Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,947,850	0	C	T	52.2%	13.0 / 28.0	23	E40K (GAA→AAA)	hdfR	flhDC operon transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base C (3/8);  new base T (12/0);  total (15/8)
Fisher's exact test for biased strand distribution p-value = 3.37e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.48e-05

GTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTGTCGTTATG  >  NC_000913/3947706‑3947998                                                                                                                                                 |                                                                                                                                                     gTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGGAAAGGGTCACACCCCGGTGATTTTTCCGttt                                                                                                                                                >  1:398037/1‑150 (MQ=255)      gAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTTACACCCCGGTGATTTTTCCGTTGTTTGa                                                                                                                                           >  2:354786/1‑151 (MQ=255)        ggTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGGAAAAGGTCACACCCAGGTGATTTTTCAGttttttgctt                                                                                                                                         >  1:8158/1‑143 (MQ=255)                   cctcctTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGGAAAGGGTCACACCCCGTTGATTTTTCAGTTGTCTGATTCGAAAGCTCa                                                                                                                               >  1:168955/1‑150 (MQ=255)                      cctTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGGAAAAGGTCACACCCCGATGATTTTTCCGTTGTTTGATTCGAAAACTCActg                                                                                                                            >  1:358495/1‑150 (MQ=255)                             ggcggcCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGAAAAGGTTCACACCCCGTTGATTTTTCAGTTGTCTGATTCGAAAGCTCACTGCTGACTgg                                                                                                                    >  2:107398/1‑151 (MQ=255)                                 gcCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGGAAAGGGTCACACCCAGTTGATTTTTCAGTTGTCTGATTCGAAAACTCACTGCTGACTGGGGCa                                                                                                                >  2:338427/1‑151 (MQ=255)                                    tGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAGGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGAt                                                                                                             <  2:163074/151‑1 (MQ=255)                                    tGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGAt                                                                                                             <  1:272087/151‑1 (MQ=255)                                            gCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGAAAAGGGTCACACCCCGTTTATTTTTCAGTTTTCTGGTTTGGAAACTCACTGCTGACTGGGTCAGATAGAGGGAt                                                                                                     >  2:279701/1‑151 (MQ=255)                                                       tttCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAAGGTTACACCCCGTTGGTTTTTCAGTTGTTTGGTTTGAAAGATCACTGCTGTCTGGGGCAGATAGAGCGATTCTGCCGCTCg                                                                                          >  1:344641/1‑151 (MQ=255)                                                       tttCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAAGGTCACACCCAGGTGATTTTTCAGTTGTCTTATTTGAAAACTCACTGCTGACTGGGGCAGATAGAGCGATTTAGCCGCTCg                                                                                          >  2:411633/1‑151 (MQ=255)                                                                 aGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGAAAAAGGTCACACCCAGTTGATTTTTTCGTTGTCTGATTTGAAAACTCACTGCTGACTGGGGCAGATAGAGCGATTCAGCCGCCCGACCCAAGTGa                                                                                >  1:300686/1‑151 (MQ=255)                                                                  ggCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGGAAAGGTTCACACCCAGTTGATTTTTCAGTTGTCTGATTTGAAAACTCACTGCTGACTGGGGCAGATAAAAGGGTTTAGCCGCCCGGCCcaaaggaa                                                                               >  2:300017/1‑146 (MQ=255)                                                                                  cGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTc                                                               <  2:156694/151‑1 (MQ=255)                                                                                                             tgtgGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATc                                    <  2:356070/151‑1 (MQ=255)                                                                                                               tgGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATcc                                   <  2:359442/150‑1 (MQ=255)                                                                                                                      tGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGc                            <  2:400414/150‑1 (MQ=255)                                                                                                                            ggTTCACACCCAGTTGATTTACCAGCTGTCTGATTCGATATCTCACTGCTGACTGGGCCAGACATAGCGATTAAGCCGCTCGGCGAATGAGACGCGCTGGTCTAACTTCCAGGATAGATTTTAATAATTCCGTATTCACAGTGCTCTCCg                      >  1:258573/1‑150 (MQ=255)                                                                                                                             gTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCa                    >  1:130501/1‑151 (MQ=255)                                                                                                                                 acacCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAat                <  1:335899/151‑1 (MQ=255)                                                                                                                                  cacCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAatt               >  2:262171/1‑151 (MQ=255)                                                                                                                                               ttCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTGTCGTTATg  <  2:413776/151‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                     GTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTGTCGTTATG  >  NC_000913/3947706‑3947998

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑