Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,875,532	0	A	T	30.8%	35.2 / 11.6	27	H32L (CAT→CTT)	yidX	putative lipoprotein YidX
Reads supporting (aligned to +/- strand):  ref base A (5/13);  new base T (8/0);  total (13/14)
Fisher's exact test for biased strand distribution p-value = 1.65e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.41e-01
Rejected as consensus: Frequency below/above cutoff threshold.

TGTTGTACTACAATTTAGATCACAAAAAGAACAATGCATAAAAAAATGACATGCGTCGGGCAGAAATCTGAAAAGGGATATCAGGCGCTAAACAGGAGGGAAAGAAGAGTATGCTTTCAACGGCTTAGCTACTCGTTTAAAGGATTAATCATGAAGTTGAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTCCCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCTCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACACCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGTAGGGGAATCGCTGGATTACCTTATCACTGATGGTGCCGATGACATCGTTAAGATGCTCAATGATCCAGCACTTAACCGGCACAATATTCAGGTTGCCGATGACGCAAGATTTGTTTTAAATGCGGGGAAAAAGAAATTTACCGG  >  NC_000913/3875288‑3875778                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                                       tgtggtACTACAATTTAGATCACAAAAAGAACAATGCATAAAAAAATGTCATGCGTCGGGCAGAAATCTGAAAATGGATATCAGGCGCTAAACAGGAGAGAAAGAATAGTATGTTTTCAAGGGCTTAGCTACTCTTTTAAAGTATTAATCGTTAAGTTTAATTTTAAGGGATTTTTTAAGTCTGCCTGTTTATTCCCGCTGTTGCTGATTCTTGCAGGCTGTATCGCGTATGCTGTGGTTTCCCGTACCg                                                                                                                                                                                                                                                   <  2:320831/246‑1 (MQ=255)     gtACTACAATTTAGATCACAAAAAGAACAATGCATAAAAAAATGACATGCGTCGGGCAGAAATCGGAAAAGGGATATCAGGCGCTAAACATGAGGGAAAGAAGAGTATGCTTTCAACGGCTTAGCTACTCGTTTAAAGGATTAATCATGAAGTTGAATTTTAAGGTATTTTTTAAGGCTGCCGGTTTATTCCCACGGGCGCTGATGCGTTCAGGCTGTATCTCGTATTCGCTGGTTTCCCATACCGCAAAg                                                                                                                                                                                                                                              <  2:73489/251‑1 (MQ=255)     gtACTACAATTTAGAACACAAAAAGAACAATGCATAAAAAAATGACAAGCGTCGGGCAGAAATCTGAAAAGGGATATCAGGCGCTAAACAGGAGGGAAAGAAGAGTATGCTTTCAACGGCTTAGCTACTCGTTTAAAGGATTAATCATGAAGTTGAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTCTCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCTCTGGTTTCCCATTCCGCAAAg                                                                                                                                                                                                                                              <  2:199850/251‑1 (MQ=255)          acAATTTAGATAACAAAAATAAAAATGCATAAAAAAATGATATGCGTCGGGCAGAAATCTAAAAAGGGATATCAGGCGCTAAACAGGGAGGAAAGAAGAGTATGCTTTAAACGGCTTAGCTACTAGTTTAAAGGATTAAGCATGAAGATGAATTTTAATGGTGTGTTTAAGGCTGCTGGTTTATTACCACGGTCGCTGATGCTTTCAGGCTGTATCTCGTATTCTCTGGTTTCCCATACCGAAAAGGGTa                                                                                                                                                                                                                                          <  2:178434/250‑1 (MQ=255)                                            aaaTGACATGCGTCGGGCAGAAATCTGAAAAGGGATATCAGGCGCTAAACAGGAGGGAAAGAAGAGTATGCTGTCAACGGCTTAGCTACTCGTTTAAAGGATTAATCATGAAGTTGAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTCCCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCTCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGAAAGGATCAATCGCAGTCAGACACCATc                                                                                                                                                                                                       <  2:200118/251‑1 (MQ=255)                                                                         aaGGGATATCAGGCGCTAAACAGGAGGGAAAGAAGAGTATGCTTTCAACGGCTTAGCTACTCGTTTAAAGGATTAATCATGAAGTTGAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTCCCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCTCTCTTTTGCTTTACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACACCATCACTGGGCTATCGCAGGCAAAAGATAGTa                                                                                                                                                                           >  1:243388/1‑250 (MQ=255)                                                                          aGGGATAGCAGTCGATAAACAGGAGGGAAATAAGAGTATTATTTCAACGGAAAAAAGACACGATTAAAAAATTAATCATGAAGGTGAATTTTAAGGTAGTTTTTAAGGCTGCCGGTTGATTCCCGTTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCTCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGAAAGTAGCAATCGCAGTCAGACACCATCACTGGGCTATCGCAGGCAATAGATAGTAAt                                                                                                                                                                         <  1:48890/251‑1 (MQ=255)                                                                            ggATATCAGGCGCTAAACAGGAGGGAAAGAAGAGTATGCTTTCAACGGCTTAGCTACTCGTTTAAAGGATTAATCATGAAGTTGAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTCCCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCTCTGGTTTGCCTTACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACACCATCACTGGGCTATCGCAGGCAAAAGATAGTAATgg                                                                                                                                                                       >  1:6568/1‑251 (MQ=255)                                                                               tatCAGGCGCTAAACAGGAGGGAAAGAAGAGTATGCTTTCAACGGCTTAGCTACTCGTTTAAAGGATTAATCATGAAGTTGAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTCCCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCTCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACACCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAAc                                                                                                                                                                    >  1:174425/1‑251 (MQ=255)                                                                                          aatcatgaatgAAAGAAGAGTTTGTTTTCAACGGCTTAGCTATACATTTAAAAGATTAATCATGAAGTTGAAGTTTAAGGAATTTTTTAAGGCTGCCAGTTTATACCCACTGGCGCTGATGCTTTCAAGCTGTATCTCGTATGCTCTGGTTTCCCATACCGCAAAGGGTAGTTTAGGAAAGTATCAATCTCAGTCAGTCACTATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAggtta                                                                                                                                                           <  1:41728/239‑4 (MQ=255)                                                                                            aCAGGAGGGAAAGAAGAGTATGCTTTCAACGGCTTAGCTACTCGTTTAAAGGATTAATCATGAAGTTGAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTCCCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCCGTCTTCTGCTTGACAAAAAAGGGAAGTTCAGGAAAGTATCATTCGCAATCAGAGACAATCACAGGGCGATGGAAGGCAAAAGATAGTAATGGAACAAAAgacaatgat                                                                                                                                                       >  1:277948/1‑243 (MQ=255)                                                                                                gaggGAAAGCAGAGTATGCTTTCAACGGCTTAGCTACTCGTTTAAAGGATTAATCATGAAGTTGAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTCCCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCTCTGTTTTCCCATACCGCAAAGGGTAGATCAGGAAAGTATCAATCGCAGTCAGACACAATCACTGGACTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTCTGTTTTTg                                                                                                                                                   >  1:63437/1‑251 (MQ=255)                                                                                                 agggaaagaaaagtattacatCAACGGCTTAGCTAATCGTTTTAAGGATTAATCATGAAGTTGAAGTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTCCCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCTCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACACCATCGCTGGGCTATCGCAGGCAAAAGATAGTAATGGATCAAAAGGCTATGTTTTTGt                                                                                                                                                  <  2:185849/231‑1 (MQ=255)                                                                                                 aggGAAAGAAGAGTATGCTTTCAACGGCTTAGCTACTCGTTTAAAGGATTAATCATTAAGTTGAATTTTAAGGGATTTTTTCAGGCTGCCGGTTTATTCCCTCTGGCGCTGATGCTTGCAGGCTGTATCTCGTATGCTCTGGTTTCCCATGCCGCAAAGGTTAGTTCAGGAAAGTATCAAGCGCAGTCAGACAAAATGACTGGGCTAGCGCGGGCAAAAGATAGTAAGGGAATAAATGGTTTTGtttttt                                                                                                                                                   <  2:63437/250‑2 (MQ=255)                                                                                                     aaaGAAGAGTATGCTTTCAACGGCTTAGCTACTCGTTTAAAGGATTAATCATGAAGTTGAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTCCCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCTCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACACCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGTAggg                                                                                                                                              <  2:188351/251‑1 (MQ=255)                                                                                                     aaaGAAGAGTATGCTTTCAACGGCTTAGCTACTCGTTTAAAGGATTAATCATGAAGTTGAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTCCCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCCGTGGTCTGCCTGACAGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACACCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGTAggg                                                                                                                                              >  1:281924/1‑251 (MQ=255)                                                                                                              tATGCTTTCAACGGCTTAGCTACTCGTTTAAAGGATTAATCATGAAGTTGAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTCCCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCCCTCGTTTCCCTTACCGCAAAAGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACACCATCACTGCGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGTAGGGGAATCGCTg                                                                                                                                     >  1:263837/1‑251 (MQ=255)                                                                                                                                   aCTCGTTTAAAGGATTAATCATGAAGTTGAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTCCCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCCCTGGTCTCCCTGACAGCAAAGGGAAGTTCAGGAAAGTATCAATCGCAGTCAGACACCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGTAGGGGAATCGCTGGATTACCTTATCACTGATGGt                                                                                                                >  1:111389/1‑251 (MQ=255)                                                                                                                                        tttAAAGGATTAATCATGAAGTTGAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTCCCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCCGTCTTTTGCTTGAAAACAAAGGGAAGTTCAGGAAAGTATCAATCTCAGTAAGACACCATCATTGGAATATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGTAGGGGAATCGCTGGATTCCTTTATCACTGCTGGTGCCg                                                                                                            >  1:170583/1‑250 (MQ=255)                                                                                                                                                   aaTCATGAAGTTGCATTTTAAGGGCTTTTTTAAGGCTGCCGGTTTATTCCCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCTCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACACCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAgg                                                                                                                                                              >  2:60115/1‑189 (MQ=255)                                                                                                                                                   aaTCATGAAGTTGAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTCCCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCTCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACACCATCACTGGGCTATCGCAGGCAAAAGAGAGTAATGGAACAAAAgg                                                                                                                                                              <  1:60115/189‑1 (MQ=255)                                                                                                                                                                           aTTTTTTAAGGCTGCCGGTTTATTCCCACTGGCTCTGATGTTTTCAGGCTGTATCTCGTATGCTCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTGAGACACCATCACTGGGCTATCGCAGGCAAAAGATAGTAATTGAATAAAAGGCTATGTTTTTGTAGGGGAATCGCTGGATTAACTTATCACTGATGGTGCCGATGACATCGTTAAGATGCTCTATGATCCAGCGCttt                                                                        <  2:6568/251‑2 (MQ=255)                                                                                                                                                                                      cggtcggagtattcccaacgtcgcTGATGCGTTCAGGTGGTAACTAGTATGCTCATGTTTCCCAGACCGCAAAGGGGAGTTCAGGAAAGTAAAAATCGCAGACAGACAACAGCACTGGGCGATCGCAGGAAAAAGATAGTAATGGAACAAAATGTTATGTTTTTGTAGGGGAATTGCTGGATTACCTGATCACTGATGGTGCCGATGACATCGTTAAGATGTTCAATGAGCCAGCACTTAATCGGAACAat                                                             <  2:14421/230‑1 (MQ=255)                                                                                                                                                                                                                aTGCTTTCAGGCTGTATCTCGTATGCCGTCTTCTGCTTGACCGCAAAGAATAGTGCAGGCAAGTATCAATCGCAGTCCGTCACCATCCCCACGCTATCGCAGGCAAAAGATAGTACTGGCACAAAGGGCCATGTTGTTGAAGGGGAATCGCTGGATTACCTTATCACTGATGGAGCCGATCACATCGTTAAGATGATCATCGATCCAGCACTTCACCGGCACAATATTCATGTCGCTGATGACGCAAGAtt                                   >  1:21614/1‑251 (MQ=255)                                                                                                                                                                                                                       cAGGCTGTATCTCGTATGCTCTGGTTTCCCATACCGCACAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACACAATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGTAGGGGAATCGCTGGATTACCTTATCACTGATGGTGCCGATGACATCGTTAAGATGCTCACTGATCCAGCACTTAACCGGCACAATATTCAGGTTGCCGATGACGCAAGATTTGtttt                             >  2:31711/1‑250 (MQ=255)                                                                                                                                                                                                                                   cGTATGCTCTGGTTTCCCATACCGAAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCCGACACCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGTAGGGGAATCGCTGGATTACCTTATCACTGATGGTGCCGATGACATCGTTAAGCTGCTCAATGATCCAGCACTTAACCGGCACAATATTCAGGTTGCCGATGACGCAAGATTTGTTTTAAATGCGGGGaa                 >  2:57919/1‑250 (MQ=255)                                                                                                                                                                                                                                                    cATACCGAAAAGGGTAGTTCATGAAAGGATCAATCACAGTCAGACACCAACAATGGGCTATCGCAGGCAAAAGATAGTACTGGAACAAAAGGCTATGTTGTTGTAGGGGAATCGCTGGAGTACCTTAGCAATGATGGTGCCGATGACAGCGTTAATATGCTCAATGATCCAGCACTTAACCGTCACAATATTCGGGTTGCTGATGACGCAAGATTTGTTTTAAATGCGGGGAAAAAGTATTTTACCgt  <  2:240391/248‑2 (MQ=255)                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                                       TGTTGTACTACAATTTAGATCACAAAAAGAACAATGCATAAAAAAATGACATGCGTCGGGCAGAAATCTGAAAAGGGATATCAGGCGCTAAACAGGAGGGAAAGAAGAGTATGCTTTCAACGGCTTAGCTACTCGTTTAAAGGATTAATCATGAAGTTGAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTCCCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCTCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACACCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGTAGGGGAATCGCTGGATTACCTTATCACTGATGGTGCCGATGACATCGTTAAGATGCTCAATGATCCAGCACTTAACCGGCACAATATTCAGGTTGCCGATGACGCAAGATTTGTTTTAAATGCGGGGAAAAAGAAATTTACCGG  >  NC_000913/3875288‑3875778

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑