Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,429,692	0	T	A	58.3%	10.1 / 20.7	24	L215Q (CTA→CAA)	stfR	putative prophage side tail fiber protein StfR
Reads supporting (aligned to +/- strand):  ref base T (5/5);  new base A (10/4);  total (15/9)
Fisher's exact test for biased strand distribution p-value = 4.03e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.69e-01
Rejected as consensus: Frequency below/above cutoff threshold.

GATGCTGCGGACTCAGCACGCGCAGCCAGCACGTCAGCCGGACAGGCCGCGTCGTCGGCTCAGTCAGCGTCTTCCAGCGCAGGAACGGCATCAACAAAGGCCACTGAAGCATCAAAAAGTGCTGCCGCTGCAGAGTCCTCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCACATCTGCATCCACCGCGACCACGAAGGCATCAGAAGCTGCGACCTCGGCCCGGGATGCGGCGGCCTCAAAAGAAGCGGCAAAATCATCAGAAACGAACGCATCATCAAGCGCCAGTAGTGCAGCTTCCTCGGCAACGGCGGCAGGAAATTCCGCGAAGGCGGCAAAAACGTCCGAGACGAACGCCAGGTCTTCTGAAACGGCAGCGGGACAGAGCGCCTCGGCTGC  >  NC_000913/1429487‑1429932                                                                                                                                                                                                              |                                                                                                                                                                                                                                                 natgcaactgACTCAGCACGCGCCGCCAGCACGTCCGCCGGACAGGCTGCATCGTCAGATCAGGAGGCGTCCTCCGGCGCAGCAGCGGCATCAGCAAAGGCAACTGAAGCGGAAAAAAGTGCCGCAGCCGCAGAGTCCTCAAAAAACGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGCCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGCCTGCCTCCACCGCGGCCACGa                                                                                                                                                                                                            >  1:41801/10‑244 (MQ=255)                         gtcagcACGTCAGCCGGACAGGCCGCGTCGTCGGCTCAGTCAGCGTCTTCCAGCGCAGGAACGGCTTCAACAAAGGCCACTGAAGCATCAAAAAGTGCTGCCGCTGCAGAGTCCTCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCACATCTGCATCCACCGCGACCACGACGGCATCAGCAGCTGCGACCTCGGCCCggc                                                                                                                                                                              >  1:167813/3‑249 (MQ=255)                                     gCCGGACAGGCCGCGTCGGCGGCTCAGTCAGCGTCTTCAAGCGCAGGAACGGCATCAAAAAAGGCCACTGAAGCGTCAAAAAGTGCTGCCGCTGCTGAGTCCTCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTAAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCACATCTGCATCCACCGCGACCACGAAGGCATCAGAAGCTGCGACCTCGGCACGGGATGCGGCGGCCTc                                                                                                                                                                 >  1:164482/1‑251 (MQ=255)                                                cgcgTCGTCGGCTCAGTCAGCGTCTTCCAGCGCAGGAACGGCATCAACAAAGGCCACTGAAGCATCAAAAAGTGCTGCCGCTGCAGAGTCCTCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCACAGCTGCATCCACCGCGACCACGAAGGCATCAGAAGCTGCGACCTCGGCCCGGGATGCGGCGGCCTCAAAAGAAGCgn                                                                                                                                                      <  1:39427/251‑2 (MQ=255)                                                                   gCGTCCTCCGGCGCAGAAGCGGCATCAGCAAAGGCCACTGAAGCGGAAAAACGTGACGCAGCCGCAGAGTCCTCAAAAAACGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCCGCGTCACAACACTCAGTCGCCACGTCTGCCTCCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCTCAAAAGAGGCAGCAACATCATCAGAaacga                                                                                                                                    >  1:220073/1‑250 (MQ=255)                                                                          ccAGCGCAGGAACGGCATCACCAAAGGCCACTGAAGCATCAAAAAGTGCTGCCGCTGCAGAGTCATCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCACATCTGCATCCACCGCGACCACGAAGGCATCAGAAGCTGCGACCTCGGCCCTGGATGCGGCGGCCTCAAAAGAAGCGGCAAAATCATCAGAAACGAACGcatc                                                                                                                             <  1:153280/250‑1 (MQ=255)                                                                                  gaagcGGCATCAGCAAAGGCCCCTGAAGCGGAAAAAAGTGCCGCAGCCGCAGAGTCCTCAAAAAACGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCTCCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCTCAAAAGAGGCAGCAAAATCATCAGAAACGACCGCATCATCAAgtgc                                                                                                                    >  1:171214/5‑248 (MQ=255)                                                                                                     ccACTGAAGCGGAAAAAAGTGCCGCAGCCGCAGAGTCCTCAAAAAACGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCTCCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCTCAAAAGAGGCAGCAAAATCATCAGAAACGAACGCATCATCAAGTGCCGGTCGTGCAGCTTCCTCg                                                                                                 >  1:114493/1‑251 (MQ=255)                                                                                                      cACTGAAGCATCAAAAAGTGCTGCCGCTGCAGAGTCCTCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCACATCTGCATCCAc                                                                                                                                                                                                                       <  1:71496/132‑1 (MQ=255)                                                                                                        ctgaagcggaaaaaaGTGCCGCAGCCGCAGAGTCCTCAAAAAACGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCTCCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCTCAAAAGAGGCAGCAAAATCATCAGAAACGAACGCATCATCAAGTGCCGGTCGTGCAGCTTCCTCGGc                                                                                               >  1:58033/11‑250 (MQ=255)                                                                                                                  aaaaaGTGCCGCAGCCGCAGAGTCCTCAAAAAACGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCTCCACcgcggn                                                                                                                                                                                                                 <  1:52435/126‑3 (MQ=255)                                                                                                                           cgcagccgCAGAGTCCTCAAAAAACGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCTCCACCGCGGCCACGaaag                                                                                                                                                                                                         >  1:10665/8‑123 (MQ=255)                                                                                                                               gCTGCAGAGTCCTCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCACATCTGCATCCACCGCGACCACGAAGGCATCAGAAGCTGCGACCTCGGCCCGGGATGCGGCGGCCTCAAAAGAAGCGGCAAAATCATCAGAAACGAACGCATCATCAAGCGCCAGTAGTGCAGCTTc                                                                                                     >  1:49396/1‑221 (MQ=255)                                                                                                                                                 aacgcgGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCTCCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCTCAAAAGAGGCAGCAAAATCATCAGAAACGAACGCATCATCAAGTGCCGGTCGTGCAGCTTCCTCGGCAACGGCGGCAGAAAATTCTGCCAGGGCGGCAAAAACGTCCga                                                     <  1:13941/249‑1 (MQ=255)                                                                                                                                                    gcggcgGCCTCCAGGGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCTCTACAATCAGCAGCCACATCTGCATCCACCGCGan                                                                                                                                                                                                                 <  1:129618/92‑2 (MQ=255)                                                                                                                                                    gcggcgGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCACATCTGCATCCACCGCGAc                                                                                                                                                                                                                 >  2:129618/1‑92 (MQ=255)                                                                                                                                                    gcggcgGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCTCCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCTCAAAAGAGGCAGCAAAATCATCAGAAACGAACGCATCATCAAGTGCCGGTCGTGCAGCTTCCTCGGCAACGGCGGCAGAAAATTCTGCCAGGGCGGCAAAAACGTCCGAGAc                                                  <  1:187355/251‑1 (MQ=255)                                                                                                                                                      ggcggcCACCATTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCATCACCCACATCTGCAGCCTCCGCGACCACGAATCCATAAGAATCTGCAACCTCGGCCCTGGATGTGGCTGCCTCAAAAAAAGCGGCAAAATCACCAGAAACGAACGCATCATCAAGCGCCAGTAGTGCa                                                                                                          <  1:99487/193‑1 (MQ=255)                                                                                                                                                              ncaGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCTCCACCGCGGCCACGaaagc                                                                                                                                                                                                        >  1:131113/2‑88 (MQ=255)                                                                                                                                                              ccaGTGCCGGCGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGGCACAACAATCAGCCGCCACGTCTGCCTCCACCGCGGCCACGaaagc                                                                                                                                                                                                        <  2:131113/91‑4 (MQ=255)                                                                                                                                                                          nggcgAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCACATCTGCATCCACCGCGACCACGAAGGCATCAGAAGCTGCGACCTCGGCCCGGGATGCGGCGGCCTCAAAAGAAGCGGCAAAATCATCAGAAACGAACGCATCATCAAGCGCCAGTAGTGCAGCTTCCTCGGCAACGGCGGCAGGAAATTCCGCGAAGGCGGCAAAAACGTCCGAGACGAAc                                              >  1:55416/2‑233 (MQ=255)                                                                                                                                                                                                  ntgcAGCGTCACAACAATCAGCCGCCACGTCTGCCTCCACCGCGGCCACGAACGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCTCAAAAGAGGCAGCAAAATCATCAGAAACGAACGCATCATCAAGTGCCGGTCGTGCAGCTTCCTCGGCAACGGCGGCAGAAAATTCTGCCAGGGCGGCAAAAACGTCCGAGACGAATGCCAGGTCATCTGAAACAGCAGCGGAACGGAGCGCCTctgcc    >  1:23259/4‑247 (MQ=255)                                                                                                                                                                                                    gcAGCGTCACAACAATCAGCCGCCACGTCTGCCTCCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCTTCAAAAGAGGCAGCAAAATCATCAGAAACGAACGCATCATCAAGTGCCGGTCGTGCAGCTTCCTCGGCAACGGCGGCAGAAAATTCTGCCAGGGCGGCAAAAACGTCCGAGACGAATGCCAGGTCATCTGAAACAGCAGCGGAACGGAGCGCCTctgccgc  >  1:205725/2‑245 (MQ=255)                                                                                                                                                                                                     cAGCGTCACAACAATCAGCCGCCACGTCTGCCTCCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCTCAAAAGAGGCAGCAAAATCATCAGAAACGAACGCATCATCACGTGCCGGTCGTGCAGCTTCCTCGGCAACGGCGGCAGAAAATTctg                                                                           >  1:218537/1‑175 (MQ=255)                                                                                                                                                                                                              |                                                                                                                                                                                                                                                 GATGCTGCGGACTCAGCACGCGCAGCCAGCACGTCAGCCGGACAGGCCGCGTCGTCGGCTCAGTCAGCGTCTTCCAGCGCAGGAACGGCATCAACAAAGGCCACTGAAGCATCAAAAAGTGCTGCCGCTGCAGAGTCCTCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCACATCTGCATCCACCGCGACCACGAAGGCATCAGAAGCTGCGACCTCGGCCCGGGATGCGGCGGCCTCAAAAGAAGCGGCAAAATCATCAGAAACGAACGCATCATCAAGCGCCAGTAGTGCAGCTTCCTCGGCAACGGCGGCAGGAAATTCCGCGAAGGCGGCAAAAACGTCCGAGACGAACGCCAGGTCTTCTGAAACGGCAGCGGGACAGAGCGCCTCGGCTGC  >  NC_000913/1429487‑1429932

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑