Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,578,287	0	T	C	61.1%	7.4 / 17.3	18	E147G (GAA→GGA)	gntR	d‑gluconate inducible gluconate regulon transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base T (5/2);  new base C (0/11);  total (5/13)
Fisher's exact test for biased strand distribution p-value = 2.45e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.92e-04

ATGATAGTACGTTCGTCGAGACGTGCGCCGAGATAGGCAATGTGGCGATGCCCGCGAGCAATAATGGCAGTGGTCATCTGGCGTGCTGCTTCAAAGTTATCAAAACCGACGGCGATATCAAGGCATGGCGACTTGCTGTCCATCAGTTCCACCACGGGAATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGGAGAGCATGGATTCGAGGCGTTCTTGCTCCATTTCCGGTTTATAACCG  >  NC_000913/3578140‑3578424                                                                                                                                                    |                                                                                                                                          atgatAGTACGTTCGTCGAGACGTGCGCCGAGATAGGCAATGTGGCGATGCCCGCGAGCAATAATGGCAGTGGTCATCTGGCGTGCTGCTTCAAAGTTATCAAAACCGACGGCGATATCAAGGCATGGCGACTTGCTGTCCATCAGTTcca                                                                                                                                        >  2:198475/1‑151 (MQ=255)             tcgtcgAGACGTGCGCCGAGATAGGCAATGTGGCGATGCCCGCGAGCAATAATGGCAGTGGTCATCTGGCGTGCTGCTTCAAAGTTATCAAAACCGACGGCGATATCAAGGCATGGCGACTTGCTGTCCATCAGTTCCACCACGGGAATAc                                                                                                                            <  1:75438/151‑1 (MQ=255)              cgtcgAGACGTGCGCCGAGATAGGCAATGTGGCGATGCCCGCGAGCAATAATGGCAGTGGTCATCTGGCGTGCTGCTTCAAAGTTATCAAAACCGACGGCGATATCAAGGCATGGCGACTTGCTGTCCATCAGTTCCACCACGGGAATAc                                                                                                                            >  1:10704/1‑150 (MQ=255)                     aCGTGCGCCGAGATAGGCAATGTGGCGATGCCCGCGAGCAATAATGGCAGTGGTCATCTGGCGTGCTGCTTCAAAGTTATCAAAACCGACGGCGATATCAAGGCATGGCGACTTGCTGTCCATCAGTTCCACCACGGGAATACCCGCCAc                                                                                                                     <  1:28253/150‑1 (MQ=255)                            ccGAGATAGGCATTGTGGCGATGCCCGCGAGAAATAATGGCAGTGGTCATCTGGCGTGCTGCTTAAAATTTACAAAACCCGACGGCGATATAAAGGCAGGGCGACTTGCTGTCCATCAGTCCCCCCACGGGAATACCCGCCACTTCAatca                                                                                                             <  1:245610/151‑1 (MQ=255)                            ccGAGATAGGAATGGGGGGGATCCCCGCAACAAAAAAGGGCGGTGGTCATCGGGCGTGCTGTTTAAAATTTAAAAAACCCGCCGGCGAAATAAAGGCGGGGCGCCTTGCTGTCCACCATTCCCCCCACGGGAATACCCGCCACTTCAatca                                                                                                             <  2:245681/151‑1 (MQ=255)                              gagaTAGGCAATGTGGCGATGCCCGCGAGCAATAATGGCAGTGGTCATCTGGCGTGCTGCTTCAAAGTTATCAAAACCGACGGCGATATCAAGGCATGGCGACTTGCTGTCCATCAGTTCCACCACGGGAATACCCGCCACTTCAatcat                                                                                                            >  2:229924/1‑150 (MQ=255)                                      cAATGTGGCGAGCCCCGCGAGAAATAAGGGCAGTGGTCATCGGGCGTGCTGCTTAAAATTTAACAAACCCGACGGCGATATCAAGGCATGGCGCTTTGCTGTCCATCGGTCCCCCCAGGGAAATACCCGCCACTTCAATCATCTTTAAgg                                                                                                    <  2:177567/150‑1 (MQ=255)                                      cAATGGGGGGAGCCCCGCGAGAAATAAGGGCGGTGGTCATCTGGCGTGCTGCTTAAAATTTAACAAACCCGACGGCGATATCAAGGCAGGGCGACTTGCTGTCCATCAGTCCCCCCACGGAAATACCCGCCACTTCAATCATCTTTAAgg                                                                                                    <  2:281419/150‑1 (MQ=255)                                      aattgtgGGGACCCCCGCAAGCAATAAGGGCAGGGGTCATCTGGCGTGCTCCTCAAAATTTAAAAAACCCGCCGGCAAAATAAAGGCAGGCCCACTTGCTCCCCATCATTCCCCCCGGGGAAATCCCCGCCACTTCAATCATCTTTAAgg                                                                                                    <  2:173234/147‑1 (MQ=255)                                                    cggggagaAATAAGGGCGGGGGTCTTCTGGGGTGCTGTTTAAAATTTAAAAAACCCGAGGGCAATACAAGGGCAGGGCGATTTGCTGCCCATCAGTCCCCCCAGGGGAATCCCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTggg                                                                                     <  1:26818/147‑1 (MQ=255)                                                       cgAGAAATAATGGCAGTGGTCATCGGGCGTGCTGCTTAAAAGTTACCAAACCCGCCGGCAATATCAAGGCAGGGCGACTTGCTGTCCATCATTCCCACCACGGAAATCCCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTa                                                                                   <  1:244128/150‑1 (MQ=255)                                                       agagaAATAAGGGCAGGGGTCATCGGGGGTGCTCCTAAAAAGTAAAAAAACCCGACGCCAATATCAAGGCATGCCGATTTGCTCTCCAGCAGTCCCCCCGGGGGAATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTa                                                                                   <  2:113588/149‑1 (MQ=255)                                                                           cATCTGGCGTGCTGCTTCAAAGTTATCAAAACCGACGGCGATATCAAGGCATGGCGACTTGCTGTCCATCAGTTCCACCACGGGAATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCg                                                              >  1:178463/1‑151 (MQ=255)                                                                                          ttaaaatttaaaaaaaCCGAGGGCGATATAAGGGCATGGCGACTTGCTGTCCATCATTCCCCCCACGGAAATCCCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGgag                                               <  1:265755/139‑1 (MQ=255)                                                                                          ttaaaaTTTATCAAACCCGCCGGCGATAACAAGGCATGGCGCTTTGCTGTCCATCAGTCCCCCCAGGGAAATCCCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGgag                                               <  2:109648/148‑1 (MQ=255)                                                                                                           cgcgggggATATAAAGGGAGGGCGCCTTGCTGCCCATCAGTCCCACCAGGGGAATCCCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGGAGAGCATGGATTCGAGGCg                              <  1:29352/144‑1 (MQ=255)                                                                                                                                       gCTGTCCATCAGTTCCACCACGGGAATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGGAGAGCATGGATTCGAGGCGTTCTTGCTCCATTTCCGGTTTATAACCg  >  2:295316/1‑151 (MQ=255)                                                                                                                                                    |                                                                                                                                          ATGATAGTACGTTCGTCGAGACGTGCGCCGAGATAGGCAATGTGGCGATGCCCGCGAGCAATAATGGCAGTGGTCATCTGGCGTGCTGCTTCAAAGTTATCAAAACCGACGGCGATATCAAGGCATGGCGACTTGCTGTCCATCAGTTCCACCACGGGAATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGGAGAGCATGGATTCGAGGCGTTCTTGCTCCATTTCCGGTTTATAACCG  >  NC_000913/3578140‑3578424

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑