Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	431,972	0	C	A	60.0%	‑2.5 / 10.1	10	Q295K (CAA→AAA)	thiL	thiamine‑phosphate kinase
Reads supporting (aligned to +/- strand):  ref base C (4/0);  new base A (0/6);  total (4/6)
Fisher's exact test for biased strand distribution p-value = 4.76e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.23e-03
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

GTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGA  >  NZ_CP009273/431900‑432048                                                                         |                                                                             gtgCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATc                                                             >  1:16810/1‑90 (MQ=255)           tGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCttt                                                   >  1:239876/1‑90 (MQ=255)               ccGGGGCGCGTGGGATGTGGCTCGCGCCCCCGGGGGCGTCCTTTTTCCTTGTAGCGGGAAAATGACCGCCGATATCGAAGGGCTTTGttt                                               <  1:289996/90‑1 (MQ=255)                                              cTGGGCGTCCCTTTTCCCTGTATGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGAc                <  2:16810/90‑1 (MQ=255)                                               tGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACt               >  1:114833/1‑90 (MQ=255)                                               ggggCGTCCCTTTTCCTGGTATGGGGAAAATGCCCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACt               <  1:152547/89‑1 (MQ=255)                                               ggggCGTCCCTTTTCCCTGTATGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACt               <  2:115277/89‑1 (MQ=255)                                                   cGTCCCTTTTCCTTGTGTCGGAAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGaa           <  2:93851/90‑1 (MQ=255)                                                       ccGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGa       >  2:196726/1‑90 (MQ=255)                                                            tACCTGTAGGGGAAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGa  <  2:173819/90‑1 (MQ=255)                                                                         |                                                                             GTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGA  >  NZ_CP009273/431900‑432048

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 6 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑