Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,897,051	0	C	A	60.0%	‑2.2 / 12.2	10	intergenic (+318/+1055)	ygcE/queE	FGGY‑family carbohydrate kinase/7‑carboxy‑7‑deazaguanine synthase QueE
Reads supporting (aligned to +/- strand):  ref base C (0/4);  new base A (6/0);  total (6/4)
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.

TATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTCATTAGCCTCAAAACAAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAACAAGCTTA  >  NZ_CP009273/2896996‑2897118                                                        |                                                                    tatCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTCATTAGCCTCAAAACAAAGACAAACTTCCa                                   <  2:485687/90‑1 (MQ=255)       tATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTCATTAGCCTCAAAACAAAGACAAACTTCCAGATtta                             <  1:356530/90‑1 (MQ=255)                     aTTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTCATTAGCCTCAAAACAAAGACAAACTTCCAGATTTATTACTTAACCAATg               <  2:609069/90‑1 (MQ=255)                       tcatcaACAGCGTATAGAGGCGGTTATGTAAAAACACCCATTTTCCTCCAAACAAAAAAAAAAATTCAGATTTTTTTATTTAACAATGaa             >  1:329813/1‑90 (MQ=255)                             aCAGCGTATAGAGGCGGTTATTTAAAAACACTCATTAGCCTCCAAAAAAAAAAAAAATTCCAAATTTTTTTCTTTAACAAAGAATAaaaa       >  1:331808/1‑90 (MQ=255)                              cAGCGTATAGAGGCGGTTTTTTAAAAAAACTCATTATCCTCAAAAAAAAAAAAAAAATCCAGATTTTTTTTTTAAACAAAAAATAaaaaa      >  2:397876/1‑89 (MQ=255)                               aGCGTATAGAGGCGGTTTTGTAAAAACACTCATTAACCTCAAAAAAAAAAAAAACTTCCAGATTTTTTTTTTTACCAATTAATAaaaaac     >  1:486563/1‑88 (MQ=255)                               aGCGTATAGAGGCGGTTATGTAAAAACACTCCTTAGCCTCAAAAAAAAAACAAAATTCCAGATTTTTTTCTTAAACAAATAATAaaaaac     >  1:17015/1‑88 (MQ=255)                                gCGTATAGAGGCGGTTTTTTAAAAACACTCATTATCCTCCAAAAAAAAAAAAAAATCCAGATTTTTTATTTAAACAAAAAATAaaaaaat    >  2:297904/1‑87 (MQ=255)                                  gTATAGAGGCGGTTATGTAAAACCACTCATTAGCCTCAAAACAAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAACAAGCTTa  <  2:329813/90‑1 (MQ=255)                                                        |                                                                    TATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTCATTAGCCTCAAAACAAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAACAAGCTTA  >  NZ_CP009273/2896996‑2897118

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑