Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913578,5740AC50.0% ‑2.6 / 12.1 15intergenic (+6/+26)rzpD/borDputative prophage endopeptidase RzpD/prophage lipoprotein BorD
Reads supporting (aligned to +/- strand):  ref base A (1/6);  new base C (3/4);  total (4/11)
Fisher's exact test for biased strand distribution p-value = 5.59e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.65e-01
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

TGCACATCAAAGCAGTCTGTCAGTCAGTGCGTGAAGCCACCACGGCCTCCGGCGTGGATAATGCAGCCTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAGAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCTGGGTTTCTGTTTTAACAACATTTTCTGCGCCGCCACAAATTTTAGCTGCATCGACAGTTTTCTTCTGCCCAATTCCAGAAACGAAGAAATGATGGGTGATGGTTTCCTTTGGTGCTACTGCTGTCTGTTTGTTTTG  >  NC_000913/578384‑578821
                                                                                                                                                                                              |                                                                                                                                                                                                                                                       
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)
                                                                                                                                                                                             gACCATTTCTATGGGCAACTCATGCAATTATGTTGAGCAATACGCGCGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCTGTGTTTTTGGTTTAACACCATGTTCTGCGCCGCCACAAGTTGTAGCTGCAGCGACAGTTTTCTTCTACCCAATTCCAGAAACGAAGAAATGATGTGTTTTGGGTTCCTTTGGTTCTACTGCTGTCTGTTTGTTTTg  <  1:150054/249‑1 (MQ=255)
                                                                                                                                                                                             gACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCTGGGTTTCTGTTTTAACAACATTTTCTGCGCCGCCACAAATTTTAGcn                                                                                           <  1:104953/160‑2 (MQ=255)
                                                                                                                                                                                             gACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCTGGGTTTCTGTTTTAACAACANTTTNNNnnccnn                                                                                                         >  2:104953/1‑144 (MQ=255)
                                                                                                                                                                                              |                                                                                                                                                                                                                                                       
TGCACATCAAAGCAGTCTGTCAGTCAGTGCGTGAAGCCACCACGGCCTCCGGCGTGGATAATGCAGCCTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAGAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCTGGGTTTCTGTTTTAACAACATTTTCTGCGCCGCCACAAATTTTAGCTGCATCGACAGTTTTCTTCTGCCCAATTCCAGAAACGAAGAAATGATGGGTGATGGTTTCCTTTGGTGCTACTGCTGTCTGTTTGTTTTG  >  NC_000913/578384‑578821

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: ‑