Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	581,056	0	A	G	33.3%	14.9 / 12.5	21	T75A (ACA→GCA)	nohD	putative DNA‑packaging protein NohD
Reads supporting (aligned to +/- strand):  ref base A (9/5);  new base G (4/3);  total (13/8)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.27e-01
Rejected as consensus: Frequency below/above cutoff threshold.

GCAATGGAAGTCAACAAAAAGCAGCTGGCTGACATTTTCGGTGCGAGTATCCGTACCATTCAGAACTGGCAGGAACAGGGAATGCCCGTTCTGCGAGGCGGTGGCAAGGGTAATGAGGTGCTTTATGACTCTGCCGCCGTCATAAAATGGTATGCCGAAAGGGATGCTGAAATTGAGAACGAAAAGCTGCGCCGGGAGGTTGAAGAACTGCTGCAGGCCAGCGAGACAGATCTCCAGCCAGGGACTATTGAGTACGAACGCCATCGACTTACGCGTGCGCAGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGATCCCCCTGTCGGTGCAGCGGCGTTTTCCGGAACTGGAA  >  NC_000913/580831‑581265                                                                                                                                                                                                                                  |                                                                                                                                                                                                                  gCAATGGAAGACAACAAAAAGCAGCTGGCTGACATTTTCGGTGCGAGTATCCGTACCATTCAGAACTGGCAGGAACAGGGAATGCCCGTTCTGCGAGGCGGTGGCAAGGGAAATGAGGTGCTTTATGACTCTGCCGCCGTCATAAAATGGTATGCCGAAAGGGATGCTGAAATTGAGAACGAAAAGCTGCGCAGGGAGGTTGAAGAACTGCTGCAGGCCAGCGAGACAGATCTCCAGCCAgggcaaacgcg                                                                                                                                                                                          >  1:145029/1‑243 (MQ=255)            naacaaAAAGCAGCTGGCTGACATTTTCGGTGCGAGTATCCGTACCATTCAGAACTGGCAGGAACAGGGAATGCCCGTTCTGCGAGGCGGTGGCAAGGGTAATGAGGTGCTTTATGACTCTGCCGCCGTCATAAAATGGTATGCCGAAAGGGATGCTGAAATTGAGAACGAAAAGCTGCGCCGGGAGGTTGAAGAACTGCTGCAGGCCAGCGAGACAGATCTCCAGCCAGGGACTATTGAGCACGAACGcc                                                                                                                                                                               >  1:34488/2‑251 (MQ=37)             aacaaAAAGCAGCTGGCTGACATTTTCGGAGCGAGTATCCGTACCATTTAGAACTGGCAGGAACGGGGAATGCCCGTTCTGCGAGGCGGTGGCAAGGGTACTGAGGTGCTTTATGACTCTGCCGCCGTCATAACATGGAATGCCGAAAGAGATGCTGAAATTGAGAACGCAAAGCTGCGCCGGGAGGTTGAAGAACTGCTGCAGGCCAGCGAGACAGAACTCCAGCCAGGGTGTATTGAGGACGAACGcc                                                                                                                                                                               >  1:86837/1‑250 (MQ=11)               caaAAAGCAGCTGGCTGACATTTTCGGAGTGAGTATCGGTACCATTCAGAACTGGCAGGAACAGGGCATGCCCGTTTTGCGAGGCGGTGGCAAGGGTCATGAGGCGCTTTATGACTCTGCCGCCGTCATAAACTGGTATGCCGATTGGGATGCTGAAATTGAGAACGAAAAGCTGCGCCGGGCGGTTGAAGAACTGCTGCAGGCCAGCGCGACCGATCTCCAGCCCGGGACTATTGAGTACgcaacccatc                                                                                                                                                                            >  1:166830/1‑242 (MQ=11)                                aCATTTTCGGTGCGAGTATCCGTACCATTCAGAACTGGCAGGAACAGGGAATGCCCGTTCTGCGAGGCGGTGGCAAGGGTAATGAGGTGCTTTATGACTCTGCCGCCGTCATAAAATGGTATGCCGAAAGGGATGCTGAAATTGAGAACGAAAAGCTGCGCCGGGAGGTTGAAGAACTGCGGCAGGCCAGCGAGGCAGATCTCCAGCCAGGAACTATTGAGTACGAACGCCATCGACTTACGCGTgcgc                                                                                                                                                             >  1:39986/1‑249 (MQ=18)                                 cATTTTCGGTGCGAGTATCCGTACCATTCAGAACTGGCAGGAACAGGGAATGCCCGTTCTGCGAGGCGGTGGCAAGGGTAATGAGGTGCTTTATGACTCTGCCGCCGTCATAAAATGGTATGCCGAAAGGGATGCTGAAATTGAGAACGAAAAGCTGCGCCGGGAGGTTGAAGAACTGCGGCAGGCCAGCGAGGCAGATCTCCAGCCAGGAACTATTGAGTACGAACGCCATCGACTTACGCGTGCGCAgn                                                                                                                                                          <  1:31012/251‑2 (MQ=16)                                    tttCGGTGCGAGTATCCGTACCATTCAGAACTGGCAGGAACAGGGAATGCCCGTTCTGCGAGGCTGTGGCAAGGGTAATGAGGTGCTTTATGACTCTGCCGCCGTCATAAAATGGTATGCCGAAAGGGATGCTGAAATTGAGAACGAAAAGCTGCGCCGGGAGGTTGAAGAACGGCGGCAGGCCAGCGAGGCAGATCTCCAGCCAGGAACTATTGAGTACGAACGCCATCGACTTACGCGTGCGCAGGcc                                                                                                                                                        <  1:110686/250‑1 (MQ=255)                                                          aTTCAGAACTGGCAGGAACAGGGAATGCCCGTTCTGCGAGGCGGTGGCAAGGGTAATGAGGTGCTTTATGACTCTGCCGCCGTCATAAAATGGTATGCCGAAAGGGATGCTGAAATTGAGAACGAAAAGCTGCGCCGGGAGGTTGAAGAACTGCTGCAGGCCAGCGAGACAGATCTCCAGCCAGGGACTATTGAGTACGAACGCCATCGACTTACGCGTGCGCAGGCCGATGCACAGGAGCTGAAAAATGc                                                                                                                                 <  1:133417/251‑1 (MQ=38)                                                                            cAGGGAATGCCCGTTCTGCGAGGCGGTGGCAAGGGTAATGAGGTGCTTTATGACTCTGCAGCCGTCATAAAATGGAATGCCGAAAGGGATGCTGAAATTGAGAACGAAAAGATGCGCCGGGAGGTTGAAGAACTGCTGCAGGCCAGAGAGACAGATCTCAAGCCAGGGACTATTGAGTACGAACGCCATCGACTTACGCGTGCGCAGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAgt                                                                                                               >  1:124846/1‑251 (MQ=255)                                                                                               gAGGCGGTGGCAAGGGTAATGAGGTGCTTTATGACTCTGCCGCCGTCATAAAATGGTATGCCGAAAGGGGTGCTGAAATTGAGAACGAAAAGCTGCGCCGGGAGGTTGAAGAACTGCGGCAGGCCAGCGAGGCAGATCTACAGCCAGGGACTATTGAGTACGAACGCCATCGACTTACGCGTGCGCAGGCCGACGCACAGGAACTGAAGAATGCCAGCGACTCCGCTGCAGGGGTGGAAACAGCATTCTGt                                                                                            >  1:111945/1‑251 (MQ=11)                                                                                                        gCAAGGGTAATGAGGTGCTTTATGACTCTGCCGCCGTCATAAAATGGTATGCCGAAAGGGATGCTGAAATTGAGAACGAAAAGCTGCGCCGGGAGGTTGAAGAACTGCGGCAGGCCAGCGAGGCAGATCTCCAGCCAGGAACTATTGAGTACGAACGCCATCGACTTACGCGTGCGCAGGCCGa                                                                                                                                                      <  1:76764/184‑1 (MQ=255)                                                                                                            gggTAATGAGGTGCTTTATGACTCTGCCGCCGTCATAAAATGGTATGCCGAAAGGGATGCTGAAATTGAGAACGAAAAGCTGCGCCGGGAGGTTGAAGAACTGCTGCAGGCCAGCGAGACAGATCTCCAGCCAngg                                                                                                                                                                                                  >  2:106472/1‑136 (MQ=255)                                                                                                                                   ctGCCGCCGTCATAAAATGGTATGCCGAAAGGGATGCTGAAATTGAGAACGAAAAGCTGCGCCGGGAGGTTGAAGAACTGCTGCAGGCCAGCGAGACAGATCTCCAGCCAGGGACTATTGAGTACGAACGCCATCGACTTACGCGTGCGCAGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAAttn                                                          <  1:106472/249‑2 (MQ=39)                                                                                                                                     gccgccGTCATAAAATGGTATGCCGAAAGGGATGCTGAAATTGAGAACGAAAAGCTGCGCCGGGAGGATGAAGCACTGCGGCAGGCCAGCGAGGCAGATCTCCAGCCAGGAACTCTTGAGTCCGAACGCCATCGACTTAcg                                                                                                                                                                    >  1:152477/1‑141 (MQ=11)                                                                                                                                          cgTCATAAAATGGTATGCCGAAAGGGATGCTGAAATTGAGAACGAAAAGCTGCGCCGGGAGGTTGAAGAACTGCTGCAGGCCAGCGAGACAGATCTCCAGCCAGGGACTATTGAGTACGAACGCCATCGACTTACGCGTGCGCAGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATtc                                                 <  1:51516/251‑1 (MQ=38)                                                                                                                                             cATAAAATGGTATGCCGAAAGGGATGCTGAAATTGAGAACGAAAAGCTGAGCCGGGAGGTTGAAGAAATGCGGAAGGCCAGCGAGGCAGATCTCCAGCCAGGAACTATTGAGTACGAACGCCATCGAATTACGCGTGCGTAGGCAGACGCACAGGAAATGCAGAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATGGAAGGTGAAATTGCCAGTATTCTCg                                              >  1:169205/1‑251 (MQ=11)                                                                                                                                                             gAAAGGGATGCTGAAATTGAGAACGAAAAGCTGCGCCGGGAGGTTGAAGAACTGCTGCAGGCCAGCGAGACAGATCTCCAGCCAGGGACTATTGAGTACGAACGCCATCGACTTACGCGTGCGCAGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGGCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGATCCCCCTGTc                              <  1:82737/251‑1 (MQ=21)                                                                                                                                                                  ggATGCTGAAATTGAGAACGAAAAGCTGCGACGGGAGGTTGAAGAACTGCTGCAGGCCAGCGAGACAGATCTCCAGCCAGGGACTATTGAGTACGAACGCCATCGACTTACGCGTGCGCAGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGATCCCCCTGTCGGTGc                         >  1:144876/1‑251 (MQ=21)                                                                                                                                                                               gagaACGAAAAGCTGCGCCGGGAGGTTGAAGAACTGCTGCAGGCCAGCGAGACAGATCTCCAGCCAGGGACTATTGAGTACGAACGCCATCGACTTACGCGTGCGCAGGCCGATGCACAGGAGCTGATAAAGGCCAGAGACTCCGCTGAAGTGGTGGAAACCTCATTCTTTACTTTCGTGCGGTCGCGGAGCGCAGGTGAAATTGCCAGGATTCTCGACGGGAGCCCCCTGTCGGTGCAGCGGCGTTTTcc            <  1:112507/251‑1 (MQ=11)                                                                                                                                                                                                                         nccAGCGAGACAGATCTCCAGCCAGGGACTATTGAGTACGAAAGCCATCGACTTACGCGTGCGCAGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGAc                                            >  1:30095/2‑177 (MQ=17)                                                                                                                                                                                                                           cAGCGAGACAGATCTCCAGCCAGGGACTATTGAGTAAGAAAGCCATCGACTTACGCGTGCGCAGGCCGCTGCACAGGAGCTGAAAAATGACAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTAGTGCTGTCGCGGATCGCAGGTGAAATTGACAGTATTCTCGACGGGATCCCCCTGTCGGTGCAGCGGCGTTTTCCGGAACTGGaa  >  1:164140/1‑217 (MQ=11)                                                                                                                                                                                                                                  |                                                                                                                                                                                                                  GCAATGGAAGTCAACAAAAAGCAGCTGGCTGACATTTTCGGTGCGAGTATCCGTACCATTCAGAACTGGCAGGAACAGGGAATGCCCGTTCTGCGAGGCGGTGGCAAGGGTAATGAGGTGCTTTATGACTCTGCCGCCGTCATAAAATGGTATGCCGAAAGGGATGCTGAAATTGAGAACGAAAAGCTGCGCCGGGAGGTTGAAGAACTGCTGCAGGCCAGCGAGACAGATCTCCAGCCAGGGACTATTGAGTACGAACGCCATCGACTTACGCGTGCGCAGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGATCCCCCTGTCGGTGCAGCGGCGTTTTCCGGAACTGGAA  >  NC_000913/580831‑581265

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑