Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,429,360	0	C	T	52.9%	‑4.6 / 16.1	17	R104R (CGC→CGT)	stfR	putative prophage side tail fiber protein StfR
Reads supporting (aligned to +/- strand):  ref base C (2/6);  new base T (6/3);  total (8/9)
Fisher's exact test for biased strand distribution p-value = 1.53e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.54e-01
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

CAATCCAGCTGAAAGCAAAACGTAACAGCACCACGGTGGTGGTGAACACGCTGGCCTCAGAAAATCCGGATGAAGCCGGGCGTTACAGCATGGACGTTGAGTACGGTCAGTACAGCGTTATTCTGTTGGTGGAAGGATTCCCGCCGTCACATGCCGGGACCATTACCGTGTATGAAGATTCTCAACCCGGTACGCTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGTCCGGAGGCACTGCGCCGTTTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGCGGTGGCACAGAACACGGCAGCCGCGAAGAAGTCAGCCAGTGATGCCAGCACATCAGCCCGTGAGGCGGCAACCCATGCGGCTGATGCTGCGGACTCAGCACGCGCAGCCAGCACGTCAGCCGGACAGGCCGCGTCGTCGGCTCAGTCAGCGTCTTCCAGCGCAGGAACGGCATCAACAAAGGCCACTGAAGCATCAAAAAGTGCTG  >  NC_000913/1429110‑1429610                                                                                                                                                                                                                                                           |                                                                                                                                                                                                                                                           caATCCAGCTGAAAGCAAAACGTAACAGCACCACGGTGGTGGTGAACACGCTGGCCTCAGAAAATCCGGATGAAGCCGGGCGTTACAGCATGGACGTTGAGTACGGTCAGTACAGCGTTATTCTGTTGGTGGAAGGATTCCCGCCGTCACATGCCGGGACCATTACCGTGTATGAAGATTCTCAACCCGGTACGCTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGTCCGGAGGCACTgcgc                                                                                                                                                                                                                                                            >  1:169723/1‑251 (MQ=255)                                               cacGTTGGCCTAAGAAAATCCGGATGAAGCCGGGCGTTACAGCAGGGAGGTGGAGTACGGTCAGTACAGCGTTATTCTGTGGGTGGAAGGCTTCCCGCCGTCACATGCCGGGACCATTACCGTGTATGAAGATTCTCAACCCGGTACGCTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGTCCGGAGGCACTGCGCCGTTTTGAACGGATGGTGGAAGAGGTGGTGCGTAACGCGTCCGCgg                                                                                                                                                                                                              <  1:172378/251‑1 (MQ=255)                                                       gcTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTAAAGTGTCATCCTGCAGGTTGACGGTTTTCCACCATCGCACGCCGGGACCATCACCGTGTATGAAGCTTCACAACCGGGGACGCTGAATGATTTTCTCTGTGCAATGACGGAGGATGATGCCCGGCCGGAGGTGCTGCGTCGTATTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGt                                                                                                                                                                                                                    >  1:150114/2‑237 (MQ=255)                                                       cctaaGAAAATCCGGATGAAGCCGGGCATTCCAGCATGGACGTTGAGTACGGTCGGTACAGCGGTATTCTGTTGGTGGATGGTTTCCCGCCGTCACATGCCGTGACCACTACCGTGTATGAAGAGTCCCAACCCGGTACGCTGAATGATTGTCTCGGTGACATGACGGAGGATGATGCCCGTCCGGAGGCCCTGCGCCGTTTTGAACTGATGGTGGACGAGGTGGGGCTTAACGCGTGCGCGGTGGCACAg                                                                                                                                                                                                      <  1:16949/247‑1 (MQ=255)                                                              gaaTCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTACAGTGTCATCCTGCAGGTTGACGGTTTTCCACCATCGCACGCCGGGACCATCACCGTGTATGAAGATTCACAACCGGGGACGCTGAATGATTTTCTCTGTGCCATGACGGAGGATGATGCCCGGCCGGAGGTGCTGCGTCGTCTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGGGGTGGCACAGagtacgg                                                                                                                                                                                               >  1:93871/2‑245 (MQ=255)                                                                    ggATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGCCAGTACAGTGTCATCCTGCAGGTTGACGGTTTTCCCCCATCGCACGCCGGGACCATCACCGTGTATGCAGATTCACAACCGGGGACGCTGAATGATTTTCTCTGTGCCATGACGGAGGATGATGCCCGGCCGGAGGTGCTGCGTCGTCTTGAACTGATGGTGGCAGAGGTGGAGCGTAACGCGTCCGTGGTGGCACAGAGTACGGCAgacg                                                                                                                                                                                         >  1:29840/1‑248 (MQ=255)                                                                              gggCGTTACAGCATGGACGTTGAGTACGGTCAGTACAGCGTTATTCTGTTGGTGGAAGGATTCCCGCCGTCACATGCCGGGACCATTACCGTGTATGAAGATTCTCAACCAGGTACGCTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGTCCGGAGGCACTGCGCCGTTTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGCGGTg                                                                                                                                                                                                            <  1:17771/222‑1 (MQ=255)                                                                                  gTTACAGCATGGCTGTGGAGTACGGTCAGTACAGTGTCATCCTGCAGGTTGACGGTTTTCCACCATCGCACGCCGGGACCATCACCGTGTATGAAGATTCACAACCGGGGACGCTGAATGATTTTCTCTGTGCCATGACGGAGGCTGACGCCCGGCCGGAGGTGCTGCGTCGTCTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGTGGTGGCACAGAGTACGGCAGACGCGAAGAAATCAGcc                                                                                                                                                                           >  1:218268/1‑251 (MQ=255)                                                                                  gTTACAGCATGGATGTGGAGTACGGTCAGTACAGTGTCATCCTGCAGGTTGACGGTTTTCCACCATCGCACGCCGGGACCATCACCGTGTATGAAGATTCACAACCGGGGACGCTGAATGATTTTCTCTGTGCCATGACGGAGGATGATGCCCGGCCGGATGTGCTGCGTCGTCGTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGTGGTGGCACAGAGTACGGCAGACGCGAAGAAATCAGcc                                                                                                                                                                           <  1:73144/251‑1 (MQ=255)                                                                                  gTTACAGCATGGACGTTGAGTACGGTCAGTACAGCGTTATTCTGTTGGTGGAAGGATTCCCGCCGTCACATGCCGGGACCATTACCGTGTATGAAGATTCTCAACCCGGTACGCTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGTCCGGAGGCACTGCGCCGTTTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGCGGTGGCACAGAACACGGCAGCCGCGAAGAAGTCAGcc                                                                                                                                                                           >  1:99726/1‑251 (MQ=255)                                                                                                                                               gccgTTACATGCCGGGACCATTACCGTGTATGAAGATTCTCAACCCGGTACGCTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGTCCGGAGGCACTGCGCCGTTTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGCGGTGACACAGAACACGGCAGcc                                                                                                                                                                                          >  1:16872/1‑175 (MQ=255)                                                                                                                                                ccatcgcacgCCGGGACCATCACCGTGTATGAAGATTCACAACCGGGGACGCTGAATGATTTTCTCTGTGCCATGACGGAGGATGATGCCCGGCCGGAGGTGCTGCGTCGTCTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGTGGTGGCCCAGa                                                                                                                                                                                                     <  1:4876/154‑1 (MQ=255)                                                                                                                                                      caTGCCGGGACCATTACCGTGTATGAAGATTCTCAACCCGGTACGCTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGTCCGGAGGCACTGCGCCGGTTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGCGGTGGCACAGAACACGGCAGCCGCGAAGAAGTCAGCCAGTGATGCCAGCACATCAGCCCGTGAGGCGGCAACCCATGCGGCTGATGCTGCGGACTCAGCACgcgc                                                                                                       <  1:148192/251‑1 (MQ=255)                                                                                                                                                      caTGCCGGGACCATGACCGTGTATGAAGATTCTCAACCCGGTACGCTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGGCCGGAGGCACTGCGCCGTTTTGAACTGATGGTGGAAGAGGTGGCTCGTAACGCGTCCGCGGTGGCACAGAACACGGCAGCCGCGAAGAAGTCAGCCAGTGATGCCAGCACATCAGCCCGTGAGGCGGCAACCCATGCGGCTGATGCTGCGGCCTCAGCACgcgc                                                                                                       <  1:148199/251‑1 (MQ=255)                                                                                                                                                      caTGCCGGGAACATTACCGTGTATGAAGATTCTCAACCCGGTACGCTGAATGATTGTCTCGGTTCCATGACGGAGGATGATGCCCGTCCGGAGGCACTGCACCGTTTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGCGGTGGCACAGAACACGGCAGCCGCGAAGAAGTCAGCCATTGATGCCCGCACATCAGCCCGTGAGGCTGCAACCCATGCGGCTGATGCTGCGGACTCAGCACgcgc                                                                                                       <  1:148193/251‑1 (MQ=255)                                                                                                                                                              gACCATCACCGTGTATGCAGATTCACAACTGGGGACGCTGAATGATTTTCTCTGTGCCATGACGGAGGATGATGCCCGGCCGGAGGTGCTGCGTCGTCTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCgtggtg                                                                                                                                                                                                            >  1:66169/1‑142 (MQ=255)                                                                                                                                                                                                                                   tgatgCCCGGCCGGAGGTGCTGCGTCGTCTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGAGGTGGCACAGAGTACGGCAGACGCGAAGAAATCAGCCGGCGATGCCAGTGCATCAGCTGCTCAGGTCGCGGCCCTTGTGACTGATGCAACTGACTCAGCACGCGCCGCCAGCACGTCCGCCGGACAGGCTGCATCGTCAGCTCAGGAAGCGTCCTCCGGCGCAGAAGCGGCATCAGCAAAgg                          >  1:97650/1‑251 (MQ=255)                                                                                                                                                                                                                                       gCCCGGCCGGAGGTGCTGCGTCGTCTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGTGGTGGCACAGAGTACGGCAGACGCGAAGAAATCAGCCGGCGATGCCAGTGCATCAGCTGCTCAGGTCGCGGCCCTTGTGACTGATGCAACTGACTCAGCACGCGCCGCCAGCACGTCCGCCGGACAgg                                                                                <  1:197851/193‑1 (MQ=255)                                                                                                                                                                                                                                                           ccGTTTTGAACTGATGGTGGAAGAGGAGGCGCGTAACGCGTCCGCGGTGGCACAGAAACCGGCAGCAGCGAAGGAGGCAGACAGTGATGCCAGCACATAAGCCCGTTAGGCCGCAACCCATGCGGCTGATGCTGCGGACTCAGCACGCGACGCCCGCCCGTCCGCCGGGCAGGCCGCGTCGTCGGCTCAGTCAGCGTCTTCCAGCGCAGGAACGGCATCAACAAAAGCCACTGAAGCATCaaaaaaggctt  >  1:208791/1‑245 (MQ=255)                                                                                                                                                                                                                                                           |                                                                                                                                                                                                                                                           CAATCCAGCTGAAAGCAAAACGTAACAGCACCACGGTGGTGGTGAACACGCTGGCCTCAGAAAATCCGGATGAAGCCGGGCGTTACAGCATGGACGTTGAGTACGGTCAGTACAGCGTTATTCTGTTGGTGGAAGGATTCCCGCCGTCACATGCCGGGACCATTACCGTGTATGAAGATTCTCAACCCGGTACGCTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGTCCGGAGGCACTGCGCCGTTTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGCGGTGGCACAGAACACGGCAGCCGCGAAGAAGTCAGCCAGTGATGCCAGCACATCAGCCCGTGAGGCGGCAACCCATGCGGCTGATGCTGCGGACTCAGCACGCGCAGCCAGCACGTCAGCCGGACAGGCCGCGTCGTCGGCTCAGTCAGCGTCTTCCAGCGCAGGAACGGCATCAACAAAGGCCACTGAAGCATCAAAAAGTGCTG  >  NC_000913/1429110‑1429610

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: ‑