Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,429,724	0	A	G	47.1%	‑5.2 / 16.0	17	T226A (ACC→GCC)	stfR	putative prophage side tail fiber protein StfR
Reads supporting (aligned to +/- strand):  ref base A (6/3);  new base G (3/5);  total (9/8)
Fisher's exact test for biased strand distribution p-value = 3.47e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.21e-01
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

ACCCATGCGGCTGATGCTGCGGACTCAGCACGCGCAGCCAGCACGTCAGCCGGACAGGCCGCGTCGTCGGCTCAGTCAGCGTCTTCCAGCGCAGGAACGGCATCAACAAAGGCCACTGAAGCATCAAAAAGTGCTGCCGCTGCAGAGTCCTCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCACATCTGCATCCACCGCGACCACGAAGGCATCAGAAGCTGCGACCTCGGCCCGGGATGCGGCGGCCTCAAAAGAAGCGGCAAAATCATCAGAAACGAACGCATCATCAAGCGCCAGTAGTGCAGCTTCCTCGGCAACGGCGGCAGGAAATTCCGCGAAGGCGGCAAAAACGTCCGAGACGAACGCCAGGTCTTCTGAAACGGCAGCGGGACAGAGCG  >  NC_000913/1429475‑1429922                                                                                                                                                                                                                                                          |                                                                                                                                                                                                       aCCCATGCGGCTGATGCTGCGGACTCAGCACGCGCAGCCAGCACGTCAGCCGGACAGGCCGCGTCGTCGGCTCAGTCAGCGTCTTCCAGCGCAGGAACGGCATCAACAAAGGCCACTGAAGCATCAAAAAGTGCTGCCGCTGCAGAGTCCTCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCACATCTGCATCCACCGCGAc                                                                                                                                                                                                       <  1:143354/251‑1 (MQ=255)       gtgactgatgcaactgACTCAGCACGCGCCGCCAGCACGTCCGCCGGACAGGCTGCATCGTCAGCTCAGGAAGCGTCCTCCGGCGCAGAAGCGGCATCAGCAAAGGCCACTGAAGCGGAAACAAGTGCCGCAGCCGCAGAGTCCTCAAAAAACGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCTCCACCGCGGCCACGa                                                                                                                                                                                                  >  1:68768/16‑250 (MQ=255)        cGGCTGATGCTGCGGACTCAGCACGCGCAGCCAGCACGTCAGCCGGACAGGCCGCGTCGTCGGCTCAGTCAGCGTCTTCCAGCGCAGGAACGGCATCAACAAAGGCCACTGAAGCATCAAAAAGTGCTGCCGCTGCAGAGTCCTCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCACATCTGCATCCACCGCGACCACGa                                                                                                                                                                                                  >  1:130102/1‑249 (MQ=255)                    cGGACTCAGCACGCGCAGCCAGCACGTCAGCCGGACAGGCCGCGTCGTCGGCTCAGTCAGCGTCTTCCAGCGCAGGAACGGCATCAACAAAGGCCACTGAAGCATCAAAAAGTGCTGCCGCTGCAGAGTCCTCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCACATCTGCATCCACCGCGACCACGAAGGCATCAGAAGCt                                                                                                                                                                                    <  1:141916/251‑1 (MQ=255)                               cgcgCCGCCAGCACGTCCGCCGGACAGGCTGCATCGTCAGCTCAGGAAGCGTCCTCCGGCGCAGAAGCGGCATCAGCAAAGGCCACTGAAGCGGAAAAAAGTGCCGCAGCCGCAGAGTCCTCAAAAAACGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCTCCACCGCGGCCACGAAAGCGTCAGaggccgccacttcagc                                                                                                                                                                         >  1:38114/1‑236 (MQ=255)                                                          gctgcatcgtcaGCTCAGGAAGCGTCCTCCGGCGCAGAAGCGGCATCAGCAAAGGCCACTGAAGCGGAAATAAGTGCCGCAGCCGCAGAGTCCTCAAAAAACGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCATAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCAGGTCTGCCTCCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCTCAAaagaggn                                                                                                                                              <  1:17472/245‑4 (MQ=255)                                                                      gCTCAGTCAGCGTCTTCCAGCGCAGGAACGGCATCAACAACGGCCACTGAAGCCTCAAAAAGTGCTGCCGCTGCAGAGTCCTCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTACGCGTCACTACAATCAGCAGCCACATCTGCATCCACCGCGACCACGAAGGCATCAGAAGCTGCGACCTCgg                                                                                                                                                                          >  1:165650/1‑211 (MQ=255)                                                                                     cccAGCGCAGGAACGGCATCATCAAAGGACACTGAAGCATCAAAAAGTGCTGCCGCTGCAGAGTCCTCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCACATCGGCATCCACCGCGACCACGAAGGCATCAGATGCTGCGACCTCGGCCCGGGATGCGGCGGCCTCAAAAGAAGCGGAAAAATCATCAGAAACGAACGcatc                                                                                                                   <  1:112128/250‑1 (MQ=255)                                                                                                                  cactgaagcggaaaaaaGTGCCGCAGCCGCAGAGTCCTCAAAAAACGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCTCCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCTCAAAAGAGGCAGCAAAATCATCAGAAACGAACGCATCATCAAGTGCCGGTCGTGCAGCTTCCTCgg                                                                                      <  1:50016/239‑1 (MQ=255)                                                                                                                                          cGCTGCAGAGTCCTCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCACATCTGCATCCACCGCGACCACGAAGGCATCAGAAGCTGCGACCTCGGCCCGGGATGCGGCGGCCTCAAAAGAAGCGGCAAAATCATCAGAAACGAACGCATCATCAAGCGCCAGTAGTGCAGCTTCCTCGGCAACGGCGGCAGGAAATTCcgcg                                                               >  1:141218/1‑250 (MQ=255)                                                                                                                                                                      gcCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCCCATCTGCCTCCACCGCGACCACGACGGCATCAGAAGCTGCGACCTCGGCCCGGGATGCGGCGGCCTCCACAGAAGCGGCCAAATCATCAGACCCGAACGCATCATCAAGCGCCAGAAGTGCAGCTTCCTCGGCAACGGCGGCAGGAAATTcc                                                                  >  1:115410/1‑219 (MQ=255)                                                                                                                                                                          ccaGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCACATCTGCATCCACCGCGACCACGAAGGCATCAGAAGCTGCGACCTCCGCCCGGGATGCGGCGGCCTCAAAAGAAGCGGCAAAAACATCAGAAACGAACGCATCATCAAGCGCCAGTAGTGCAGCTTCCTCGGCAACGGCGGCAGGAAATTCCGCGAAGGCGGCAAAAACGTCCGAGACGAACGCCAgg                              >  1:162161/1‑251 (MQ=255)                                                                                                                                                                                  ggTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCTCCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCTCAAAAGAGGCAGCAAAATCATCAGAAACGAACGCATCATCAAGTGCCGGTCGTGCAGCTTCCTCGGCAACGGCTGCAGAAAATTCTGCCAGGGCGGCAAAAACGTCCGAGACGAATGCCAGGTCATCTGa                      <  1:93418/251‑1 (MQ=255)                                                                                                                                                                                  ggTGCGGCGAAAACGACAGAAACGAATGCTTCAGCGTCACTACAATCAGTAGCCAAAGCTGAATCCACCGCGACCACGACGGCATCAGAAGCTGCGACCTCGGCCCGGGATGCGGCGGCATCAAAAGAAGCGGCAAAATCATCAGAGACGCACGCATCATCACACGACAGTAGTGCAGCTTCCTCGGCAACGGCGGCAGGAAATTCCGCGAAGGAGGCAAAAACTTCCGAGACGAACGcacggtattctg                       >  1:126172/1‑239 (MQ=255)                                                                                                                                                                                                      aaCGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCTCCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCTCAAAAGAGGCAGCAAAATCATCAGAAACGAACGCATCATCAAGTGCCGGTCGTGCAGCTTCCTCGGCAACGGCGGCAGAAAATTCTGCCAGGGCGGCAAAAACGTCCGAGACGAATGCCAGGTCATCTGAAACAGCAGCGGAACGGAgcg  <  1:115983/251‑1 (MQ=255)                                                                                                                                                                                                                                               cctCCACCGCGGCCACGACAGCGTCANAGGCCGNNACNTCAGCACGAGATGCGGTGGNCTNNNANNNGNCTGCANAGNNATCAGAAACNAACGCATCATCAAGTGCCGGTCGTGCAGCTTCCTCGGc                                                                                     >  2:35675/3‑127 (MQ=255)                                                                                                                                                                                                                                               cctCCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCTCAAAAGAGGCAGCAAAATCATCAGAAACGAACGCATCATCAAGTGCCGGTCGTGCAGCGTCCTCGGc                                                                                     <  1:35675/125‑1 (MQ=255)                                                                                                                                                                                                                                                          |                                                                                                                                                                                                       ACCCATGCGGCTGATGCTGCGGACTCAGCACGCGCAGCCAGCACGTCAGCCGGACAGGCCGCGTCGTCGGCTCAGTCAGCGTCTTCCAGCGCAGGAACGGCATCAACAAAGGCCACTGAAGCATCAAAAAGTGCTGCCGCTGCAGAGTCCTCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCACATCTGCATCCACCGCGACCACGAAGGCATCAGAAGCTGCGACCTCGGCCCGGGATGCGGCGGCCTCAAAAGAAGCGGCAAAATCATCAGAAACGAACGCATCATCAAGCGCCAGTAGTGCAGCTTCCTCGGCAACGGCGGCAGGAAATTCCGCGAAGGCGGCAAAAACGTCCGAGACGAACGCCAGGTCTTCTGAAACGGCAGCGGGACAGAGCG  >  NC_000913/1429475‑1429922

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑