Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,356,201	0	T	G	55.0%	6.5 / 16.0	20	T304P (ACC→CCC)	sapA	antimicrobial peptide transport ABC transporter periplasmic binding protein
Reads supporting (aligned to +/- strand):  ref base T (4/5);  new base G (11/0);  total (15/5)
Fisher's exact test for biased strand distribution p-value = 8.13e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.41e-01

TCATAGGCCCACGAGGCGCGCGGTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGTGTTAAATGCCAGATAGGCGACGTT‑CATCCCAGGACGCAGCGTTAAACGCAAGCGCGGGTCGTCACGCAAAATGGATAGCTGGCTGGCAGCAGGCCAGGCCAGAACGTCGCATTCCCCGGTCAGGAGTTTCGACAGACGTCCGGTGCCGCC  >  NC_000913/1356059‑1356351                                                                                                                                               |                                                                                                                                                        tCATAGGCCCACGAGGCGCGCGGTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGTGTTAAATg                                                                                                                                                 >  2:714787/1‑151 (MQ=255) tCATAGGCCCACGAGGCGCGCGGTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGTGTTAAATg                                                                                                                                                 <  1:668831/151‑1 (MQ=255)      ggCCCACGAGGCGCGCGGTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGGGTTAAATGCCAGa                                                                                                                                            >  2:420743/1‑151 (MQ=255)            cGAGGCGCGCGGTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGTGTTAAATGCCAGATAGGCg                                                                                                                                      <  2:221752/151‑1 (MQ=255)                   cgcgGTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGTGTTAAATGCCAGATAGGCGACGTT‑c                                                                                                                               <  2:110892/150‑1 (MQ=255)                       gTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGGGGTAAATGGCAGATAGGCGACGTT‑TATcc                                                                                                                           >  1:518411/1‑150 (MQ=255)                                      ccgTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGTGTTAAATGCCAGATAGGCGACGTT‑CATCCCAGGACGCAGCGTTaa                                                                                                           >  2:334504/1‑151 (MQ=255)                                                  tACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGGGGTAAATGCCAGATAGGGGACGTT‑CATCCCAGGACGCAGCGTTAAACGCAAGCGCgg                                                                                               >  2:409167/1‑151 (MQ=255)                                                      ataataGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGTGTTAAATGCCAGATAGGCGACGTT‑CATCCCAGGACGCAGCGTTAAACGCAAGCGCGGggcg                                                                                           >  2:421707/1‑151 (MQ=255)                                                        aataGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGGGTTAAATTCCAGATAGGCGACGTT‑CATCCCAGGACGCAGCGGTTAACGCAAGCGCGGggcgg                                                                                          >  2:424249/1‑149 (MQ=255)                                                          taGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTTGGGGGGTTGAAAACACGAAAGGGGCGGTTCCACCCCAGG‑CGCAGCGGTAAAAACAAACGCGGggcggcc                                                                                        >  1:372920/1‑147 (MQ=255)                                                          taGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGGGGTAAATGCCAGATAGGCGACGTT‑CATCCCAGGGCGCAGCGTTAAACGCAAGCGCGGGGCGGCa                                                                                        >  2:329452/1‑150 (MQ=255)                                                                gATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTTGCGGGGTTTAAAGCCAGATAGGCGGCGTT‑CATCCCCGGACGCAGCGTTAAAAGCAAGCGCGGGGCGGCAAGCaaaa                                                                                 >  2:627685/1‑151 (MQ=255)                                                                gATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGTGTTAAATGCCAGATAGGCGACGTT‑CATCCCAGGACGCAGCGTTAAACGCAAGCGCGGGTCGTCACGCaaaa                                                                                 >  2:223566/1‑151 (MQ=255)                                                                    gCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGGGTTAAATGCCAGATAGGCGACGTT‑CATCCCAGGACGCAGCGGTAAACGCAAACGCGGGGCGTCACGCAAAATGGa                                                                             >  2:736146/1‑151 (MQ=255)                                                                    gCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGGGGTAAATGCCCGATAGGCGACGTT‑CATCCCCGGACGCAGCGTTAAACGCAAGCGCGGGGCGTCACGCAAAATGGa                                                                             >  1:280868/1‑151 (MQ=255)                                                                                ggTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGGGTTAAATGCCAGATAAGCGACGTT‑CATCCCCGGACGCAGCGTTAAACGCAAGCGCGGGTCGGCACGCAAAATGGATAGctggctgg                                                                  >  2:475964/1‑150 (MQ=255)                                                                                ggTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGGGGTAAATGCCCGATAGGCGCCGTT‑CATCCCCGGGCGCAGCGGTAAACGCAAGCGCGGGTCGTCACGCAAAAAGGATAGctggctggg                                                                 >  1:465430/1‑150 (MQ=255)                                                                                                             cGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGTGTTAAATGCCAGATAGGCGACGTT‑CATCCCAGGACGCAGCGTTAAACGCAAGCGCGGGTCGTCACGCAAAATGGATAGCTGGCTGGCAGCAGGCCAGGCCAGAACGTCGCATTccc                                    <  1:595839/151‑1 (MQ=255)                                                                                                                    caggtttattTAGCGGCGGTTTGGCGGTTTGAAATGCCAGATAGGCGACGTT‑CATCCCAGGACGTAGCGTTAAACGCACGCGCGGTTCGTCTCGCAAATTGGATAGCTGGCTGACAGCATGCCAGGTTAGAACTTCGCATTCCCCGGt                                <  1:302805/143‑1 (MQ=255)                                                                                                                                               tgtTAAATGCCAGATAGGCGACGTT‑CATCCCAGGACGCAGCGTTAAACGCAAGCGCGGGTCGTCACGCAAAATGGATAGCTGGCTGGCAGCAGGCCAGGCCAGAACGTCGCATTCCCCGGTCAGGAGTTTCGACAGACGTCCGGTgccgcc  <  1:646633/151‑1 (MQ=255)                                                                                                                                               |                                                                                                                                                        TCATAGGCCCACGAGGCGCGCGGTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGTGTTAAATGCCAGATAGGCGACGTT‑CATCCCAGGACGCAGCGTTAAACGCAAGCGCGGGTCGTCACGCAAAATGGATAGCTGGCTGGCAGCAGGCCAGGCCAGAACGTCGCATTCCCCGGTCAGGAGTTTCGACAGACGTCCGGTGCCGCC  >  NC_000913/1356059‑1356351

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑