Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,356,201	0	T	G	60.0%	27.9 / 35.4	26	T304P (ACC→CCC)	sapA	antimicrobial peptide transport ABC transporter periplasmic binding protein
Reads supporting (aligned to +/- strand):  ref base T (0/10);  new base G (15/0);  total (16/10)
Fisher's exact test for biased strand distribution p-value = 3.06e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.14e-06

GTCATAGGCCCACGAGGCGCGCGGTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGCGTTAAACGCAAGCGCGGGTCGTCACGCAAAATGGATAGCTGGCTGGCAGCAGGCCAGGCCAGAACGTCGCATTCCCCGGTCAGGAGTTTCGACAG  >  NC_000913/1356058‑1356336                                                                                                                                                |                                                                                                                                        gTCATAGGCCCACGAGGCGCGCGGTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGGGTTaaaa                                                                                                                                  >  2:276236/1‑150 (MQ=255)    aTAGGCCCACGAGGCGCGCGGTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGTGTTAAATGcc                                                                                                                               <  2:55364/151‑1 (MQ=255)                      cgGTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGGGGTAAATGCCAGATAAGCGACGTTCAt                                                                                                              >  1:264562/1‑150 (MQ=255)                        gTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTTGCGGGGTTAAATGCCAGATAGGCGACGGTTATcc                                                                                                            >  2:352667/1‑150 (MQ=255)                        gTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTTGCGGCGGTAAATATCCGACAGGCGACGGTCAttc                                                                                                            >  2:645186/1‑148 (MQ=255)                        gTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATCAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTTGGGGGGGTAAATGCCAGATAGGCGACGTTCATcc                                                                                                            >  2:228760/1‑150 (MQ=255)                         tAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGTGTTAAATGCCAGATAGGCGACGTTCATccc                                                                                                           <  2:601922/150‑1 (MQ=255)                           aaaTAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAgg                                                                                                        <  2:584512/151‑1 (MQ=255)                                    ccgccgTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGCGt                                                                                               <  1:614894/151‑1 (MQ=255)                                          tttCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGCGTTAAAc                                                                                          <  1:201001/150‑1 (MQ=255)                                                     ccATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGGGTTAAATGCCAGATAAGCGACGGTCATCCCCGGACGCAGCGTTAAACGCAAGCGCGGgt                                                                              >  2:159732/1‑151 (MQ=255)                                                           taGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGGTTGGCGGGGGTTAAAGCCCCAGAGGGGGCGGTTTTCCCCGGAAGCAGCGTTTAAAGCCAGAGCcggggggcaa                                                                        >  1:33383/1‑144 (MQ=255)                                                                ggATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGGGTTAAATGCCAGATAGGCGACGTTCATCCCCGGACGCAGCGTTTAAAGCAAGCGCGGGTCGTCACGCaaa                                                                   >  2:622099/1‑151 (MQ=255)                                                                ggATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGGGTTAAATGCCAGATAGGCGACGGTCCTCCCCGGACGCAGCGGTAAAAGCAAACGCGGGGCGTCACGCaaa                                                                   >  2:93534/1‑151 (MQ=255)                                                                                 ggTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGGGGGGGTAAATGCCAGAAAGGGGAAGGTTATTCCAGGGCGCAGCGTTTAACGCAAGCGCGGGGGGGCACGCAAAATGGATAGgtggctggg                                                  >  1:435457/1‑150 (MQ=255)                                                                                 ggTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGGGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGCGTTAAACGCAAGCGCGGGTCGTCACGCAAAATGGATAGctggctgg                                                   >  2:577104/1‑150 (MQ=255)                                                                                         aTCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGCGTTAAACGCAAGCGCGGGTCGTCACGCAAAATGGATAGCTGGCTGGCAGcaggcc                                          <  1:251445/151‑1 (MQ=255)                                                                                                gTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGGGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGCGTTAAACGCAAGCGCGGGTCGTCACGCAAAATGGATAGCTGGCTGGCAGCAGgccaggccag                                   >  2:531350/1‑151 (MQ=255)                                                                                                gTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGATTGGGGGGGGTAAATGACAGATAGGGGGCGGTTATCCCCGGACGCAGCGGTAAAAGCAAGCGCGGGGCGTCCCGCAAAACGGATAGCTGGCTGGGAGCAGggccgggcag                                   >  1:382167/1‑151 (MQ=255)                                                                                                   ccAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGCGTTAAACGCAAGCGCGGGTCGTCACGCAAAATGGATAGCTGGCTGGCAGCAGGCCAGGCCAGAAc                                <  1:455902/151‑1 (MQ=255)                                                                                                         cATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGGGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCCGCGTTAAACGCAAGCGCGGGGCGTCACGCAAAATGGATAGCTGGCTGGCAGCAGGCCAGGCCAGAACGTCGCa                          >  2:495212/1‑151 (MQ=255)                                                                                                                       ggATTATTTAGCGGCGGTTTGGCGGGGTTTAATTCCAAATAGGGGGCCGTTATCCCCGGGCGCAGCGGTTAAAGCAAGCGCGGGGTGGCACGCCAAAAGGGTAGCTGGGTGGCCACCGGGCCGGCCAGAACGTCCCAATCCCCCGTCAggg            >  1:637086/1‑150 (MQ=255)                                                                                                                            attTAGCGGCGGTTTGGGGGGGTTAAAAGGCAGATAAGAGGAGTTTATCCCCGGGCGCAGGGGTAAACGCAAGAGCGGGTCGGCACGCAAAATGGATAGCTGGCTGGCAGCAGGGCAGGCCAGAACGCCGCAATCCCCGGTCGGGAGgtt        >  1:380575/1‑150 (MQ=255)                                                                                                                             tttAGCGGCGGTTTGGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGCGTTAAATGCAAGCGCGGGTCGTCACGCAAAATGGATAGCTGGCTGGCAGCAGGCCAGGCCAGAACGTCGCATTCCCCGGTCAGGAGTTTCg      <  2:337878/151‑1 (MQ=255)                                                                                                                               tAGCGGCGGTTTGGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGCGTTAAACGCAAGCGCGGGTCGTCACGCAAAATGGATAGCTGGCTGGCAGCAGGCCAGGCCAGAACGTCGCATTCCCCGGTCAGGAGTTTCGAc    <  2:453084/151‑1 (MQ=255)                                                                                                                                  cggcggTTTGGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGCGTTAAACGCAAGCGCGGGTCGTCACGCAAAATGGATAGCTGGCTGGCAGCAGGCCAGGCCAGAACGTCGCATTCCCCGGTCAGGAGTTTCGACAg  <  2:99030/150‑1 (MQ=255)                                                                                                                                                |                                                                                                                                        GTCATAGGCCCACGAGGCGCGCGGTAAAATAGAGGCCGCCGTTTCAGCCGTACCATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGTTTGGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGCGTTAAACGCAAGCGCGGGTCGTCACGCAAAATGGATAGCTGGCTGGCAGCAGGCCAGGCCAGAACGTCGCATTCCCCGGTCAGGAGTTTCGACAG  >  NC_000913/1356058‑1356336

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: ‑