Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,429,750	0	C	T	50.0%	‑5.2 / 12.1	14	T234T (ACC→ACT)	stfR	putative prophage side tail fiber protein StfR
Reads supporting (aligned to +/- strand):  ref base C (3/4);  new base T (7/0);  total (10/4)
Fisher's exact test for biased strand distribution p-value = 6.99e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.65e-01
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

GCATCAAAAAGTGCTGCCGCTGCAGAGTCCTCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCACATCTGCATCCACCGCGACCACGAAGGCATCAGAAGCTGCGACCTCGGCCCGGGATGCGGCGGCCTCAAAAGAAGCGGCAAAATCATCAGAAACGAACGCATCATCAAGCGCCAGTAGTGCAGCTTCCTCGGCAACGGCGGCAGGAAATTCCGCGAAGGCGGCAAAAACGTCCGAGACGAACGCCAGGTCTTCTGAAACGGCAGCGGGACAGAGCGCCTCGGCTGCGGCAGGCTCAAAAACAGCGGCTGCGTCGTCTGCCAGTGCAGC  >  NC_000913/1429595‑1429974                                                                                                                                                            |                                                                                                                                                                                                                                 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)                                              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)                                                                                                           nagcCACATCTGCATCCACCGCGACCACGAAGGCATCAGAAGCTGCGACCTCGGCCCGGGATGCGGCGGCCTCAAAAGAAGCGGCAAAATCATCAGAAACGAACGCATCATCAAGCGCCAGTAGTGCAGCTTCCTCGGCAACGGCGGCAGGAAATTCCGCGAAGGCGGCAAAAACGTCCGAGACGAACGCCAGGTCTTCTGAAACgg                                                                     >  1:78197/2‑207 (MQ=255)                                                                                                                               ncgNCCACGAAGGCAGCAGNAGCTGCGACCTCGGCCCGGGATGCGGCGGCCTCAAAAGAAGCGGNNANNNCNGCAGAaac                                                                                                                                                                                <  2:173866/79‑1 (MQ=255)                                                                                                                               gcgACCACGAAGGCATCAGAAGCTGCGACCTCGGCCCGGGATGCGGCGGCCTCAACAGAAGCGGCAAAATCATCAGAaac                                                                                                                                                                                >  1:173866/1‑80 (MQ=255)                                                                                                                                  aCCACGAAGGCATCAGAAGCTGCGACCTCGGCCCGGGATGCGGCGGCCTCAAAAGAAGCGGCAAAATCATCAGAAACGAACGCATCATCAAGCGCCAGTAGTGCAGCTTCCTCGGCAACGGCGGCAGGAAAGTCCGCGAAGGCGGCAAAAACGTCCGAGACGAACGCCAGGTCTTCTGAAACGGCAGCGGGACAGAGCGCCGCGGCTGCGGCAGGCTCAAAAACAGCGGCTGCGTCGTCTGCCAGTGCacc  <  1:226784/251‑3 (MQ=255)                                                                                                                                            nntCNNNNNCTGNGACCTCGGCCCGGGATGCGGCGGCCTCAAAAGAAGCGGCAAAATCATCAGAAACGAACGCATCGTCAAGCGCCAGTAGTGCAGCTTCCTCGGCAACGGCGGCAGGAAATTCCGCGAAGGCGGCAAAAACggcc                                                                                                 <  2:152306/144‑4 (MQ=255)                                                                                                                                                            |                                                                                                                                                                                                                                 GCATCAAAAAGTGCTGCCGCTGCAGAGTCCTCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCACATCTGCATCCACCGCGACCACGAAGGCATCAGAAGCTGCGACCTCGGCCCGGGATGCGGCGGCCTCAAAAGAAGCGGCAAAATCATCAGAAACGAACGCATCATCAAGCGCCAGTAGTGCAGCTTCCTCGGCAACGGCGGCAGGAAATTCCGCGAAGGCGGCAAAAACGTCCGAGACGAACGCCAGGTCTTCTGAAACGGCAGCGGGACAGAGCGCCTCGGCTGCGGCAGGCTCAAAAACAGCGGCTGCGTCGTCTGCCAGTGCAGC  >  NC_000913/1429595‑1429974

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑