA‑AGATAACGACTAt                                                                                                                      >  2:234595/1‑149 (MQ=255)                       cTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAG‑TCGCGAA‑AAA‑AGATAACGACTAttttt                                                                                                                  >  1:455611/1‑149 (MQ=255)                          cgcTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAG‑TCGCGAA‑AAA‑AGATAACGACTATTTTtctc                                                                                                               >  2:418368/1‑149 (MQ=255)                           gcTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAG‑TCGCG‑AAAAA‑AGATAACGACTATTTTTCTCa                                                                                                              >  1:399472/1‑149 (MQ=255)                                     aTCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAG‑TCGCG‑AAAAA‑AGATAACGACTATTTTTCTCATTTTGCAGTg                                                                                                    >  1:398943/1‑149 (MQ=255)                                     aTCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCAGGATTTTCTGGTTTCCAG‑TCGCGAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTg                                                                                                    <  2:534282/149‑1 (MQ=255)                                         aGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGCTTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCCG‑TCGCGAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTTccct                                                                                                >  2:117016/1‑147 (MQ=255)                                               aGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAG‑TCGCGAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGtt                                                                                          >  1:695039/1‑149 (MQ=255)                                                    gCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAG‑TCGCGAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTca                                                                                     <  1:418368/149‑1 (MQ=255)                                                      aagaagTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAG‑TCGCGAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGc                                                                                                   <  1:623744/133‑1 (MQ=255)                                                      aagaagTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAG‑TCGCGAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGc                                                                                                   >  2:623744/1‑133 (MQ=255)                                                                 aaCTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAG‑TCGCGAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTg                                                                        >  2:579254/1‑149 (MQ=255)                                                                    tgactgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTGCCAG‑TCGCGAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATACACACCTTGCTa                                                                     >  2:326232/1‑149 (MQ=255)                                                                      actgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAG‑TCGCGAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAAt                                                                   <  2:304244/149‑1 (MQ=255)                                                                      actgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAG‑TCGCGAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAAt                                                                   >  2:401280/1‑149 (MQ=255)                                                                      actgaTATCCAGAGATTTCTTCGAGCAAGATTTTTTCATTTATTTTCGCAGAAGGCCGGATTTTCTGGTTTCCAG‑TCGCG‑A‑AAATAGATAGCTACTATTTTTCTCATTTTGCAGTGTCATTTTGTTCCTCACCTGCACACAGTGGTAAt                                                                   >  2:285152/1‑149 (MQ=255)                                                                        tgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAG‑TCGCG‑AAAAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGa                                                                 >  1:204589/1‑149 (MQ=255)                                                                          atatCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAG‑TCGCGAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATCGTTCCTAACATGCCCACATTGGTAATGaaa                                                               >  2:433603/1‑149 (MQ=255)                                                                              ccAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAG‑TCGCG‑AAAAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGaaaaaaa                                                           >  1:555110/1‑149 (MQ=255)                                                                                agagATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAG‑TCGCG‑AAAAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGa                                                         >  2:701648/1‑149 (MQ=255)                                                                                        cttcGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAG‑TCGCGAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACAt                                                                                  <  1:568814/116‑1 (MQ=255)                                                                                        cttcGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAG‑TCGCG‑AAAAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACAt                                                                                  >  2:568814/1‑116 (MQ=255)                                                                                           cGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAG‑TCGCGAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAg                                              <  1:701648/149‑1 (MQ=255)                                                                                             aGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAG‑TCGCGAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACAATGGTAATGAAAAAAAGACAAAACACGAgat                                            >  2:66607/1‑147 (MQ=255)                                                                                                aaTATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAG‑TCGCGAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAg                                         >  1:129409/1‑149 (MQ=255)                                                                                                     gTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAG‑TCGCGAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTACTGAAAAAAAGACAAAACACGAGGTAAGGCGCa                                    >  2:467053/1‑149 (MQ=255)                                                                                                     gTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAG‑TCGCG‑AAAAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTGATGAAAAAAAGACAAAAGACGAGGTAAGGCGCa                                    >  2:467033/1‑149 (MQ=255)                                                                                                      ttttCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAG‑TCGCGAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCaa                                   >  1:335038/1‑149 (MQ=255)                                                                                                          ccTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAG‑TCGCGAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGc                               <  1:139704/149‑1 (MQ=255)                                                                                                            tttATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAG‑TCGCGAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACaaaa                                                    <  2:65432/126‑1 (MQ=255)                                                                                                            tttATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAG‑TCGCGAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACaaaa                                                    >  1:65432/1‑126 (MQ=255)                                                                                                            tttATTTCTCCTGCAGGCCGGATTTTCTGGTTTCCAG‑TCGCGAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCAGATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGTGCAATAGCCa                             <  2:454604/149‑1 (MQ=255)                                                                                                              tATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAG‑TCGCG‑AAAAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGt                           <  1:401280/149‑1 (MQ=255)                                                                                                                                       tGGTTTCCAG‑TCGCGAA‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGt  >  1:71030/1‑149 (MQ=255)                                                                                                                                                       |                                                                                                                                        ATTTTATTGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAG‑TCGCG‑C‑AAA‑AGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGT  >  NC_000913_3_vch_tpiA/1543873‑1544154

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑