Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,356,201	0	T	G	61.9%	8.2 / 20.5	21	T304P (ACC→CCC)	sapA	antimicrobial peptide transport ABC transporter periplasmic binding protein
Reads supporting (aligned to +/- strand):  ref base T (1/7);  new base G (13/0);  total (14/7)
Fisher's exact test for biased strand distribution p-value = 6.88e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.81e-03

GTCATAGGCCCACGAGGCGCGCGGTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGCGTTAAACGCAAGCGCGGGTCGTCACGCAAAATGGATAGCTGGCTGGCAGCAGGCCAGGCCAGAACGTCGCATTCCCCGGTCAGGAGTTTCGACAGACGTC  >  NC_000913/1356058‑1356341                                                                                                                                                |                                                                                                                                             gTCATAGGCCCACGAGGCGCGCGGTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGGGTTaaaa                                                                                                                                       >  1:596643/1‑150 (MQ=255)             cGAGGCGCGCGGTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGTGTTAAATGCCAGATAGGCg                                                                                                                           <  1:284088/151‑1 (MQ=255)                      cgGTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGTGTTAAATGCCAGATAGGCGACGTTCAt                                                                                                                   >  1:623586/1‑150 (MQ=255)                      cgGTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGGGTTAAAAGCCAGATAGGCGACGGTCAt                                                                                                                   >  1:608955/1‑150 (MQ=255)                        gTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTTGGGGGGGTTAATGTCAGAAAGGGGAGGTTCATcc                                                                                                                 >  2:381126/1‑150 (MQ=255)                        gTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTTGCGGGGGTAAATGCCCGATAGGCGACGTTCATcc                                                                                                                 >  1:130921/1‑150 (MQ=255)                        gTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGTGTTAAATGCCAGATAGGCGACGTTCATcc                                                                                                                 <  2:439136/150‑1 (MQ=255)                        gTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGGGTTAAAAGCCAGATAGGCGGCGTTTATcc                                                                                                                 >  2:387736/1‑150 (MQ=255)                             aTAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGAc                                                                                                           <  2:440523/151‑1 (MQ=255)                             aTAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGAc                                                                                                           <  1:126520/151‑1 (MQ=255)                             aTAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGAc                                                                                                           <  1:417906/151‑1 (MQ=255)                                               gCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGGGGGGTTAAATGGCAGGTAGGCGACGGTCATCCCAGGACGCAGCGTTAAAAGCAAgg                                                                                         >  1:276355/1‑150 (MQ=255)                                                     ccATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTTGCGGGGTTAAATGGCAGAAAGGCGACGTTTATCCCAGGACGCAGCGTTAAACGCAAGCGCgggg                                                                                   >  2:335124/1‑150 (MQ=255)                                                       ataataGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGGGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGCGTTAAACGCAAGCGCGGggcg                                                                                 >  1:102271/1‑151 (MQ=255)                                                                ggATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGGGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGCGTTAAACGCAAGCGCGGGTCGTCACGCaaa                                                                        >  1:250791/1‑151 (MQ=255)                                                                       aTCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGGGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGCGTTAAACGCAAGCGCGGGGCGTCACGCCAAATGGGTa                                                                 >  1:517116/1‑151 (MQ=255)                                                                            gcgcTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGCGTTAAACGCAAGCGCGGGTCGTCACGCAAAATGGATAgc                                                               <  2:583031/148‑1 (MQ=255)                                                                                        aaTCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGGGTTAAAAGCCAGATAGGCGACGTTCCTCCCCGGACGCAGCGTTAAAAGCAAGCGCGGGGCGTCACGCAAAATGGGTAGCTGGCTGGCAGcagg                                                 >  1:581277/1‑150 (MQ=255)                                                                                            gCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTTGCGGGGGTAAATGCCAGAAAAGCGGCGGTCATCCCCGGACGCAGCGGTAAACGCAAGCGCGGGGCGTCACGCAAAATGGATAGCTGGGTGGCAGcaggcccgg                                            >  2:376964/1‑151 (MQ=255)                                                                                                          aTGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGGGTTAAATGCCAGATAGGCGGCGTTTATCCCCGGGCGCCGCGGTAAAAGCAAGCGCGGGGCGTCACGCCAAAAGGATAGAGGGCTGGCAGCAGGGCAGGGCCGGACGGCGCAt                              >  2:269546/1‑151 (MQ=255)                                                                                                                                       gTTTGGCGGTGTTAAATGCCGGATAGGCGACGTCCATCCCAGGACGCAGCGTTAAACGCAAGCGCGAGTCGTCACGCAAAAGGGATAGCTGGCTGGCAGCAGGCCAGGCCAGAACGTCGCATTCCCCGGTCAGGAGTGCCGACAGACGTc  <  2:508026/150‑1 (MQ=255)                                                                                                                                                |                                                                                                                                             GTCATAGGCCCACGAGGCGCGCGGTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGCGTTAAACGCAAGCGCGGGTCGTCACGCAAAATGGATAGCTGGCTGGCAGCAGGCCAGGCCAGAACGTCGCATTCCCCGGTCAGGAGTTTCGACAGACGTC  >  NC_000913/1356058‑1356341

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑