Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,429,114	0	C	T	50.0%	‑5.5 / 17.8	19	I22I (ATC→ATT)	stfR	putative prophage side tail fiber protein StfR
Reads supporting (aligned to +/- strand):  ref base C (7/2);  new base T (3/6);  total (10/9)
Fisher's exact test for biased strand distribution p-value = 1.53e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.41e-01
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

TGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAGTTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGTTCAGGCGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGTGTACTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACAATCCAGCTGAAAGCAAAACGTAACAGCACCACGGTGGTGGTGAACACGCTGGCCTCAGAAAATCCGGATGAAGCCGGGCGTTACAGCATGGACGTTGAGTACGGTCAGTACAGCGTTATTCTGTTGGTGGAAGGATTCCCGCCGTCACATGCCGGGACCATTACCGTGTATGAAGATTCTCAACCCGGTACGCTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGTCCGGAGGCAC  >  NC_000913/1428906‑1429355                                                                                                                                                                                                                 |                                                                                                                                                                                                                                                  tgagatTGCTTAGGAAGGCCCCGGGAGTGGCGACTGCCGCACTGACGGTTTCATCGTGGGTGTCGTTAATAAGTTCGGATTAGCCAGGTAAACCAGTTTTATGACAGCCCGCCGGTTCAGGCGGGCTTTTTTGTGGGGTGAATAGGGCATTAAAGATGTCAGGGGTACTTAAAGACGGCCCAGTAAAACCGGTACAGAACGGCACAACGCAGCTGAAAGCAAAACTTAACAGCCCCACGGTGGTGGTGaa                                                                                                                                                                                                          <  1:167834/246‑1 (MQ=255)        gCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGCTTCATCGTGGGTGTCGGTTATAAGTTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGTTCCGGCGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGTGTACTGAAAGACGGAACAGGAACACCGGTACAGAACTGCACACTCCAGCTGACAGCAAAACGtc                                                                                                                                                                                                                                >  1:181552/1‑220 (MQ=255)            aTGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAGTTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGTTCAGGCGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGTGTACTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACAATCCAGCTGAAAGCAAAACGTAACAGCACCACGGTGGTGGTGa                                                                                                                                                                                                           >  1:18462/1‑238 (MQ=255)                 ggctccGGCAGTGGCGACTGGCGTACTGACGGATTCATCGTTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGGGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGc                                                                                                                                                                                                                           <  1:274910/213‑1 (MQ=255)                                              cggattCATCGTTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACACGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATg                                                                                                                                                            <  1:292511/247‑1 (MQ=255)                                                                                            cacaGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTAAGGAGTCCTGACAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACggtggtgg                                                                                                                                                                                                              >  1:324851/1‑155 (MQ=255)                                                                                                gtgtTATGACAGCCCGCCGGTTCAGGCGGGCTTTTTTTTGGGGGGAATATGGCGGTAAAGATTTCCGGGGTACTGAAAGACGGCACAGGAAACCCGGTACAGAACTGCAAAATCCAGCTGAAAGCAAAACGTAACAGCACCACGGGGGTGGAGaa                                                                                                                                                                                                          >  1:102211/1‑155 (MQ=255)                                                                                                                                       ggggTGAATATGGCAGGAATGATTTCAGGGGTACTGAAAGACGGCACATGAAAACCTGTACAGAACTGCACAATCCAGCTGAAAGCa                                                                                                                                                                                                                                       <  1:135659/87‑1 (MQ=255)                                                                                                                                                 tGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGGGGTGAACACGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGTATGTGGAGTACGGTCAGTACAgtgtcatcctgcagg                                                                                                                       <  1:85965/189‑15 (MQ=255)                                                                                                                                                  ngCAGTAAAGATTTCAGGTGTACTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACAATCCAGCTGAAAGCAAAACGTAACAGCACCACGGTGGTGGTGAACACGCTgg                                                                                                                                                                                                  >  1:194900/2‑113 (MQ=255)                                                                                                                                                  ngCAGTAAAGATTTCAGGTGTACTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACAATCCAGCTGAAAGCAAAACGTAACAGCACCACGGCGGAGGTGAACACGCTGGCCTCAGAAAATCCGGATGAAGCCGGGCGTTACAGCATGGACGTTGAGTACGGTCAGTACAGCGTTATTCTGTTGGTGGAAGGATTCCCGCCGTCACATGCCGGGACCATTACCGTGTATGAAGATTCTCAACCCGGt                                                         >  1:37631/2‑250 (MQ=255)                                                                                                                                                  ggCAGTAAAGATTTCAGGTGTACTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACAATCCAGCTGAAAGCAAAACGTAACAGCACCACGGTGGTGGTGAACACGCTgg                                                                                                                                                                                                  <  2:194900/113‑1 (MQ=255)                                                                                                                                                     aGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGGGAACACGGTGGGCTCAGAGAATCTGGATTAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTACAgtgtcatcctgca                                                                                                                         <  1:173338/183‑13 (MQ=255)                                                                                                                                                      gTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGGAACAGCACCACGGTGGTGGTGAACACGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTACAGTGTCATCCTGCAGGTTGACGGTTTTCCACCATCGCACGCCGGGACCATCACCGTGTATGAAGATTCACAACCGGGGACGCt                                                    <  1:3097/251‑1 (MQ=255)                                                                                                                                                                  ngagtccTGAAAGACGGCACATGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACACGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTACAGTGTCATCCTGCAGGTTGACGGTTTTCCACCATCGCACGCCGGGACCATCACCGTGTATGAAGATTCACAACCGGGGACGCTGAATGATTTtct                                        >  1:81213/7‑251 (MQ=255)                                                                                                                                                                       ccTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACACGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTACAGTGTCATCCTGCAGGTTGACGGTTTTCCACCATCGCACGCCGGGACCATCACCGTGTATGAAGATTCACAACCGGGGACGCTGAATGATTTTCTCtgtg                                   >  1:70723/2‑251 (MQ=255)                                                                                                                                                                                ctgCACAGGAAAACCGGTACAGAACTGCACAATCCAGCTGAAAGCAAAACGTAACAGCACCACGGTGGTGGTGAACCCGCTGGCCTCAGAAAATCCGGATGAAGCCGGGCGTTACAGCATGGACGTTGAGTACGGTCAGTACAGCGTTATTCTGTTGGTGGAAGGATTCCCGCCGTCACATGCCGGGACCATTACCGTGTATGAAGATTCTCAACCCGGTACGCTGAATGATTTTCTCGGTGCCATGACgg                          >  1:315901/3‑251 (MQ=255)                                                                                                                                                                                     caGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACACGGTGGGCTCAGATAATCCGGATGAAGCCGGGCGTTACAGTATGGATGTGGAGTan                                                                                                                                                <  1:82020/128‑2 (MQ=255)                                                                                                                                                                                                        cTGCACAATCCAGCTGAAAGCAAAACGTAACAGCACCACGGTGGTGGTGAACACGCTGGCCTCAGAAAATACGGATGAAGCCGGGCGTTACAGCATGGACGTTGAGTACGGTCAGTACAGCGTTATTCTGTTGGTGGCAGGATTCCCGCCGTCACATGCCGGGACCATTACCGTGTATGAAGATTCTCAACCCGGTACGCTGAATGCTTTTCTCAGTGCCATGACGGAGGATGATGCCCGTCCGGAGGCAc  >  1:313721/1‑251 (MQ=255)                                                                                                                                                                                                                 |                                                                                                                                                                                                                                                  TGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAGTTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGTTCAGGCGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGTGTACTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACAATCCAGCTGAAAGCAAAACGTAACAGCACCACGGTGGTGGTGAACACGCTGGCCTCAGAAAATCCGGATGAAGCCGGGCGTTACAGCATGGACGTTGAGTACGGTCAGTACAGCGTTATTCTGTTGGTGGAAGGATTCCCGCCGTCACATGCCGGGACCATTACCGTGTATGAAGATTCTCAACCCGGTACGCTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGTCCGGAGGCAC  >  NC_000913/1428906‑1429355

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑