Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	904,961	0	T	G	40.0%	19.9 / 10.7	25	C17G (TGT→GGT)	amiD	N‑acetylmuramoyl‑L‑alanine amidase D
Reads supporting (aligned to +/- strand):  ref base T (3/12);  new base G (10/0);  total (13/12)
Fisher's exact test for biased strand distribution p-value = 1.08e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

CGTTGGCGGACGTTCCGGTGCGTATGAAAAAGAACTGCGTAAAGCACGGGAGATCGCCTTTGAGGAATTAGGCTCCCAGGCGCGGGCGCTGGGGGCCGATGCCGTCGTCGGTATTGATATCGACTACGAAACGGTCGGGCAAAACGGCAGTATGCTGATGGTTAGCGTCAGCGGTACGGCGGTGAAAACGCGTCGATGAGAAGATTCTTCTGGCTGGTCGCTGCCGCTCTGTTATTGGCAGGGTGTGCAGGCGAAAAAGGCATTGTCGAGAAAGAGGGATATCAG‑CTTGATACCCGACGCCAGGCGCAGGCGGCGTATCCGCGCATTAAAGTGCTGGTGATCCACTACACCGCAGATGATTTTGATAGCTCGCTGGCGACACTGACCGATAAGCAGGTCAGCTCGCATTATCTGGTCCCTGCGGTACCACCGCGATACAACGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAAGAACTGG  >  NC_000913/904718‑905201                                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                                  cGTTGGCGGACGTTCCGGTGCGTATGAAAAAGAACTGCGTAAAGCACGGGAGATCGCCTTTGAGGAATTAGGCTCCCAGGCGCGGGCGCTGGGGGCCGATGCCGTCGTCGGTATTGATATCGACTACGAAACGGTCGGGCAAAACGGCAGTATGCTGATGGTTAGCGTCAGCGGTACGGCGGGGAAAACGCGTCGGTGGGGAGAATCTTCTGGCTGGGCGCCTCCGCCCTTTTATTTGCAGGgtggggagg                                                                                                                                                                                                                                            >  2:13637/1‑245 (MQ=255)            gTTCCGGTGCGTATGAAAAAGAACTGCGTAAAGCACGGGAGATCGCCTTTGAGGAATTAGGCTCCCAGGCGCGGGCGCTGGGGGCCGATGCCGTCGTCGGTATTGATATCGACTACGAAACGGTCGGGCAAAACGGCAGTATGCTGATGGTTAGCGTCAGCGGTACGGCGGTGAAAAAGCGTCGATGAGGAGATTCTTCTGGCTGGTCGCTGCCGCTCTGTTATTGGGAGGGGGTGCCGGGGAAAAAGGcc                                                                                                                                                                                                                                 >  1:313847/1‑250 (MQ=255)             ttCCGGTGCGTATGAAAAAGAACTGCGTAAAGCACGGGAGATCGCCTTTGAGGAATTAGGCTCCCAGGCGCGGGCGCTGGGGGCCGATGCCGTCGTCGGTATTGATATCGACTACGAAACGGTCGGGCAAAACGGCAGTATGCTGATGGTTAGCGTCAGCGGTACGGCGGTGAAAACGCGTCGATGAGAAGATTCTTATGGCTGGTCGCTGCCGCTCTGTTATTGGGAGGGGGTGGAGGCGGAAAAGGCAt                                                                                                                                                                                                                                >  1:305978/1‑251 (MQ=255)                  gTGCGTATGAAAAAGAACTGCGTAAAGCACGGGAGATCGCCTTTGAGGAATTAGGCTCCCAGGCGCGGGCGCTGGGGGCCGATGCCGTCGTCGGTATTGATATCGACTACGAAACGGTCGGGCAAAACGGCAGTATGCTGATGGTTAGCGTCAGCGGTACGGCGGTGAAAAAGCGTCGATGAGAAGATTTTTCTTGCTGGGCGCTGCCGCTCTGTTATTGGCAGGGGGGGGCGGGGAAAAAAGCATTGTCg                                                                                                                                                                                                                           >  2:204389/1‑251 (MQ=255)                                         aaaGCACGGGAGATCGCCTTTGAGGAATTAGGCTCCCAGGCGCGGGCGCTGGGGGCCGATGCCGTCGTCGGTATTGATATCGACTACGAAACGGTCGGGCAAAACGGCAGTATGCTGATGGTTAGCGTCAGCGGTACGGCGGTGAAAACGCGTCGATGAGAAGATTCTTCTGGCTGGTCGCTGCCGCTCTGTTATTGGCAGGGTGTGCAGGCGAAAAAGGCATTGTCGAGAAAGAGGGATATCAG‑CTTGa                                                                                                                                                                                                    <  2:249982/250‑1 (MQ=255)                                              aCGGGAGATCGCCTTTGAGGAATTAGGCTCCCAGGCGCGGGCGCTGGGGGCCGATGCCGTCGTCGGTATTGATATCGACTACGAAACGGTCGGGCAAAACGGAAGTATGCTGATGGTTAGCGTCAGCGGTACGGCGGTGAAAAAGCGTCGATGAGAAGATTCTTCTGGGTGGTCGCTGCCGCTCTGTTATTGGCAGGGGGTGCAGGCGGAAAAGGCATTGGCGGGGAAGAGGGATATCAG‑CTTGATAcccc                                                                                                                                                                                              >  1:211263/1‑250 (MQ=255)                                                                            ccAGGCGCGGGCGCTGGGGGCCGATGCCGTCGTCGGTATTGATATCGACTACGAAACGGTCGGGCAAAACGGCAGTATGCTGATGGTTAGCGTCAGCGGTACGGCGGTGAAAACGCGTCGGTGGGAAGATTTTTCTGGCTGGTCGCCGCCGCTCTGTTATTGGCAGGGGGTGGAGGCGAAAAAAGCATTGTGGGGAAAGAGGGGAATCAAACTT‑ATACCCGACGCCAGGCGCCGggggcgggtccccgcac                                                                                                                                                                >  2:49899/1‑240 (MQ=255)                                                                                  gcgGGCGCTGGGGGCAGATGCCGTCGTCGGTATTGATATCGACTACGAAACGGTCGGGCAAAACGGCAGTATGCTGATGGTTAGCGTCAGCGGTACGGCGGTGAAAACGCGTCGATGAGAAGATTCTTCTGGCTGGTCGCTGCCGCTCTGTTATTGGCAGGGTGTGCAGGCGAAAAAGGCATTGTCGAGAAAGAGGGATATCAG‑CTTGATACCCGACGCCAGGCGCAGGCGGCGTATCCGCGCATTAAAGt                                                                                                                                                          <  2:174752/251‑1 (MQ=255)                                                                                       cgcTGGGGGCCGATGCCGTCGTCGGTATTGATATCGACTCAGAAACCGTCGGGCACAACGGCAGTATGCTGATGGTTAGCGTCAGCGGTACGGCGGTGAAAACGCGTCCATGAGAAGATTCTTCTGGCTGGTCGCTGCCGCTCTGTTATTGGCAGGGGGTGCAGGCGGAAAAGGCATTGTCGAGAAAGAGGGATATCAG‑CTTGATACCCCACGCCACGCGCAGGCGGCGTATTCGCCCCTTAAAGTGCTgg                                                                                                                                                     >  1:31608/1‑251 (MQ=255)                                                                                           gggggCCGATGCCGTCGTCGGTATTGATATCGACTACGAAACGGTCGGGCAAAACGGCAGTATGCTGATGGTTAGCGTCAGCGGTACGGCGGTGAAAACGCGTCGATGAGAAGATTCTTCTGGCTGGTCGCTGCCGCTCTGTTATTGGCAGGGTGTGCAGGCGAAAAAGGCATTGTCGAGAAAGAGGGATATCAG‑CTTGATACCCGACGCCAGGCGCAGGCGGCGTATCCGCGCATTAAAGTGCTGGTGa                                                                                                                                                  <  1:204886/250‑1 (MQ=255)                                                                                                     gCCGTCGTCGGTATTGATATCGACTACGAAACGGTCGGGCAAAACGGCAGTATGCTGATGGTTAGCGTCAGCGGTACGGCGGTGAAAACGCGTCGATGAGAAGATTCTTCTGGCTGGTCGCTGCCGCTCTGTTATTGGCAGGGTGTGCAGGCGAAAAAGGCATTGTCGAGAAAGAGGGATATCAG‑CTTGATACCCGACGCCAGGCGCAGGCGGCGTATCCGCGCATTAAAGTGCTGGTGATCCACTacac                                                                                                                                        <  2:144741/250‑1 (MQ=255)                                                                                                     gCCGTCGTCGGTATTGATATCGACTACGAAACGGTCGGGCAAAACGGCAGTATGCTGATGGTTAGCGTCAGCGGTACGGCGGTGAAAACGCGTCGATGAGAAGATTCTTCGGGCTGGTCGCTGCCGCTCTGTTATTGGCAGGGTGTGCAGGCGAAAAAGGCATTGTCGAGAAAGAGGGATATCAG‑CTTGATACCCGACGCCAGGCGCAGGCGGCGTATCCGCGCATTAAAGTGCTGGTGATCCACTacac                                                                                                                                        <  2:4977/250‑1 (MQ=255)                                                                                                                                   aCGGTCGGGCAAAACGGCAGTATGCTGATGGTTAGCGTCAGCGGTACGGCGGTGAAAACGCGTCGATGAGAAGATTCTTCTGGCTGGTCGCTGCCGCTCTGTTATTGGCAGGGTGTGCAGGCGAAAAAGGCATTGTCGAGAAAGAGGGATATCAG‑CTTGATACCCGACGCCAGGTGCAGGCGGCGTATCCGCGCATTAAAGTGCTGGTGATCCACTACACCGCAGATGATTTTGATAGCTCGCTGGCGaca                                                                                                         <  2:152062/251‑1 (MQ=255)                                                                                                                                              aaaCGGCAGTATGCTGATGGTTAGCGTCAGCGGTACGGCGGTGAAAACGCGTCGATGAGAAGATTTTTCTGGCTGGTCGCTGCCGCTCTGTTATTGGCAGGGGGTGCCGGCGGAAAAAGCATTGTCGGGAAAGAGGGATATCAG‑CTTGTTACCCCACGCCCGGCGCCGGCGGCGGATCCGCGCATTTAAGTGCTGGTGGTCCCCTACACCGCCGATGATTTTTTTAGCTCGCTGGGGACACTGAcccaaa                                                                                               >  2:184712/1‑246 (MQ=255)                                                                                                                                                aCGGCAGTATGCTGATGGTTAGCGTCAGCGGTACGGCGGTGAAAAAGCGTCGATGAGAAGATTCTTCTGGCTGGTCGCTGCCGCTCTGTTATTTGCAGGGGGTGCAGGCGAAAAAAGCATTGTCGGGAAAAAGGGGTATCAG‑CTTTATACCCGACGCCAGGCGCAGGCGGCGGATCCGCGCATTAAAGTGCTGGGGAACCACTACACCGCCGAAGATTTTGATAGCCCGCTGGCGACACTGACCGATAAGc                                                                                            >  1:232791/1‑251 (MQ=255)                                                                                                                                                       tATGCTGATGGTTAGCGTCAGCGGTACGGCGGTGAAAAACCGTCCGTGTGAAGATTCTTCTGGCGGGGCGCCGCCGCCCTGTTATTGGCAGGGGGTTCAGGCGAAAAAGGCCATGTCGAGGCAGAAGGATATCCG‑CCTGATACCCGCCGCCAGGCGCAGGCGGGGTATCCCCGCCTTAAAAGGCTGGGGATCCCCGCAACCGCCGATGATTTTTGTAGCTCGCTTGCGACACTGACCGCTAAGCAGGTccg                                                                                     >  2:52385/1‑249 (MQ=255)                                                                                                                                                        aTGCTGATGGTTAGCGTCAGCGGTACGGCGGTGAAAACGCGTCGATGAGAAGATTCTTCTGGCTGGTCGCTGCCGCTCTGTTATTGGCAGGGTGTGCAGGCGAAAAAGGCATTGTCGAGAAAGAGGGATATCAG‑CTTGATACCCGACGCCAGGCGCAGGCGGCGTATCCGCGCATTAAAGTGCTGGTGATCCACTACACCGCAGATGATTTTGATAGCTCGCTGGCGACACTGACCGATAAGCAGGTCAGc                                                                                    <  1:49899/251‑1 (MQ=255)                                                                                                                                                              aTGGTTAGCGTCAGCGGTACGGCGGTGAAAACGCGTCGATGAGAAGATTCTTCTGGCTGGTCGCTGCCGCTCTGTTATTGGCAGGGTGTGCAGGCGAAAAAGGCATTGTCGAGAAAGAGGGATATCAG‑CTTGATACCCGACGCCAGGCGCAGGCGGCGTATCCGCGCATTAAAGTGCTGGTGATCCACTACACCGCAGATGATTTTGATAGCTCGCTGGCGACACTGACCGATAAGCAGGTCAGCTCGCAt                                                                              <  1:184712/251‑1 (MQ=255)                                                                                                                                                                     gcggcAGCGGTACGGCGGTGAAAACGCGTCGATGAGAAGATTCTTCTGGCTGGTCGCTGCCGCTCTGTTATTGGCAGGGTGTGCAGGCGAAAAAGGCATTGTCGAGAAAGAGGGATATCAG‑CTTGATACCCGACGCCAGGCGCAGGCGGCGTATCCGCGCATTAAAGTGCTGGTGATCCACTACACCGCAGATGATTTTGATAGCTCGCTGGCGACACTGACCGATAAGCAGGTCAGCTCGCATTATCTgg                                                                       <  2:313847/247‑1 (MQ=255)                                                                                                                                                                      cGTCAGCGGTACGGCGGTGAAAACGCGTCGATGAGAAGATTCTTCTGGCTGGTCGCTGCCGCTCTGTTATTGGCAGGGTGTGCAGGCGAAAAAGGCATTGTCGAGAAAGAGGGATATCAG‑CTTGATACCCGACGCCAGACGCAGGCGGCGTATCCGCGCATTAAAGTGCTGGTGATCCACTACACCGCAGATGATTTTGATAGCTCGCTGGCGACACTGACCGATAAGCAGGTCAGCTCGCATTATCTGGt                                                                      <  1:13637/251‑1 (MQ=255)                                                                                                                                                                            gggTACGGCGGTGAAAACGCGTCGATGAGAAGATTCTTCTGGCTGGTCGCTGCCGCTCTGTTATTGGCAGGGTGTGCAGGCGAAAAAGGCATTGTCGAGAAAGAGGGATATCAG‑CTTGATACCCGACGCCAGGCGCAGGCGGCGTATCCGCGCATTAAAGTGCTGGTGATCCACGACACCGCAGATGATTTTGATAGCTCGCTGGCGACACTGACCGATAAGCAGGTCAGCTCGCATTATCTGGTCCCTGc                                                                <  2:151068/250‑1 (MQ=255)                                                                                                                                                                                        gAAAACGCGTCGATGAGAAGATTCTTCTGGCTGGTCGCTGCCGCTCTGTTATTGGCAGGGTGTGCAGGCGAAAAAGGCATTGTCGAGAAAGAGGGATATCAG‑CTTGATACCCGACGCCAGGCGCAGGCGGCGTATCCGCGCATTAAAGTGCTGGTGATCCACTACACCGCAGATGATTTTGATAGCTCGCTGGCGACACTGACCGATAAGCAGGTCAGCTCGCATTATCTGGTCCCTGCGGTACCACcgcg                                                    >  1:259017/1‑251 (MQ=255)                                                                                                                                                                                                  cGATGAGAAGATTCTTCTGGCTGGTCGCTGCCGCTCTGTTATTGGCAGGGTGTGCAGGCGAAAAAGGCATTGTCGAGAAAGAGGGATATCAG‑CTTGATACCCGACGCCAGGCGCAGGCGGCGTATCCGCGCATTAAAGTGCTGGTGATCCACTACACCGCAGATGATTTTGATAGCTCGCTGGCGACACTGACCGATAAGCAGGTCAGCTCGCATTATCTGGTCCCTGCGGTACCACCGCGATACAACgg                                           <  1:204389/250‑1 (MQ=255)                                                                                                                                                                                                          agaTTCTTCTGGCTGGTCGCTGCCGCTCTGTTATTGGCAGGGTGTGCAGGCGAAAAAGGCATTGTCGAGAAAGAGGGCTATCAG‑CTTGATACCCGACGCCAGGCGCAGGCGGCGTATCCGCGCATTAAAGTGCTGGTGATCCACTACACCGCAGATGATTTTGATAGCTCGCTGGCGACACTGACCGATAAGCAGGTCAGCTCGCATTATCTGGTCCCTGCGGTACCACCGCGATACAACGGTAAACcgcg                                  >  2:208660/1‑251 (MQ=255)                                                                                                                                                                                                                        ggTCGCTGCCGCTCTGTTATTGGCAGGGTGTGCAGGCGAAAAAGGCATTGTCGAGAAAGAGGGATATCAG‑CTTGATACCCGACGCCAGGCGCAGGCGGCGTATCCGCGCATTAAAGTGCTGGTGATCCACTACACCGCAGATGATTTTGATAGCTCGCTGGCGACACTGACCGATAAGCAGGTCAGCTCGCATTATCTGGTCCCTGCGGTACCACCGCGATACAACGGTAAACCGCGCATCTGGCAACTgg                    >  2:270236/1‑251 (MQ=255)                                                                                                                                                                                                                                          aTTGGCAGGGGGTGCAGGCGGAAAAGGCATTGTCGAGAAAGAGGGGTATCAG‑CTTGATACCCGACGCCAGGCGCAGGCGGCGTATCCGCGCATTAAAGAGGTGGTGCTCCACTACACCGCAGATGATTTTGATAGCTCGCTGGCGACACTGAACGGTAAGCAGGTCAGCTCGCATTATCTGGTCCCTGCGGTACCACCGCGATACAACGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAAGAActgg  >  2:279040/1‑251 (MQ=255)                                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                                  CGTTGGCGGACGTTCCGGTGCGTATGAAAAAGAACTGCGTAAAGCACGGGAGATCGCCTTTGAGGAATTAGGCTCCCAGGCGCGGGCGCTGGGGGCCGATGCCGTCGTCGGTATTGATATCGACTACGAAACGGTCGGGCAAAACGGCAGTATGCTGATGGTTAGCGTCAGCGGTACGGCGGTGAAAACGCGTCGATGAGAAGATTCTTCTGGCTGGTCGCTGCCGCTCTGTTATTGGCAGGGTGTGCAGGCGAAAAAGGCATTGTCGAGAAAGAGGGATATCAG‑CTTGATACCCGACGCCAGGCGCAGGCGGCGTATCCGCGCATTAAAGTGCTGGTGATCCACTACACCGCAGATGATTTTGATAGCTCGCTGGCGACACTGACCGATAAGCAGGTCAGCTCGCATTATCTGGTCCCTGCGGTACCACCGCGATACAACGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAAGAACTGG  >  NC_000913/904718‑905201

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑