Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,429,692	0	T	A	55.6%	‑2.7 / 19.8	18	L215Q (CTA→CAA)	stfR	putative prophage side tail fiber protein StfR
Reads supporting (aligned to +/- strand):  ref base T (5/3);  new base A (8/2);  total (13/5)
Fisher's exact test for biased strand distribution p-value = 6.08e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.15e-01
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

CTGATGCTGCGGACTCAGCACGCGCAGCCAGCACGTCAGCCGGACAGGCCGCGTCGTCGGCTCAGTCAGCGTCTTCCAGCGCAGGAACGGCATCAACAAAGGCCACTGAAGCATCAAAAAGTGCTGCCGCTGCAGAGTCCTCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCACATCTGCATCCACCGCGACCACGAAGGCATCAGAAGCTGCGACCTCGGCCCGGGATGCGGCGGCCTCAAAAGAAGCGGCAAAATCATCAGAAACGAACGCATCATCAAGCGCCAGTAGTGCAGCTTCCTCGGCAACGGCGGCAGGAAATTCCGCGAAGGCGGCAAAAACGTCCGAGACGAACGCCAGGTCTTCTGAAACGGCAGCGG  >  NC_000913/1429485‑1429913                                                                                                                                                                                                                |                                                                                                                                                                                                                              cTGATGCTGCGGACTCAGCACGCGCAGCCAGCACGTCAGCCGGACAGGCCGCGTCGTCGGCTCAGTCAGCGTCTTCCAGCGCAGGAACGGCATCAACAAAGGCCACTGAAGCATCAAAAAGTGCTGCCGCTGCAGAGTCCTCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCACATCTGCATCCACCGCGACCACGAAGGc                                                                                                                                                                                     >  1:11855/1‑250 (MQ=255)                cAGCACGCGCCGCCAGCACGTCCGCCGGACAGGCTGCATCGTCAGCTCAGGAAGCGTCCTCCGGCGCAGAAGCGGCATCAGCAAAGGCCACTGAAGCGGAAAAAAGTGCCGCAGCCGCAGAGTCCTCAAAAAACGCGGCGGCTCCGAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATcagccgn                                                                                                                                                                                                                   <  1:52334/205‑4 (MQ=255)                           gccagcACGTCAGCCGGACAGGCCGCGTCGTCGGCTCAGTCAGCGTCTTCCAGCGCAGGAACGGCATCAACAAAGGCCACTGAAGCATCAAAAAGTGCTGCCGCTGCAGAGTCCTCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTAc                                                                                                                                                                                                                             >  1:240338/1‑184 (MQ=255)                                                           ggCTCAGTCAGCGTCTTCCAGCTCAGTAACGGCATCAACAAAGGCCACTGAAGCATCAAAAAGTGCTGCCGCTTCAGATTCCTTAAAAAGCGCGGCGTCCCCCAGTGCCGGTGCGGCGAAAACTTCAGAAACGAATGCTTCAGCGTCACTACAATCagcagcn                                                                                                                                                                                                                  <  1:32007/163‑2 (MQ=255)                                                                          nnccNNNNNAGGNACGTCATCAACAAAGGCCACTGAAGCATCAAAAAGTGCTGCCGCTGCAGAGTCCTCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATcagcag                                                                                                                                                                                                                    <  2:148913/144‑1 (MQ=255)                                                                                              cagcaaAGGCCACTGAAGCGGAAAAAAGTGCCGCAGCCGCAGAGTCCTCAAAAAACGCGGCGACCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCTCCACcgcg                                                                                                                                                                                                >  1:4436/4‑146 (MQ=255)                                                                                                ncaaAGGCAACTGAAGAATCAAAAAGTGCTGCCGCTGCAGAGTCCTCAAACAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGACACATCTGCATCCACcgc                                                                                                                                                                                                 >  1:204811/2‑143 (MQ=255)                                                                                                            naaGCATCAAAAAGTGCTGCCGCTGCAGAGTCCTCAAGAAGCGCGGCGGACACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCACATCTGCATCCACCGCGACCAc                                                                                                                                                                                           >  1:55105/2‑137 (MQ=255)                                                                                                               gCATCAAAAAGTGCTGCCGCTGCAGAGTCCTCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCACATCTGCATCCACCGCGACCACGAAGGCATCAGAAGCTGCGACCTCGGCCCGGGATGCGGCGGCCTCAAAAGAAGCGGCAAAATCATCAGAAACGAACGCATCATCAAGCGCCAGTAGTGCAGCTTCCTCGGCAAcggn                                                                      <  1:159553/251‑2 (MQ=255)                                                                                                                  taaaaaaGTGCCGCAGCCGCAGAGTCCTCAAAAAACGCGGCGTCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCTCCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCTCCAAAGAGGCAGCACAATCATCAGAAACGAACGCATCATCAAGTGCCGGTCGTGCAGCTTCCTCGGCAACggcggc                                                                   >  1:60269/3‑251 (MQ=255)                                                                                                                  gaaaaaaGTGCCGCAGCCGCAGAGTCCTCAAAAAACGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCTCCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCTCAAAAGAGGCAGCAAAATCATCAGAAACGAACGCATCATCAAGTGCCGGTCGTGCAGCTTCCTCGGCAACgtcggc                                                                   >  1:60261/3‑251 (MQ=255)                                                                                                                      aaaGTGCCGCAGCCGCAGAGTCCTCAAAAAACGCGGCGGCCACCAGTGCCGGTGCGGCAAACACGTCAGAAACGATTGCTGCAGCGTCACAACAAACAGCCACCACGTCTGACTCCACCGCGGCCACGACAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCTCACAAGAGGCAGCAAAATCATCAGAAACGAACACATCATCAAGTGCCGCTCGTGCAGACTCCACGGCAACGGCGGCAga                                                                >  1:192098/1‑249 (MQ=255)                                                                                                                              gcagccgCAGAGTCCTCAAAAAACGCGGCGGCCACCAGTGCCGGTGCGGCGCAAACGTCAGAAACGAATGCTCCAGCGTCACAACAATCAGCAGCCACGTCTGCCTCCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCTCAGAAGAGGCAGCAAAATCATCAGAAACGAACGCATCATCAAGTGCCGGTCGTGCAGCTTCCTCGGCAACGGCGGCAGAAAATTctgc                                                       >  1:144298/7‑248 (MQ=255)                                                                                                                                              nnaaaaACNNGGCGGCCACCAGAGCCGGTGCGGCGAAAACGTCAGAAACGAATGCGGCAGCGTCAAAACAATCAGCTGCCACGTCTGCCTCCCCcgag                                                                                                                                                                                                <  2:4436/96‑3 (MQ=255)                                                                                                                                                            nccaccaGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCTCCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCTCACAAGAGGCAGCAAAATCATCAGAAACGAACGCATCATCAAGTGCCGGTCGTGCAGCTTCCTCGGCAACGGCGGCAGAAAATTCTGCCAGGGCGGCAAAAACGTCCGAgaagaatgc                         >  1:149891/2‑248 (MQ=255)                                                                                                                                                             ncaccaGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCTCCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCTCAGAAGAGGCAGCAAAATCATCAGAAACGAACGCATCATCAAGTGCCGGTCGTGCAGCTTCCTCGGCAACGGCGGCAGAAAATTCTGCCAGGGCGGCAAAAACGTcc                                    >  1:76165/2‑239 (MQ=255)                                                                                                                                                             ccaccaGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCTCCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCTCAAAAGAGGCAGCAAAATCATCAGAAACGAACGCATCATCAAGTGCCGGTCGTGCAGCTTCCTCGGCAACGGCGGCAGAAAATTctgccagg                                                   >  1:105078/1‑217 (MQ=255)                                                                                                                                                                                   aaCGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCACATCTGCATCCACCGCCACCACGAAGACATCAGCAGCTGCGACCTCGGCCCGAGATGCGGCCGCCTCAAAAGAAGCGGCAAAATCATCAGAAACGAACGCATCATCAAGCGCCAGTAGTGCAGCTTCCTCGGCAACGGCGGCAGGAAATTCCGCGAAGGCGGCAACAACGTCCGAGACGAACGCCAGGTCTTCTGAAACGGAAGCgg  >  1:126517/1‑251 (MQ=255)                                                                                                                                                                                                                |                                                                                                                                                                                                                              CTGATGCTGCGGACTCAGCACGCGCAGCCAGCACGTCAGCCGGACAGGCCGCGTCGTCGGCTCAGTCAGCGTCTTCCAGCGCAGGAACGGCATCAACAAAGGCCACTGAAGCATCAAAAAGTGCTGCCGCTGCAGAGTCCTCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCACATCTGCATCCACCGCGACCACGAAGGCATCAGAAGCTGCGACCTCGGCCCGGGATGCGGCGGCCTCAAAAGAAGCGGCAAAATCATCAGAAACGAACGCATCATCAAGCGCCAGTAGTGCAGCTTCCTCGGCAACGGCGGCAGGAAATTCCGCGAAGGCGGCAAAAACGTCCGAGACGAACGCCAGGTCTTCTGAAACGGCAGCGG  >  NC_000913/1429485‑1429913

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑