Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,875,532	0	A	T	33.3%	23.8 / 14.9	27	H32L (CAT→CTT)	yidX	putative lipoprotein YidX
Reads supporting (aligned to +/- strand):  ref base A (8/10);  new base T (9/0);  total (17/10)
Fisher's exact test for biased strand distribution p-value = 8.83e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.64e-01
Rejected as consensus: Frequency below/above cutoff threshold.

AATGCATAAAAAAATGACATGCGTCGGGCAGAAATCTGAAAAGGGATATCAGGCGCTAAACAGGAGGGAAAGAAGAGTATGCTTTCAACGGCTTAGCTACTCGTTTAAAGGATTAATCATGAAGTTGAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTC‑CCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCTCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACA‑CCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGTAGGGGAATCGCTGGATTACCTTATCACTGATGGTGCCGATGACATCGTTAAGATGCTCAATGATCCAGCACTTAACCGGCACAATATTCAGGTTGCCGATGACGCAAGATTTGTTTTAAATGCGGGGAAAAAGAAATTT  >  NC_000913/3875320‑3875773                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                   aaTGCATAAAAAAATGACATGCGTCGGGCAGAAATCTGAAAAGGGATATCAGGCGCTAAACAGGAGGGAAAGAAGAGTATGCTTTCAACGGCTTAGCTACTCGTTTAAAGGATTAATCATGAAGTTGAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTC‑CCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCTGTGGTTTGCCTTACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGt                                                                                                                                                                                                              >  1:354946/1‑251 (MQ=255)                      cGTCGGGCAGAAATCTGAAAAGGGATATCAGGCGCTAAACAGGAGGGAAAGAAGAGTATGCTTTCAACGGCTTAGCTACTCGTTTAAAGGATTAATCATGAAGTTGAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTC‑CCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAGTAGATCAGGAAAGTATCAATCGCAGTCAGAAA‑CCATCACTGGGCTAt                                                                                                                                                                                        >  1:374763/1‑251 (MQ=255)                              aGAAATCTTAAAATGGAAATAAGGCGCTAAACAGGAGGGAAAGAAGAGTATGCTTTCAAAGGCTTAGCTACTCGTTTAAAGGATTAAGCATGAAGTTGAATTTTAAGGGATTTTTTAAGGCTTCCTGTTTATTC‑CCACTGGCTCTGATGCTTTCAGGCTGTATCTCGTATGCTCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGAAATTATCAATCGCAGTCAGTCA‑CCATCACTGGGCTATCGCATGCa                                                                                                                                                                                <  2:333212/251‑1 (MQ=255)                                             gATATCAGGCGCTAAACAGGAGGGAAAGAAGAGGATGTTTTCAACGGCTTAGCTAATCGTTTAAAGGATTAATAATGAAGTTGAATTTTAAGGGATTTTTTAAGGCTTCCGGTTTATTC‑CCACTGGCGCTGAGGCTTTCAGGCTGTATCTCGTATGCTCTGGTTTCCCATACCTCAAAGGGTAGTTCAGTAAAGTATCAATCGCAGTCAGACA‑CCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGa                                                                                                                                                                 <  2:257695/251‑1 (MQ=255)                                                         caataaggaggTAAAGAATATGATGCTTTCAACGGCTTAATTACTAGGTGAAAGGATTAAACATGAAGTTGAATTTTAAGGGATTGTTTAAGACTGCCGGTAGATTCACCA‑TGGCGCTGATGCTTTCAGGCTGTATCTCGTATGTTCTGGTTTCCCATACCGCTAAGGGTAGTTCAGGAAAGTATCAATCGAAGTCAGACA‑CCATCACTGGGCTATCGCAGGCAAAAGATAGTAAGGGAACAACAGGCTAt                                                                                                                                                     <  2:49/246‑1 (MQ=255)                                                             cAGGAGGGAAAGAAGAGTATGCTTTCAACGGCTTAGCTACTCGTTTAAAGGATTAATCATGAAGTTGAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTC‑CCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACA‑CCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTATGttt                                                                                                                                                 >  1:80877/1‑251 (MQ=255)                                                                  gggAAAGAAGAGTATGCTTTCAACGGATTAGCTACTCGTTTAAAGGATTAATCATGAAGTTGAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTC‑CCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCTCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGTAAGTATCAATCGCAGTCAGACA‑CCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGt                                                                                                                                             >  2:119535/1‑250 (MQ=255)                                                                               aTGCTTTCAAAGGCTTAGCTACTTGTTTAAAGGATTAATCATGAAGGTGAAAATTAAGGGAATTTTTAAGGCTGCCGGTTTATTC‑CCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCTCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACA‑CCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGTAGGGGAATCGCTgg                                                                                                                               <  1:14564/251‑1 (MQ=255)                                                                                         cGGCTTAGCTACTCGTTTAAAGGATTAATCATGAAGTTGAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTC‑CCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCTCTCGTCTCCTTTACCGCAAAGGGTAGTTCAGGAAAGACTCAATCGCAGTCAGACA‑CCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGTAACAAAAGGCTATGTTTTTGTAGGGGAATCGCTGGATTACCTTAt                                                                                                                     >  1:2849/1‑251 (MQ=255)                                                                                                   aCTCGTGTAAAGGATTAACCATGAAGTTTAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTAATC‑CCACTGGCTCTGATGCTGTCAGGCTGTATCTCGTATGCTCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACA‑CCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGTAGGGGAATCGCTGGATTACCTTATCACTGATGGt                                                                                                           <  1:235208/251‑1 (MQ=255)                                                                                                                aTTAATCATGAAGTTGAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTC‑CCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCTCTGGTTTGCCATACCGAAAAGGGAAGTTCAGGAAAGTCTCAATCGCAGTCAGACA‑CAATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGTAGGGGAATCGCTGGCTTACCTTATCACTGATGGTGCCGATGACaacg                                                                                              >  1:50575/1‑248 (MQ=255)                                                                                                                       aTGAAGTTGAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTC‑CCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCTCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACA‑CCATCACTGGGCTATCGCAGGCAAACGATAGTAATGGAACAAAAGGCTATGTTTTTGTAGGGGAATCGCTGGATTACCTTATCACTGATGGTGCCGATGACATCGTTa                                                                                           >  2:314425/1‑247 (MQ=255)                                                                                                                         gAAGTTGAATTTTAAGGGCTTTTTTAAGGCTGCCGGTTTATTC‑CCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCTCTGGTTTCCCTTACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACA‑CCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGTAGGGGAATCGCTGGATTACCTTATCACTGATGGTGCCGATGACATCGTTAAGATGc                                                                                     >  1:353477/1‑251 (MQ=255)                                                                                                                           agttgtagtttAAGGGATTATTTAAGGGTGCCTGTTTATTC‑ACTCTGGCGATGATGATTTCAGGATGTAACTCGAATTCGCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTGAGACA‑CCATCTCTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGTAGGGGAATCGCTGGATTACCTTATCACTGATGGTGCCGATGACATCGTTAAGATGCTc                                                                                   <  2:252749/243‑1 (MQ=255)                                                                                                                                 aTTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTC‑CCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCCGTGTTTTCCCATACAGCAACGAGTAGTTCCGGAACGTCTCAATCGCAGTCCGACA‑CCATCACTGGGCTATCGCCGGCAAAAGCTAGAAATGGAACAAACGGCTATGCTTTTGTCGGGGACTCGCTGAATTACCATATCACTGATGGTGCCGCTGACATCGTTCAGCTGCTCAATGAt                                                                             >  1:253060/1‑251 (MQ=255)                                                                                                                                     tAAGGGAATTTTTAATGCTGCTGGTTTATTC‑CCACTTGCGCTTATGCTTACAAGCTGTAACTAGTATGCTCTGGTATCCCAAACCGCAAAGTGGAGTTCATGAAAGTATCAATCGCAGTCAGACA‑GCATCACTGGGCTATCGCAGGCAAAAGATAGTAATAGAACAAAAGGCTATGTTTTTGTAGGGGAATCGCTGGATTGCCTTATCACTGATGGTGCCGATGACATCTGTAAGATGCTCAATGATCCa                                                                          <  2:27142/250‑1 (MQ=255)                                                                                                                                               tttAAGGCTGCCGGTTTATTC‑CCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCTCTCTTTTGCTTTAACGCAAAGGGTAGTTAAGGAAAGTATCAATCGCAGTCAGACA‑CCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGTAGGGGAATCGCTGGATTACCTTATCACTGATGGTGCCGATGACATCGTTAAGATGCTCAATGATCCAGCACTTAACCg                                                               >  1:344634/1‑251 (MQ=255)                                                                                                                                                 tAAGGCTGCCGGTTTATTC‑CCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCCGTCTTCTGCTTGAAAGAAAAGGATAGATCCAGAAAGTATCAATAGCAGTCA‑ACAACCATCACTAGGCTATCGCAGGCAACAGATAGCAATGGAACAAAAGGCTAAGTGTTTGTAGGGGTATAGCTGGATTACCTTATCACTGTTGGTGCCGATGACATAGTTAAGATGCTCAAGGTTCCAGCACTTAACCgg                                                              >  1:228803/1‑250 (MQ=255)                                                                                                                                                 tAAGGCTGCCGGTTTATTC‑CCACTGGCGATGATGCTTTCAGGCTGTATCTCGTATGCTCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACA‑CCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGTAGGGGAATCGCTGGATTACCTTATCACTGATGGTTCCGATGACATCGTTAAGATGCTCAATGATCCAGCTCTTAACCgg                                                              <  2:345807/250‑1 (MQ=255)                                                                                                                                                    ggCTGCCGGTTTATTC‑CCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCCCTGGTTTCCCTTACAGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACA‑CAATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGTAGGGGAATCGCTGGATTACCTTATCACTGATGGTGCCGATGACATCGTTAAGATGCTCAATGATCCAGCACTTAACAGGcac                                                           >  1:164301/1‑250 (MQ=255)                                                                                                                                                       tGCCGGTTTATTC‑CCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCCCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGACAGTATCAATCGCAGTCAGACA‑CCATCACTGGGCTATCGCAGGCCAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGTAGGGGAATCGCTGGATTACCTTATCACTGATGGTGCCGATGACATCGTTAAGATGCTCAATGATGAAGCACTCAACCGGCACAat                                                        >  1:295755/1‑250 (MQ=255)                                                                                                                                                            gTTTATTC‑CCACTGGCTCTGATGTTTTCAGGCTGTATCTCTTATGCTCTGGGTTCCCATACCGCAAAGGGTAGTTCAGGAAAGTATCAAGCGCAGTCAGACA‑CCATCACTGGGCTAGCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTTTGTTTTTGTAGGGGAATCGCTGGATTACCTTATCACTGATGGTGCCGATGACATCTTTAAGATGCTCAATGATCCATCACTTATCCGGCACAATATTCAg                                                  <  2:269463/251‑1 (MQ=255)                                                                                                                                                                aTTC‑CCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCCGTCGTTTCCTTTACAAAAAAGGGAAGTTGAGGAAAGTCTCAATCGCAGTCAACCA‑CCATCACTGGGCAATCGCAGGCAACAGATAGTGATGGAACAAAAGGCTATGTTTTTGTAGGGGAATCGCTGGATTACCTTATCACTGATGGTGCCGATGACATAGTTAAAATGCTCAATGATCCAGCCCTAAACCGGCACAATATTCCGGTTg                                              >  1:347306/1‑251 (MQ=255)                                                                                                                                                                  cc‑ccACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCTCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACA‑CCATCACTGGGCTATCGAAGGCAAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGTAGGGGAATCGCTGGATTACCTTATCACTGATGGTGCCGATGACATCGTTAAGATGCTCAATGATCCAGCACTTAACCGGCACAATATTCAGGTTGcc                                            >  1:25933/2‑251 (MQ=255)                                                                                                                                                                                                    cGTATGCTCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACA‑CCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGTAGGGGAATCGCTGGATTACCTTATCACTGATGGTGCCGATGACATCGTTAAGATGCTCAATGATCCAGCACTTAACCGGCACAATAtt                                                     >  2:172285/1‑209 (MQ=255)                                                                                                                                                                                                    cGTATGCTCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACA‑CCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGTAGGGGAATCGCTGGATTACCTTATCACTGATGGTGCCGATGACATCGTTAAGATGCTCAATGATCCAGCACTTAACCGGCACAATAtt                                                     <  1:172285/209‑1 (MQ=255)                                                                                                                                                                                                             tGGTTTCCCATACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACA‑CCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGTAGGGGAATCGCTGGATTACCTTATCACTGATGGTGCCGATGACATCGTTAAGATGCTCAATGATCCAGCACTTAACCGGCACAATATTCAGGTTGCCGATGACGCAAGATTTGTTTTAAATGCGGGGAAAAAGAAAttt  >  1:207875/1‑251 (MQ=255)                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                   AATGCATAAAAAAATGACATGCGTCGGGCAGAAATCTGAAAAGGGATATCAGGCGCTAAACAGGAGGGAAAGAAGAGTATGCTTTCAACGGCTTAGCTACTCGTTTAAAGGATTAATCATGAAGTTGAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTC‑CCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCTCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACA‑CCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGTAGGGGAATCGCTGGATTACCTTATCACTGATGGTGCCGATGACATCGTTAAGATGCTCAATGATCCAGCACTTAACCGGCACAATATTCAGGTTGCCGATGACGCAAGATTTGTTTTAAATGCGGGGAAAAAGAAATTT  >  NC_000913/3875320‑3875773

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑