Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,669,465	0	C	A	60.0%	0.1 / 13.3	10	L240F (TTG→TTT)	yphD	ABC transporter permease
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.

GCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCG  >  NZ_CP009273/2669400‑2669540                                                                  |                                                                            gcgATGCCGTAAACCCCCAGCCCTTTTGCGGCCCCTGCGTTCCCAAACCCGGGGCGCGCCCCCAAAAAAATGCCGGTCACCGCCGCtaat                                                     <  1:79449/90‑1 (MQ=255)                cccAGCCCGTTTGCGGCACCTGCGTTCCCAGACCCGGGGGGCGCCCCCAAAAAAAGGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTa                                      <  1:111405/89‑1 (MQ=255)                cccAGACCTTTTGCGGCCCCGGCGTTCCAAGAACCGAGGCGCGCCGCAAAAAAAATCCCGGTCACCGCCGCTAATAATCCCGAAAGGGTa                                      <  1:135849/89‑1 (MQ=255)                 ccAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTaa                                     >  2:1304/1‑90 (MQ=255)                   aGACCGTTTGCGGCCCCTGCGTTCCCAAAACCGAGGCGCGCCGCAAAAAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAg                                   <  1:141245/90‑1 (MQ=255)                         tttGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGa                             >  1:183145/1‑90 (MQ=255)                                  ccTGCGTCACCAGACCCGAGGCGCGCCCCAAAAAAAATCCCGGCCCCCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCAcc                    <  1:330205/90‑1 (MQ=255)                                                    aGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTa                                      >  1:115400/1‑54 (MQ=255)                                                    aGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCg  >  1:21008/1‑90 (MQ=255)                                                    aGGCGCGCCGCCAAAAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTa                                      <  2:115400/54‑1 (MQ=255)                                                                  |                                                                            GCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCG  >  NZ_CP009273/2669400‑2669540

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑