Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	579,099	0	A	.	66.7%	0.2 / 10.6	10	intergenic (‑206/+85)	borD/ybcV	prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV
Reads supporting (aligned to +/- strand):  ref base A (1/2);  new base . (1/5);  total (2/8)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.95e-01
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

GGGCCAGCGCAGTAGCGAGTAGCATTTTTTTCATGGTGTTATTCCCGATGCTTTTTGAAGTTCGCAGAATCGTATGTGTAGAAAATTAAACAAACCCTAAACAATGA‑GTTGAAATTTCATATTGTTAATATTTATTAATGTATGCCAGGTGCGATGAATCGTCATTGTATTCCCGGATTAACTATGTCCACAGCCCTGACGGGGAACTTCTCTGCGGGAGTGTCCGGGAATAATTAAAAACGATGCACACAGGGTTTAGCGCGTACATGTATTGTATTATGCCAACACCCCGGTGCTGACACGGAAGAAACCGGACGTTATGATTTAGCGTGGAAAGATTTGTGTAGTGTTCTGAATGCTCTCAGTAAATAGTAATGAATTATCAAAGGTATAGTAATATCTTTTATGTTCGTGGATATTTGTAATCCATCGGAAAACTCCTGCTTTAGCAAGATTTTCCCTGTATTG  >  NC_000913/578860‑579327                                                                                                                                                                                                                                                 |                                                                                                                                                                                                                                     gggCCAGCGCAGTAGCGAGTAGCATTTGTTTCATGGTGTTATTCCCGATGCTTTTTGAAGTTCGCAGAATCGTATGTGTAGAAAAGTAAACAAACCCTAAACA‑TGTTGTTGAAATTTCACTTTGTTAATATTTATTAATGTATGGCATGTGCTATTAATCGTCATTGTACTCGCGTTTTAACTATGTCCACAGCCCTTACGAGGAACTTCTCTGCGGGAGTGTCTGGGAATAATTAAAA‑CGATGcacacan                                                                                                                                                                                                                          <  1:40517/251‑2 (MQ=255)                        aTTTTTTTCATTGTGTTATTCCCGATGCTTTTTGAAGTTCGCAGAATCGTATGTGTAGAAAATTAAACAAACCCTAAACAATGA‑GTTGAAATTTCATATTGTTAATATTTATTAATGTATGTCAGGTGCGATGAATCTTCATTGTATTCCCGGATTAACTATGTCCACAGCCCTGACGGGGAACTTCTCTGCGGGAGTGTCCGGGAATAATTAAAA‑CGATGCACACAGGGTTTAGCGCGTACAcgtattgn                                                                                                                                                                                                   <  1:133477/251‑2 (MQ=255)                                                               cGCAGAATCGTATGTGTAGAAAATTAAACAAACCCTAAACAATGA‑GTTGAAATTTCATATTGTTAATATTTATTAATGTATGTCAGGTGCGATGAATCGTCATTGTATTCCCGGATTAACTATGTCCACAGCCCTGACGGGGAACTTCTCTGCGGGAGTGTCCGGGAATAATTAAAA‑CGATGCACACAGGGTTTAGCGCGTACACGTATTGCATTATGCCAACGCCCCGGTGCTGACACGGAAGAAAccn                                                                                                                                                             <  1:129445/250‑2 (MQ=255)                                                                gCAGAATCGTATGTGTAGAAAATTAAACAAACCCTAAACAATGA‑GTTGAAATTTCATATTGTTAATAGTTATTAATGTATGCCAGGTGCGATGAATCGTCATTGTATTCCCGGATTAACTATGTCCACAGCCCTGACGGGGAACTTCTCTGCGGGAGTGTCCGGGAATAATTAAAAACGATGCACACAGGGTTTAGCGCGTACATGTATTGTATTATGCCAACACCCCGGTGCTGACACg                                                                                                                                                                       <  1:143852/240‑1 (MQ=255)                                                                                                                                                                 nnnnnnnnnnttNNNNNATTNACTATGTCCACAGCCCTGATGGGGAACTTCTCTGCGGGAGTGTCCGGGAATAATTAAAAACGATGCACACAGGGTTTAGCGCGTACATGTATTGTATTATGCCAACACCCCGGTGCTGACACGGAAGAAACCg                                                                                                                                                             <  2:131880/144‑1 (MQ=255)                                                                                                                                                                                                  gCCCTGACGGGGAACTTCTCTGCGGGAGTGTCCGGGAATAATTAAAAACGATGCACACAGGGTTTAGCGCGTACATGTATTGTATTATGCCAACACCCCGGTGCTGACACGGAAGAAACCGGACGTTATGATTTAGCGTGGAAAGATTTGTGTAGTGTTCTGAATGCTCTCAGTAAATAGTAATGAATTATCaa                                                                                    >  1:172881/1‑194 (MQ=255)                                                                                                                                                                                                           gggAACTTCTCTGCGGGAGTGTCCGGGAATAATTAAAA‑CGATGCACACAGGGTTTAGCGCGTACACGTATTGCATTATGCCAACGCCCCGGTGCTGACACGGAAGAAACCGGACGTTATGATTTAGCGTGGAAAGATTTGTGTAGTGTTCTGAATGCTCTCAGTAAATAGTAATTAATTATCAAAGGTATAGTAATATCtttn                                                                 <  1:61632/203‑2 (MQ=255)                                                                                                                                                                                                                cTTCTCTGCGGGATTGGCCGTGAAGAATTAAAA‑CGATTCACACAGGGTTTAGCGTGTTCACGTATTTCATTATTCCAGCGCCCCATTGCGGACACGTAAGAAACCGGATGTTATGATTTAGTTTGTAAAGTTTTGTGTAGTGGTCTTAATTCTCTCAGTAAATAGTAATGAATTATCAAAGGtn                                                                               <  1:42176/184‑2 (MQ=255)                                                                                                                                                                                                                         nggAGTGTCCGGGAATAATTAAAA‑CGATGCACACAGGGTTTAGCGCGTACACGTATTGCATTATGCCAACGCCCCGGTGCTGACACGGAAGAAACCGGACGTTATGATTTAGCGTGGAAAGATTTGTGTAGTGTTCTGAATGCTCTCAGTAAATAGTAATGAATTATCAAAGGTATAGTAATATCTTTTATGTTCATGGATATTTGTAACCCATCGGAAAACTCCTGCTTTAGCAAGATTTTCCCTGTAtt   >  1:132148/2‑251 (MQ=37)                                                                                                                                                                                                                           gAGTGTCCGGGAATAATTAAAAGCGATGCACACAGGGTTTAGCGCGTACATGTATTGTATTATGCCAACACCCCGGTGCTGACACGGAAGAAACCGGACGTTATGAGTTAGCGTGGAAAGATTTGTGTAGTGTTCTGAATTCTCTCAGGAAATAGTAATGAATTATCAAAGGTATAGTAATATCTGTTATGTTCGTGGATAGGTGTAATCCAGCGGAAAACTCCTGCTTTAGCAAGATTTTCCCTGTAtcg  <  1:209056/251‑3 (MQ=38)                                                                                                                                                                                                                                                 |                                                                                                                                                                                                                                     GGGCCAGCGCAGTAGCGAGTAGCATTTTTTTCATGGTGTTATTCCCGATGCTTTTTGAAGTTCGCAGAATCGTATGTGTAGAAAATTAAACAAACCCTAAACAATGA‑GTTGAAATTTCATATTGTTAATATTTATTAATGTATGCCAGGTGCGATGAATCGTCATTGTATTCCCGGATTAACTATGTCCACAGCCCTGACGGGGAACTTCTCTGCGGGAGTGTCCGGGAATAATTAAAAACGATGCACACAGGGTTTAGCGCGTACATGTATTGTATTATGCCAACACCCCGGTGCTGACACGGAAGAAACCGGACGTTATGATTTAGCGTGGAAAGATTTGTGTAGTGTTCTGAATGCTCTCAGTAAATAGTAATGAATTATCAAAGGTATAGTAATATCTTTTATGTTCGTGGATATTTGTAATCCATCGGAAAACTCCTGCTTTAGCAAGATTTTCCCTGTATTG  >  NC_000913/578860‑579327

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: ‑