Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,429,024	0	A	C	42.9%	‑5.5 / 13.7	14	intergenic (+40/‑25)	lomR/stfR	Rac prophage; protein LomR_1/putative prophage side tail fiber protein StfR
Reads supporting (aligned to +/- strand):  ref base A (5/3);  new base C (1/5);  total (6/8)
Fisher's exact test for biased strand distribution p-value = 1.38e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.04e-01
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

CACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGTGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAGTTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGTTCAGGCGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGTGTACTGAAAGACGGCACAGGAAAACCGGTAC‑AGAACTGCACAATCCAGCTGAAAGCAAAACGTAACAGCACCACGGTGGTGGTGAACACGCTGGCCTCAGAAAATCCGGATGAAGCCGGGCGTTACAGCATGGACGTTGAGTACGGTCAGTACAGCGTTATTCTGTTGGTGGAAGGATTCCC  >  NC_000913/1428808‑1429251                                                                                                                                                                                                                         |                                                                                                                                                                                                                                     cACGACGTGCTGACCGGAAGTGATGACGGTAGACACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGTGCAGTTTAACCCGACCGAATCCGTGGCAATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGAGTCGTTTATAAGTTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGTTCAGGCGGGCTTTTTTGTGGGGTGAATATGGCAGTa                                                                                                                                                                                                     >  1:198428/1‑250 (MQ=255)                            ggTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGAGTGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAGTTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGTTCAGGCGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGTGTAATGAAAGACGGc                                                                                                                                                                          >  1:28891/1‑250 (MQ=255)                                gCCACAGCAACACGTCTCTGGCGTGGTGAGCTGGCGTGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGTCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAGTTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCTGTTCAGGCGGGCGTTGTTGTGGGGTGAATATGGGAGTAAATATTCCAGGTGGGCTGAAAGACGGCACAgn                                                                                                                                                                     <  1:67884/251‑2 (MQ=255)                                                                     gCAGTTTAACCCGACCGAATCCGTGGCCATTGCTATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTCGGTGTCGGTTATAAGTTCTGATTCGCCAGGTAACACAGTGTTATGACCGCCCGCCGGTTCAGGCGGGCTTTTTTGTGGGGGGAATCTGGCAGTAACGATTTCAGGTGTACTGCAAGACGGc                                                                                                                                                                          >  1:188933/1‑209 (MQ=255)                                                                                                      tatTGCTTATGAAGGCTCCGGCAGTGGCGACTGGCGTACTGACGGATTCATCGTTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTgggg                                                                                                                                                                                                                   <  1:132817/135‑1 (MQ=255)                                                                                                             tATGAAGGCTCCGGCAGTGGCGACTGGCGTACTGACGGATTCATCGTTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTAC‑AGAACTGCACCATTCAGCTGAAAGCCAGACTTAACATCACCACGGTGGTGGTGAACACGGTGGnc                                                                                        <  1:181883/250‑1 (MQ=255)                                                                                                                  aGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATAGTGGGTGTCGGTTATAAGTTCTGCTTAGCCAGGTAACCCAGTGTTATGACAGCCCGACGGTTCAGGCGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGTGTACTGAAAGAc                                                                                                                                                                             >  1:149152/1‑161 (MQ=255)                                                                                                                             gTGGCGACTGGCGTACTGACGGAGTCTTCGTTGGGGTCGGTGATAAATTCTTATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTTGGCTTTGGTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCGCAGGAAAACCGGTAC‑AGACCTGCACCATTCAGCGGAAAGCCAGACGTAACAGCGCCACGGTGGTGGTGAACACGGTGGGCTCAg                                                                                    <  1:213237/238‑1 (MQ=255)                                                                                                                                gCGACTGGCGCACTGTCGGTTTCATCGTGGGTGTCGGTTATAAGTTCTGATTACACTGGGAACCCCGTGTTATGACAGACCGGCGGTTCCGGCGGGATTTTTTGTGGGGGGGATATGGCAGTAACGGTTTCATGAGTACTGAAAGACGGCCCAGGAAAACCGGTAccggaccgcccaatc                                                                                                                                            >  1:216806/1‑166 (MQ=255)                                                                                                                                      ggCGCACTGACGGTTTCATCGGGGGTGTCGGTTATAAGTTCTGATGAGCCAGGTA‑CACAGTGTTATGACAGCCCGCCGGTTCAGGCGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGTGTACTGAAAGACGGCACAGGAAAACCGGTAC‑AGAACTGCACAATCCAGCTGAAAGCAAAACTTAACAGCACCACGGTGGGGGTGAACACGCTGGCCTCAGAAAATCCGGATGAAGCCGGGc                                                               <  1:182338/249‑1 (MQ=255)                                                                                                                                                     tCATCGTTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTAGGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTTGGGTGAATATGTCAGTAAAGAtttn                                                                                                                                                                                             <  1:67977/110‑2 (MQ=255)                                                                                                                                                               ggtCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTAC‑AGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACACGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTTCAGCATg                                                    <  1:185238/235‑1 (MQ=255)                                                                                                                                                                           gTTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGTTCAGGCGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGTGTACTGAAAGACGGCACAGGAAAACCGGTAC‑AGAACTGCACAATCCAGCTGAAAGCAAAACGTAACAGCACCACGGTGGTGGTGAACACGCTGGCCTCAGAAAATCCGGATGAAgn                                                                    <  1:59139/208‑2 (MQ=255)                                                                                                                                                                                                  gtgtTATGACAGCCCGCCGGTTCAGGCGGGATTTTTTGGGGGGGGGATATGGCAGTACAGATTTCAGGGGCACTGAAAGAAGGCACAGGAAAACCGGGACCAAAAC‑GCACAATCCAGATGACAGCAAAACCGACCAGCACAACGGTGGTGGTGAACACGATGCCCTCAGAAAATCCGGATGACGCCGGGCGTTACAGCCTGGACGTTGAGCGCGGTAAGTACAGCGCTATTCTGTTGAGGGACGGATTccc  >  1:100541/1‑251 (MQ=255)                                                                                                                                                                                                                         |                                                                                                                                                                                                                                     CACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGTGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAGTTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGTTCAGGCGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGTGTACTGAAAGACGGCACAGGAAAACCGGTAC‑AGAACTGCACAATCCAGCTGAAAGCAAAACGTAACAGCACCACGGTGGTGGTGAACACGCTGGCCTCAGAAAATCCGGATGAAGCCGGGCGTTACAGCATGGACGTTGAGTACGGTCAGTACAGCGTTATTCTGTTGGTGGAAGGATTCCC  >  NC_000913/1428808‑1429251

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑