Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,177,748	0	C	A	36.0%	14.0 / 12.5	25	E55* (GAG→TAG)	nudF	ADP‑sugar pyrophosphatase
Reads supporting (aligned to +/- strand):  ref base C (14/2);  new base A (0/9);  total (14/11)
Fisher's exact test for biased strand distribution p-value = 2.69e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

GCCAGGAAACTTAACACCGGTTTGGTCCGTTTGACTATCAGTCCCGCCTCTTCAATCGCTTCGCGACGGGCAACATCTTCCACACTTTCACCCTCTTCAATCATCCCGGCAACCATCTCCAGTAGCCAAGGGGTTTCGCTGGTGTCGTACGCGGCAATCCGAATCTGCTCAATCAGCACAACTTCATCACGCACTGGGTCAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTCAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCAATAATTTCTACATCGTTTTTGCCAAATGTAACGGGCAGGTTGTCTGGCTTAAGCATTGTTAATGTCCTGGCACTAATAGTGAATTAAATGTGAATTTCAGCGACGTTTGACTGCCGTTTGAGCAGTCATGTGTTAAATTG  >  NC_000913/3177516‑3177994                                                                                                                                                                                                                                         |                                                                                                                                                                                                                                                       gCCAGGACGCTTAACACCGGTTTGGTCCGTTTGACTCTCAGTCCCGCCTCTTCAATCGCTTCGCGACGGGCAACATCTTCCACACTTTCACCCTCTTCAATCATCCCGGCAACCATCTCAAGTAGCCAAGGGGTTTCGCTGGTGTCGTACGCGGCAATCCGCATCTGCTCAATCAGCACAACTTCATCACGCACTGGGTCAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTCAAAAATTTCCCGCCGCAc                                                                                                                                                                                                                                      >  2:60753/1‑251 (MQ=255)             aaCACCGGTTTGGTCCGTTTGACTATCAGTACCGCCTCTTCAATCGCTTCGCGCCGGGCAACATCTTCCACACTTTCACCCTCTTCAATCATCCCGGCAACCATCTCCAGTAGCCAAGGGGTTTCGCTGGTGTCGTACGCGGCAATCCGAATCTGCTCAATCAGCACAACTTCATCACGCACTGGGTCAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTCaa                                                                                                                                                                                                                                                      >  2:459551/1‑223 (MQ=255)                      ttGGTCCGTTTGACTATCAGTCCCGCCTCTTCAATCGCTTCGCGACGGGCAACATCTTCCACACTTTCACCCTCTTCAATCATCCCGGCAACCATCTCCAGTAGCCAAGGGGTTTCGCTGGTGTCGTACGCGGCAATCCGAATCTGCTCAATCAGCACAACTTCATCACGCACTGGGTCAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTCAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGtt                                                                                                                                                                                                                 >  2:291421/1‑251 (MQ=255)                         cctcGTTTGACTATCCGCCCCCCCTCTTCAACCGCTTCGCGACGGGCAACATCTCCCACACTTTCCCCCTCTTCAATCACCCCGGCAACCATCCCCAGTAGCAAGGGGGTTTCGCGGGTGTCGTACGCGGCAATCCGAATCTGCTAAATCAGCACAACTTCACCACGCACGGGGTCAAAGGGTAGCAAGCCTGCGGCGTGACCGCGCTAAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGaa                                                                                                                                                                                                              <  1:16199/248‑1 (MQ=255)                           ccGTTTGACTATCAGTCCCGCCTCTTCAATCGCTTCGCGACGGGCAACATCTTCCACACTTTCACCCTCTTCAATCATCCCGGCAACCATCTCCAGTAGCCAAGGGGTTTCGCTGGTGTCGTACGCGGCAATCCGAATCTGCTCAATCAGCACAACTTCATCACGCACTGGGTCAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTCAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAAt                                                                                                                                                                                                             >  1:174376/1‑250 (MQ=255)                            cGTTTGACTATCAGTCCCGCCTCTTCAATCGCTTCGCGACGGGCAACATCTTCCACACTTTCACCCTCTTCAATCATCCCGGCAACCATCTCCAGTAGCCAAGGGGTTTCGCTGGTGTCGTACGCGGCAATCCGAATCTGCTCAATCAGCACAACTTCATCACGCACTGGGTCAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTCAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGaa                                                                                                                                                                                                              >  2:16199/1‑248 (MQ=255)                                                 tctTCAATCGCTTCGCGACGGGCAACATCTTCCACACTTTCACCCTCTTCAATCATCCCGGCAACCATCTCCAGTAGCCAAGGGGTTTCGCTGGTGTCGTACGCGGCAATCCGAATCTGCTCAATCAGCACAACTTCATCACGCACTGGGTCAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTCAAAAATTTcc                                                                                                                                                                                                                                              <  1:250578/195‑1 (MQ=255)                                                 tctTCAATCGCTTCGCGACGGGCAACATCTTCCACACTTTCACCCTCTTCAATCATCCCGGCAACCATCTCCAGTAGCCAAGGGGTTTCGCTGGTGTCGTACGCGGCAATCCGAATCTGCTCAATCAGCACAACTTCATCACGCACTGGGTCAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTCAAAAATTTcc                                                                                                                                                                                                                                              >  2:250578/1‑195 (MQ=255)                                                                cgACGGCCAACATCTTCCACACTTTCACCCTCTTCAATCATCCCGGCAACCATCTCCAGTAGCCAAGGGGTTTCGCTGGTGTCGTACGCGGCAATCCGAATCTGCTCAATCAGCACAACTTCATCACGCACTGGGTCAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTCAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGaaaaaa                                                                                                                                                                        >  1:90906/1‑250 (MQ=255)                                                                       cAACATCTTCCACACTTTCACCCTCTTCAATCATCCCGGCAACCATCTCCAGTAGCCAAGGGGTTTCGCTGGTGTCGTACGCGGCAATCCGAATCTGCTCAATCAGCACAACTTCATCACGCACTGGGTCAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTCAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCcgcg                                                                                                                                                                 >  2:51948/1‑250 (MQ=255)                                                                                   cacttcccccccctccaaccaccccGGCACCCATCCCCAGTAGCCAAGGGGTTTCGCTGGTGTCGTACGCGGCAATCCGAATCGGCTAAATCAGCACAACTTCAACACGCACTGGGTCAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTAAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTtct                                                                                                                                                    <  2:7190/229‑1 (MQ=255)                                                                                     cTTTCTCCCTCTACAATCTGCCGGGCAACCATCCCCAGCAGCCAGGGGGTTTCGCTGGTGTCGTACGCGGCAATCAGAAGCTGCTCAATCACCAAAACTTCAGCCCGCAGGGGGTAAAGGGGAAGCAAGACGGCGGCGGGCCCGCCCTCAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACTAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGttgct                                                                                                                                                    <  1:321916/249‑4 (MQ=255)                                                                                        tccccacctgcattcatcCCGGCACCCACCCCCAGTGGCCAGGGGGTCTGGCTGGTTTCGGACGCGGAAAGCCGAATTTGCTAAATCACCCCAACTTCACCACGCACTGGGTAAAAGGTGAGAAAGATGGCGGGGGGCGCGCCCTAAAAAATTCCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGAGCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTg                                                                                                                                                <  1:60753/237‑1 (MQ=255)                                                                                                                                        gcgctgggacagaccgcgGAAATCCGAATCTGCACAACCAGAACAACTTCACCCCGCCGTGGGTAAAAGGGGAGAAAGACGGCGGCGTGACCGCCCAAAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCAATAATTTCTACATCGTTTTTGCCAAATGTAACGGGCAGGTTGTCTg                                                                                                <  2:90906/236‑1 (MQ=255)                                                                                                                                            gtcctcttccgtcccaattccgatccTGCCCAACCAGCACAACTTCACCCCGCCCTGGGTAAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTAAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCAATAATTTCTACATCGTTTTTGCCAAATGTAACGGGCAGGTTGTCTGGCTTa                                                                                           <  1:10764/226‑1 (MQ=255)                                                                                                                                                 gcggccgcgGCAACCCAAATCTGCCCAACCAGCAAAACTTCACCACCCCTTGGGAAAAAGGGTAGCAAGAGGGCGGCGTGACCGCCCTAAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCAATAATTTCTACATCGTTTTTGCCAAATGTAACGGGCAGGTTGTCTGGCTTAAGCAt                                                                                      <  1:313936/246‑1 (MQ=255)                                                                                                                                                     aCGCGGCAATCCGAATCTGCTCAATCCGCACAACTTCATCACGCACTGGGTCAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTCAAAAATTTCCCGCCGCACCTCATGAATCATTTGCCCGTTGACTAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCAATAATTTCTACATCGTTTTTGCCAAATGTCACGGGCAGGTTGTCTGGCTTAAGCATTGtt                                                                                  >  1:412173/1‑251 (MQ=255)                                                                                                                                                           cAATCCGAATCTGCTCAATCAGCACAACTTCATCACGCACTGGGTCAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTCAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCAATAATTTCTACATCGTTTTTGCCAAATGTAACGGGCAGGTTGTCTGGCTTa                                                                                           >  2:10764/1‑236 (MQ=255)                                                                                                                                                                    ccTGCTCAAACAGCACACCTTCATCCCGCACGGGGTCAAAGGGACGCAAGACTCGGGCGTGCCCGCGCTAAAAAATTGCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCAATAATTTCTACATCGTTTTTGCCAAATGTAACGGGCAGGTTGTCTGGCTTAAGCATTGTTAATGTCCTGGCACTa                                                                   <  1:146142/250‑1 (MQ=255)                                                                                                                                                                       gCTCAATCAGCACAACTTCATCACGCACTGGGTCAAAGGGTAGCACGACTGCGGCGTGACCGCGCTCAAAAATTTCCCGCCGCCCCTCATGACTCATTTGCCCGTTGAATAGACGATGACGACATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTATCGTGCAATAATTTCTACATCGTTTTTGCCAAATGTAACGGGCAGGTTGTCTGGCTTaa                                                                                          >  2:208402/1‑225 (MQ=255)                                                                                                                                                                                                        aaaaGGGAACCAAGACTGCGGCGTGACCGCGCTAAAAAAGTCCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCAATAATTTCTACATCGTTTTTGCCAAATGTAACGGGCAGGTTGTCTGGCTTAAGCATTGTTAATGTCCTGGCACTAATAGTGAATTAAATGTGAATTTCAGCGACGGTTGAc                               <  2:155720/250‑1 (MQ=255)                                                                                                                                                                                                                          gggcgTGCCCGCGCCAAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCAATAATTTCTACATCGTTTTTGCCAAATGTAACGGGCAGGTTGTCTGGCTTAAGCATTGTTAATGTCCTGGCACTAATAGTGAATTAAATGTGAATTTCAGCGACTTTTGACTGCCGTTTGAGCAGTCAt             <  2:309352/250‑1 (MQ=255)                                                                                                                                                                                                                           ggcgTGACCGCGCTCAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCAATAATTTCTACATCGTTTTTGCCAAATGTAACGGGCAGGTTGTCTGGCTTAAGCATTGTTAATGTCCTGGCACTAATAGTGAATTAAATGTGAATTTCAGCGACGTTTGACTGCCGTTTGAGCAGTCAtg            >  1:23513/1‑251 (MQ=255)                                                                                                                                                                                                                               tGACCGCGCTCAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTCTAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCAATAATTTCTACATCGTTTTTGCCAAATGTAACGGGCAGGTTGTCTGGCTTAAGCATTGTTAATGTCCTGGCACTAATAGTGAATTAAATGTGAATTTCAGCGACGTTTGACTGCCGTTTGAGCAGTCATGTGtt        >  1:202775/1‑251 (MQ=255)                                                                                                                                                                                                                                     cgcTCAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCAATAATTTCTACATCGTTTTTGCCAAATGTAACGGGCAGGTTGTCTGGCTTAAGCATTGTTAATGTCCTGGCACTAATAGTGAATTAAATGTGAATTTCAGCGACGTTTGACTGCCGTTTGAGCAGTCATGTGTTAAATTg  >  1:274350/1‑251 (MQ=255)                                                                                                                                                                                                                                         |                                                                                                                                                                                                                                                       GCCAGGAAACTTAACACCGGTTTGGTCCGTTTGACTATCAGTCCCGCCTCTTCAATCGCTTCGCGACGGGCAACATCTTCCACACTTTCACCCTCTTCAATCATCCCGGCAACCATCTCCAGTAGCCAAGGGGTTTCGCTGGTGTCGTACGCGGCAATCCGAATCTGCTCAATCAGCACAACTTCATCACGCACTGGGTCAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTCAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCAATAATTTCTACATCGTTTTTGCCAAATGTAACGGGCAGGTTGTCTGGCTTAAGCATTGTTAATGTCCTGGCACTAATAGTGAATTAAATGTGAATTTCAGCGACGTTTGACTGCCGTTTGAGCAGTCATGTGTTAAATTG  >  NC_000913/3177516‑3177994

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑