Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,428,978	0	G	A	43.8%	1.8 / 13.5	16	pseudogene (183/189 nt)	lomR	Rac prophage; protein LomR_1
Reads supporting (aligned to +/- strand):  ref base G (7/2);  new base A (1/6);  total (8/8)
Fisher's exact test for biased strand distribution p-value = 4.06e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.78e-01
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

GGAACTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGTGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAGTTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGTTCAGGCGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGTGTACTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACAATCCAGCTGAAAGCAAAACGTAACAGCACCACGGTGGTGGTGAACACGCTGGCCTCAGAAAATCCGGATGAAGCCGGGCGTTACAGCATG  >  NC_000913/1428775‑1429201                                                                                                                                                                                                            |                                                                                                                                                                                                                                ngAACTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGTGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAGTTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGTTc                                                                                                                                                                                    >  1:22385/2‑249 (MQ=255)                                  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)                                                                                                                                           gCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAGTTCTGATTAGCCAGGTAACACANNGTTATgnn                                                                                                                                                                                                 >  2:7013/1‑96 (MQ=255)                                                                                                                                              tATGAAGGCTCCGGCAGTGGCGACTGGCGTACTGACGGATTCATCGTTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACTTAACATCACCACGGTGGTGGTGAACACGGTGGnc                                      <  1:181883/250‑1 (MQ=255)                                                                                                                                                   aGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATAGTGGGTGTCGGTTATAAGTTCTGCTTAGCCAGGTAACCCAGTGTTATGACAGCCCGACGGTTCAGGCGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGTGTACTGAAAGAc                                                                                                                          >  1:149152/1‑161 (MQ=255)                                                                                                                                                              gTGGCGTCTGGCGTACTGACGGATTCATCGTTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGcc                                                                                                                                                                                             <  1:12148/83‑1 (MQ=255)                                                                                                                                                              gTGGCGACTGGCGTACTGACGGATTCATCGTTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGcc                                                                                                                                                                                             >  2:12148/1‑83 (MQ=255)                                                                                                                                                              gTGGCGACTGGCGTACTGACGGAGTCTTCGTTGGGGTCGGTGATAAATTCTTATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTTGGCTTTGGTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCGCAGGAAAACCGGTACAGACCTGCACCATTCAGCGGAAAGCCAGACGTAACAGCGCCACGGTGGTGGTGAACACGGTGGGCTCAg                                  <  1:213237/238‑1 (MQ=255)                                                                                                                                                                 gCGACTGGCGCACTGTCGGTTTCATCGTGGGTGTCGGTTATAAGTTCTGATTACACTGGGAACCCCGTGTTATGACAGACCGGCGGTTCCGGCGGGATTTTTTGTGGGGGGGATATGGCAGTAACGGTTTCATGAGTACTGAAAGACGGCCCAGGAAAACCGGTAccggaccgcccaatc                                                                                         >  1:216806/1‑166 (MQ=255)                                                                                                                                                                       ggCGCACTGACGGTTTCATCGGGGGTGTCGGTTATAAGTTCTGATGAGCCAGGTA‑CACAGTGTTATGACAGCCCGCCGGTTCAGGCGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGTGTACTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACAATCCAGCTGAAAGCAAAACTTAACAGCACCACGGTGGGGGTGAACACGCTGGCCTCAGAAAATCCGGATGAAGCCGGGc             <  1:182338/249‑1 (MQ=255)                                                                                                                                                                                      tCATCGTTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTAGGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTTGGGTGAATATGTCAGTAAAGAtttn                                                                                                                                          <  1:67977/110‑2 (MQ=255)                                                                                                                                                                                                ggtCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACACGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTTCAGCATg  <  1:185238/235‑1 (MQ=255)                                                                                                                                                                                                            gTTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGTTCAGGCGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGTGTACTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACAATCCAGCTGAAAGCAAAACGTAACAGCACCACGGTGGTGGTGAACACGCTGGCCTCAGAAAATCCGGATGAAgn                  <  1:59139/208‑2 (MQ=255)                                                                                                                                                                                                            |                                                                                                                                                                                                                                GGAACTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGTGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAGTTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGTTCAGGCGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGTGTACTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACAATCCAGCTGAAAGCAAAACGTAACAGCACCACGGTGGTGGTGAACACGCTGGCCTCAGAAAATCCGGATGAAGCCGGGCGTTACAGCATG  >  NC_000913/1428775‑1429201

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑