Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	578,809	0	T	C	50.0%	‑5.5 / 18.3	20	T29A (ACA→GCA)	borD	prophage lipoprotein BorD
Reads supporting (aligned to +/- strand):  ref base T (3/7);  new base C (2/8);  total (5/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.21e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

CTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCTGGGTTTCTGTTTTAACAACATTTTCTGCGCCGCCACAAATTTTAGCTGCATCGACAGTTTTCTTCTGCCCAATTCCAGAAACGAAGAAATGATGGGTGATGGTTTCCTTTGGTGCTACTGCTGTCTGTTTGTTTTGAACAGTAAATGTCTGTTGAGCACATCCTGTAATAAGCAGGGCCAGCGCAGTAGCGAGTAGCATTTTTTTCATGGTGTTATTCCCGATGCTTTTTGAAGTTCGCAGAATCGTATGTGTAGAAAATTAAACAAACCCTAAACAATGAGTTGAAATTTCATATTGTTAATATTTATTAATGTATGCCAGGTGCGATGAATCGTCATTGT  >  NC_000913/578591‑579027                                                                                                                                                                                                                           |                                                                                                                                                                                                                           aacATGCAATTATTGTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCTGGGTTTCTGTTTTAACAACATTTTCTGCGCCGCCACAAATTTTAGCTGCATCGACAGTTTTCTTCTGCCCAATTCCAGAAACGAAGAAATGATGGGTGATGGTTTCCTTTGGTGCTACTGCTGTCTGTTTGTTTTGAACAGTAAATGTCTGTTGan                                                                                                                                                                                            <  1:200057/249‑2 (MQ=255)  tCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAAACGACCAATCCATTTCCGAATGTTTGATGGGTTTCTGTTTTAACAACATTTTCTGCGCAGCCACAAACTTTAGCTGCATCGAAAGTTTTCTTATGCCCAATTACAGAAACGAAGAAATGATGGGTGATGGTTTCCTTTGGTGCTACTGCTGTCTGTTTGTTTTGAACAGTAAATGTATGTTGAGc                                                                                                                                                                                           >  1:303254/1‑251 (MQ=255)                     aaTACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCATTCCATTTACGAATGTTTGCTGGGTTTCTGTTTTAACAACATTTTCTGCGCCGCCACAAATTTTAGCTGCATCGACAGTTTTCTTCTGCCCAATTCCAGAAACGAAGAAATGATGGGTGATGGTTTCCTTTGGTGCTACTGCTGTCTGTTTGTTTTGAACAGTAAATGTCTGTTGAGCACATCCTGTAATAAGCAgg                                                                                                                                                                        <  1:15403/251‑1 (MQ=255)                          ccacGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTGGCTGGGTTTCTGTTTTAACAACATTTTCTGCGCCGCCACAAATTTTGGCTGCATCGACAGTTTTCTTCTGCCCAATTCCAGAAACGAAGAAATGATGGGGGATGGTTTCCTTTGGTGCTACTGCTGCCGGTTTGTTTTGAACAGTAAACGTCTGTTGAGCACATCCTGTAATAAGCAGGGCCAg                                                                                                                                                                   <  1:168660/250‑1 (MQ=255)                                                                     cGAGCAATCCATTTATGAATGTTTGCTGGGTTTCTGTTTTACCAACATTTTCTGCGCCGCCACAAATTTTGGCTGCATCGACAGTTTTCTTCTGCCCAATTCCAGAAACGAATAAATGATGGGTGATGTTTTCCTTTGGTGCTTCTGCTGCCGGTTTGTTTTGAACAGTATACGTCTGTTGAGCACATCCTGTAATAAGCAGGGCCAGCGCAGTATCGATTAGCATTTTTTTCATGGTGATATTCCCGATg                                                                                                                        <  1:252358/251‑1 (MQ=255)                                                                     cGAGCAATCCATTTACGAATGTTTGCTGGGTTTCTGTTTTAACAACATTTTCTGCGCCGCCACAAATTTTGGCTGCATCGACAGTTTTCTTCTGCCCAATTCCAGAAACGAAGAAATGATGGGTGATGGTTTCCTTTGGTGCTACTGCTGCCGGTTTGTTTTGAACAGTAAACGTCTGTTGAGCACATCCTGTAATAAGCAGGGCCAGCGCAGTAGCGAGTAGCATTTTTTTCATGGTGTTATTCCCGATg                                                                                                                        <  1:252357/251‑1 (MQ=255)                                                                     cGAGCAATCCATTTACGAATGTTTGCTGGGTTTCTGTTTTAACAACATTTTCGGCGCCGCCACAAATTTTAGCTGCATCGACAGTTTTCTTCTGCCCAATTCCAGAAACGAAGAAATGATGGGTGATGGTTTCCTTTGGTGCTACTGCTGTCTGGTTGTTTTGAACAGTAAATGTCTGTTGAGCACATCCTGTAATAAGCAGGGCCAGCGCAGTAGCGAGTAGCATTTTTTTCATGGTGTTATTCCCGATg                                                                                                                        <  1:160759/251‑1 (MQ=255)                                                                                    cGAATGTTTGCTGGGTTTCTGTTTTAACAACATTTTCTGCGCCGCCACAAATTGTGGCTGCATCGACAGTTTTCTTCTGCCCTATTCCAGAAACGAAGAAATGATGGGTGATGGTTTCCTTTGGTGCTACTGCTGCCGGTTTGTTTTGAACAGTAAACGTCTGTTGAGcac                                                                                                                                                                                         <  1:132606/171‑1 (MQ=255)                                                                                                                                          tAGCTGCATCGACAGTTTTCTTCTGCCCAAGTCCAGAAACGAAGAAATGATGGGTGATGGTTTCCTTTGGTGCGACTGCTGTCTGTTTGTTTTGAACAGTAAATGTCTGTTGAGCACAGTCTGTAAGAAGCAGGGCCAGCGCAGGAGCTAGTATCAGTTTTTTCATGGTTTTATTCCCGATGCTATTTGAAGTTCGCAGAATCGGAtgtg                                                                                            <  1:220139/210‑1 (MQ=255)                                                                                                                                                naTCGACAGTTTTCTTCTGCCCAATTCCAGAAACGAAGAAATGATGGGTGATGGTTTCCTTTGGTGCTACTGCTGCCGGTTTGTTTTGAACAGTAAACGTCTGTTGAGCACATCCTGTAATAAGCAGGGCCAGAGCAGTAGCGAGTAGCATTTTTTTCATGGTGTTATTCCCGATGCTTTTTGAAGTTCGCAGAATCGTATGTGTAGAAAATTAAACAAACCCTAAACAATGAGTTGAAATTTCat                                                  >  1:37321/2‑246 (MQ=255)                                                                                                                                                                   nccAATTCCAGAAACGAAGAAATGATGGGTGATGGTTTCCTTTGGTGCTACTGCTGTCTGTTTGTTTTGAACAGTAAATGTCTGTTGAGCACATCCTGAAATAAGCAGGGCCAGCGCAGTAGCGAGTAGCATTTTTTTCATGGTGTTATTCCCGATGCTTTTTGAAGTTCGCAGAATCGTATGTGTAGAAAATTAAACAAACCCTAAACAATGAGTTGaa                                                         >  1:84339/2‑220 (MQ=255)                                                                                                                                                                       cttCCAGAAACGAAGAAATGATGGGGGATGGTTTCCTTTGGTGCTACTGATGTTGGCTTGTTTTCAACCGTAAGCGTCTGTTGAGCACATCCTGTAATAAGCAGGGCCAGCGCCGTAGCGAGAAGCGTTTTTTTCATGGGGTTATTCCCGATGCttttt                                                                                                                  >  1:159325/2‑159 (MQ=255)                                                                                                                                                                         tCCAGAAACGAAGAAATGATGGGTGATGGTTTCCTTTGGTGATACTGCTGCCGGATTGTTTTGAACAGTAAACGTCTGTTGAGCACATCCTGTAATAAGCAGGGCCAGCGCAGTAGCGAGTAGCATTTTTTTCATGGTGTTATTCCCGATGCTTTTTGAAGTTCg                                                                                                          >  1:125759/1‑165 (MQ=255)                                                                                                                                                                          ccAGAAACGAAGAAAGGATGGGTGATGGTTTCCTTTGGTGCTACTGCTGCCGGTTTGTTTTGAACAGTAAACGTCTGTTGAGCACATCCTGTAATAAGCAGGTCCAGCGCAGTAGCGAGTAGGATTTTTTTCATGGTGTTATTCCCGATGCTTTTTGAAGTTcn                                                                                                          <  1:35202/164‑2 (MQ=255)                                                                                                                                                                            aGAAACGAAGAAATGATGGGTGATGGTTTCCTTTGGTGCTACTGCTGTCTGTTTGTTTTGAACAGTAAATGTCTGTTGAGCACATCCTGTAATAAGCAGGGCCAGCGCAGTAGCGAGTAGCATTTTTTTCATGGTGTTATTCCCGATGCTTTTTg                                                                                                                 <  1:143605/155‑1 (MQ=255)                                                                                                                                                                                         tgaggggTGATGGTTTCCTTTGGTTCTACTGCTGCCGGTTTGTGTTGAGCAGTAAACGTCGGTTGAGCACAGCCTGTAATAAGCAGGGCCAGCGCAGTAGCGAGTAGCATTTTTTTCATgg                                                                                                                                      <  1:210661/117‑1 (MQ=255)                                                                                                                                                                                           atgGGTGATGGTTTCCTTTGGTGCTACTGCTGTCTGTTTGTTTTGAACAGTAAATGTCTGTTGAGCACATCCTGTAATAAGCAGGGCCAGCGCAGTAGCGAGAAGCATTTTTTTCATGGTGTTATTCCCGATGCTTTTTGAAGTTCGCAGAATCGTATGTGTAGAAAATTAAACAAACCCTAAACAATGAGTTGAAATTTCATATTGTTAATATTTATTAATGTATGCCAGGTGCGATGAATCGTCATTGt  <  1:330701/251‑1 (MQ=255)                                                                                                                                                                                           atgGGTGATGGTTTCCTTTGGTGCTACTGCTGTCTGTTTGTTTTGAACAGTAAATGTCTGTTGAGCACATCCTGTAATAAGCAGGGCCAGCGCAGTAGCGAGAAGCATTTTTTTCATGGTGTTATTCCCGATGCTTTTTGAAGTTCGCAGAATCGTATGTGTAGAAAATTAAACAAACCCTAAACAATGAGTTGAAAGTTCATATTGTTAATATTTATTAATGTATGCCAGGTGCGATGAATCGTCATTGt  <  1:330704/251‑1 (MQ=255)                                                                                                                                                                                                   tGGTTTCCTTTGGTGCTACTGCTTCCGGTTTGTTTTGAACAGTAAACGGCTGTTGAGCACATCCTGTAATAAGCAGGGCCAGCGCAGTAGCGAGTAGCAttttttt                                                                                                                                           <  1:120488/106‑1 (MQ=255)                                                                                                                                                                                                          cTTTGGTGCTACTGCTGCCGGTTTGTTTTGAAAAGNAAANNACNNTTNAGcac                                                                                                                                                                                         <  2:177366/53‑1 (MQ=255)                                                                                                                                                                                                                           |                                                                                                                                                                                                                           CTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCTGGGTTTCTGTTTTAACAACATTTTCTGCGCCGCCACAAATTTTAGCTGCATCGACAGTTTTCTTCTGCCCAATTCCAGAAACGAAGAAATGATGGGTGATGGTTTCCTTTGGTGCTACTGCTGTCTGTTTGTTTTGAACAGTAAATGTCTGTTGAGCACATCCTGTAATAAGCAGGGCCAGCGCAGTAGCGAGTAGCATTTTTTTCATGGTGTTATTCCCGATGCTTTTTGAAGTTCGCAGAATCGTATGTGTAGAAAATTAAACAAACCCTAAACAATGAGTTGAAATTTCATATTGTTAATATTTATTAATGTATGCCAGGTGCGATGAATCGTCATTGT  >  NC_000913/578591‑579027

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: ‑