Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,429,632	0	G	A	50.0%	‑6.5 / 14.5	16	S195N (AGC→AAC)	stfR	putative prophage side tail fiber protein StfR
Reads supporting (aligned to +/- strand):  ref base G (5/3);  new base A (6/2);  total (11/5)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.07e-01
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

GCCAGTGATGCCAGCACATCAGCCCGTGAGGCGGCAACCCATGCGGCTGATGCTGCGGACTCAGCACGCGCAGCCAGCACGTCAGCCGGACAGGCCGCGTCGTCGGCTCAGTCAGCGTCTTCCAGCGCAGGAACGGCATCAACAAAGGCCACTGAAGCATCAAAAAGTGCTGCCGCTGCAGAGTCCTCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCACATCTGCATCCACCGCGACCACGAAGGCATCAGAAGCTGCGACCTCGGCCCGGGATGCGGCGGCCTCAAAAGAAGCGGCAAAATCATCAGAAACGAACGCATCATCAAGCGCCAGTAGTGCAGCTTCCTCGGCAACGGCGGCAGGAAATTCCGC  >  NC_000913/1429439‑1429860                                                                                                                                                                                                  |                                                                                                                                                                                                                                     nccAGTGATGCCAGCACATCAGCCCGTGAGGCGGCAACCCATGCGGCTGATGCTGCGGACTCAGCACGCGCAGCCAGCACGTCAGCCGGACAGGCCGCGTCGTCGGCTCAGTCAGCGTCTTCCAGCGCAGGAACGTCATCAACAAAGGCCACTGAAGCATCAAAAAGTGCTGCCGCTGCAGAGTCCTCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTc                                                                                                                                                                             >  1:148913/2‑251 (MQ=255)                                               cTGATGCTGCGGACTCAGCACGCGCAGCCAGCACGTCAGCCGGACAGGCCGCGTCGTCGGCTCAGTCAGCGTCTTCCAGCGCAGGAACGGCATCAACAAAGGCCACTGAAGCATCAAAAAGTGCTGCCGCTGCAGAGTCCTCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCACATCTGCATCCACCGCGACCACGAAGGc                                                                                                                                >  1:11855/1‑250 (MQ=255)                                                              cAGCACGCGCCGCCAGCACGTCCGCCGGACAGGCTGCATCGTCAGCTCAGGAAGCGTCCTCCGGCGCAGAAGCGGCATCAGCAAAGGCCACTGAAGCGGAAAAAAGTGCCGCAGCCGCAGAGTCCTCAAAAAACGCGGCGGCTCCGAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATcagccgn                                                                                                                                                              <  1:52334/205‑4 (MQ=255)                                                                         gccagcACGTCAGCCGGACAGGCCGCGTCGTCGGCTCAGTCAGCGTCTTCCAGCGCAGGAACGGCATCAACAAAGGCCACTGAAGCATCAAAAAGTGCTGCCGCTGCAGAGTCCTCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTAc                                                                                                                                                                        >  1:240338/1‑184 (MQ=255)                                                                                                      gtcagctcaggaagCGTCCTCCGGCGCAGAAGCGGCATCAGCAAAGGCCACTGAAGCGGAAAAAAGTGCCGCAGCCGCAGAGTCCTCAAAAAACGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCAcaac                                                                                                                                                                        >  1:172022/13‑152 (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)                                                                                                                                                                                                  |                                                                                                                                                                                                                                     GCCAGTGATGCCAGCACATCAGCCCGTGAGGCGGCAACCCATGCGGCTGATGCTGCGGACTCAGCACGCGCAGCCAGCACGTCAGCCGGACAGGCCGCGTCGTCGGCTCAGTCAGCGTCTTCCAGCGCAGGAACGGCATCAACAAAGGCCACTGAAGCATCAAAAAGTGCTGCCGCTGCAGAGTCCTCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCACATCTGCATCCACCGCGACCACGAAGGCATCAGAAGCTGCGACCTCGGCCCGGGATGCGGCGGCCTCAAAAGAAGCGGCAAAATCATCAGAAACGAACGCATCATCAAGCGCCAGTAGTGCAGCTTCCTCGGCAACGGCGGCAGGAAATTCCGC  >  NC_000913/1429439‑1429860

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑