Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	578,605	0	T	G	47.1%	0.3 / 18.6	17	K97Q (AAA→CAA)	borD	prophage lipoprotein BorD
Reads supporting (aligned to +/- strand):  ref base T (2/7);  new base G (3/5);  total (5/12)
Fisher's exact test for biased strand distribution p-value = 6.20e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.45e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

TGCACATCAAAGCAGTCTGTCAGTCAGTGCGTGAAGCCACCACGGCCTCCGGCGTGGATAATGCAGCCTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAGAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCTGGGTTTCTGTTTTAACAACATTTTCTGCGCCGCCACAAATTTTAGCTGCATCGACAGTTTTCTTCTGCCCAATTCCAGAAACGAAGAAATGATGGGTGATGGTTTCCTTTGGTGCTACTGCTGTCTGTTTGTTTTGAACAGTAAATGTCTG  >  NC_000913/578384‑578836                                                                                                                                                                                                                              |                                                                                                                                                                                                                                        tGCACATCAAACCAGTCTGTCAGTCAGTGCGTGAAGCCACCACCGCCTCCTGCGTGGATAATGCAGCCTCCCCCCGACTGGCAGACCCCGCTGAACGGGATTATTTCACCCTCAGAGAGACGCTGATCACTATGCAAAAACACCTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAGAGTTGCCCATATCGATGGGCAACTCATGCAATTATTGTGAGCAATACACACGCGCTTCCAGCgg                                                                                                                                                                                                              >  1:56558/1‑249 (MQ=25)     caTCAAAGCAGTCTGTCAGTCAGTGCGTGAAGCCACCACGGCCTCCGGCGTGGATAATGCAGCCTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCGCTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAGAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCgn                                                                                                                                                                                                              <  1:41949/245‑2 (MQ=255)             cAGTCTGTCAGTCAGTGCGTGAAGCCACCACCGCCTCCGGCGTGGATAATGCAGCCTCCCCCCGACTGGCAGACGCCGCGGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATGAATGAGCAGTGCAGATAGAGTTGGCCATATCGATGGTCTTCTCATGCAATTATTGTGAGCAATACACACGCGCTTCCAGCTGAGTATAAATGCCTa                                                                                                                                                                                                <  1:88559/251‑1 (MQ=25)             cAGTCTGTCAGTCAGTGCGTGAAGCCACCACCGCCTCCGGCGTGGATAATGCAGCCTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGCTCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAGAGTTGCCCATATCGATGGGCAACTCATGCAATTATTGTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCt                                                                                                                                                                                                 >  1:158642/1‑250 (MQ=255)                           gtGCGTGAAGCCCCCACGGCCTCCGGCGTGGATAATGCAGCCTCCCCCCGACTGGCAGACACCGCTGATCGGGATTATTTCTCCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGGGCAGATAGAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTGCCATCGGAGTAGAAATGCCTAAGGTAATAAAACCg                                                                                                                                                                                  <  1:57792/251‑1 (MQ=38)                                tGAAGCCACCACCGCCTCCGGCGTGGATAATGCAGCCTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCATAAGTATAGTAATGAGCAGTGCAGATAGAGTTGCCCATAGCGATGGGCAACTCATGCAATTATTGTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGcn                                                                                                                                                                                                  <  1:17507/230‑2 (MQ=37)                                                                                                    attattTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAGAGTTGCCCATATCGAGTGGCAACTGATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATGGACGTATTTTTTCTGGGTTTCTGTTTTAACAACATTTTCTGCGCCGCCACAAATTTTGGCTg                                                                                                         <  1:82596/251‑1 (MQ=255)                                                                                                          tCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAGAGCGGACCATATCGATGGGCAACGCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCGTAAAGTAATAAAACCGAGCATTCCATTGACTAATGTTTGCTGGGTTGCTGTTTTAACAACATTTTCTGCGCCGCCACAAATTTTAGCTGCATCg                                                                                                    <  1:151854/250‑1 (MQ=255)                                                                                                              ccTCAGGGAGAGGCTGATCACTATGCAAAAACAAGTGGAAGGAACCCAGAAGGATATTAAGGAGCAGTGCAGATAGAGCTGACCATATGGATGGGCACCTCATGCAATTATTTGGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAATTAATAAAACCGAGCAATCCTTTTACAAATGTTTGCTGGGTTTCGGTTTTAACACCATTTTCTGCCCCGCCACAAATTTTAGCTGCATCGACAGt                                                                                               <  1:163139/251‑1 (MQ=255)                                                                                                                           ntGATCACTATGCAAAA‑CAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAGAGTTGCCCATATCGATGGGCAACTCATGCAATTATTGTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTAc                                                                                                                                                                    >  1:104563/2‑168 (MQ=255)                                                                                                                                cACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGGGCAGATAGAGTTGCCCATATCGATGGGCAACTCATGCAATTATTGTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCTGGGTTTCTGTTGTAACAACATTTTCTGCGCCGCCACAAATTTTGGCTGCATCGACAGTTTTCTTCTGCCCAATTc                                                                              <  1:53415/250‑1 (MQ=255)                                                                                                                                                  nnaannnnNCCANAAGTATATTAATGAGCAGTGCAGATAGAGTTGCCCATATCGATGGGCAACTCATGCAATTATTGTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTAc                                                                                                                                                                    <  2:104563/144‑1 (MQ=255)                                                                                                                                                                                          agttgcccATAGCGATGGGCAATTCATGCAATTATTGTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATGTACGAATGTTTGCTGTGTTTCTGTTTTAACAACATTTTCTGCTCCGCCACAAGTCTTGGCTGCATCGGCAGGTTTCTTCTTCCCAATGCCAGAAGCTAAGAAATGATGTGGGATGGTTTCCTTTGGTGCTACTGCTGCCGgtttgttt                   <  1:94048/245‑1 (MQ=255)                                                                                                                                                                                              gACCATTTCTATGGGCAACTCATGCAATTATGTTGAGCAATACGCGCGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCTGTGTTTTTGGTTTAACACCATGTTCTGCGCCGCCACAAGTTGTAGCTGCAGCGACAGTTTTCTTCTACCCAATTCCAGAAACGAAGAAATGATGTGTTTTGGGTTCCTTTGGTTCTACTGCTGTCTGTTTGTTTTg                 <  1:150054/249‑1 (MQ=255)                                                                                                                                                                                              gACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCTGGGTTTCTGTTTTAACAACATTTTCTGCGCCGCCACAAATTTTAGcn                                                                                                          <  1:104953/160‑2 (MQ=255)                                                                                                                                                                                              gACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCTGGGTTTCTGTTTTAACAACANTTTNNNnnccnn                                                                                                                        >  2:104953/1‑144 (MQ=255)                                                                                                                                                                                                           ggCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCTGGGTTTCTGTTTTCACAACATTTTCTGCGCCGCCACAAATTTTAGCTGCATCGACAGTTTTCTTCTGCCCAATTCCAGAAACGAAGAAATGATGGGTGATGGTTTCCTTTGGTGCTACTGCTGTCTGTTTGTTTTGAACAGTAAATGTCTg  >  1:86629/1‑251 (MQ=255)                                                                                                                                                                                                                              |                                                                                                                                                                                                                                        TGCACATCAAAGCAGTCTGTCAGTCAGTGCGTGAAGCCACCACGGCCTCCGGCGTGGATAATGCAGCCTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAGAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCTGGGTTTCTGTTTTAACAACATTTTCTGCGCCGCCACAAATTTTAGCTGCATCGACAGTTTTCTTCTGCCCAATTCCAGAAACGAAGAAATGATGGGTGATGGTTTCCTTTGGTGCTACTGCTGTCTGTTTGTTTTGAACAGTAAATGTCTG  >  NC_000913/578384‑578836

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑