Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	653,350	0	T	C	61.5%	4.8 / 12.1	13	G15G (GGA→GGG)	crcB	fluoride efflux transporter CrcB
Reads supporting (aligned to +/- strand):  ref base T (5/0);  new base C (0/8);  total (5/8)
Fisher's exact test for biased strand distribution p-value = 7.77e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.13e-03
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

GTGGGTT‑AAATCGCATACTTAACAGCCATCTCGCCACGCTTCCCGTACCACCGCCAATAAAAACTGCTAAAAGAAGTTGTAACACTGCAAAATCCTGCTATTTGATTTGTATGAGTGATA  >  NZ_CP009273/653310‑653429                                          |                                                                                gTGGGTT‑AAATCGCATACTTAACAGCCATCTCGCCACGCTTCCCGTACCACCGCCAATAAAAACTGCTAAAAGAAGTTGTAACACTGCaa                                >  2:294817/1‑90 (MQ=255)  ggggTTAAAACCGCATCCTAAACACCCATCCCCCCCCCCTCCCCGTCCCACCGCCAATAAAAACTGCTAAAAGAAGTTGTAACACTGCaa                                <  2:259406/89‑1 (MQ=255)   gggTT‑AAATCGCATAC‑TAACAGCCATCTCGCCACGCTTCCCGTACCACCGCCAATAAAAACTGCTAAAAGAAGTTGTAACACTGCAAAAt                             >  1:119844/1‑90 (MQ=255)              gCATACTTAACAGCCATCTCGCCACGCTTCCCGTACCACCGCCAATAAAAACTGCTAAAAGAAGTTGTAACACTGCAAAATCCTGCTact                    >  1:259406/1‑88 (MQ=255)               cATACTTAACAGCCATCTCGCCACGCTTCCCGTACCACCGCCAATAAAAACTGCTAAAAGAAGTTGTAACACTGCAAAATCCTGCTattt                   >  1:105290/1‑90 (MQ=255)                   ctaaaCACCCATCCCCCCCCGCTCCCCGTACCACCGCCAATAAAAACTGCTAAAAGAAGTTGTAACACTGCAAAATCCTGCTatttgatt               <  1:521157/87‑1 (MQ=255)                   ctaaaCACCAATCCCCCCCCGCTCCCCGTCCCACCGCCAATAAAAACTGCTAAAAGAAGTTGTAACACTGCAAAATCCTGCTatttgatt               <  1:373963/87‑1 (MQ=255)                        cAGCCATCTCGCCACGCTCCCCGTCCCACCGCCAATAAAAACTGCTAAAAGAAGTTGTAACACTGCAAAATCCTGCTATTTGATTTGTAt          <  1:144235/90‑1 (MQ=255)                           ccttctcGCCACGCTCCCCGCCCCACCGCCAATAAAAACTGCTAAAAGAAGTTGTAACACTGCAAAATCCTGCTATTTGATTTGTATGAg       <  1:104902/87‑1 (MQ=255)                             aTCTCGCCACGCTTCCCGTACCACCGCCAATAAAAACTGCTAAAAGAAGTTGTAACACTGCAAAATCCTGCTATTTGATTTGTATGAGTg     >  1:209209/1‑90 (MQ=255)                                cccccACGCTCCCCGTCCCACCGCCAATAAAAACTGCTAAAAGAAGTTGTAACACTGCAAAATCCTGCTATTTGATTTGTATGAGTGATa  <  1:208303/87‑1 (MQ=255)                                ccGCCCCACTCCCCGTACCCCCGCCAATAAAAACTGCTAAAAGAAGTTGTAACACTGCAAAATCCTGCTATTTGATTTGTATGAGTGATa  <  2:396482/89‑1 (MQ=255)                                ccGCCACGCCCCCCGTCCCACCGCCAATAAAAACTGCTAAAAGAAGTTGTAACACTGCAAAATCCTGCTATTTGATTTGTATGAGTGATa  <  2:296181/89‑1 (MQ=255)                                          |                                                                                GTGGGTT‑AAATCGCATACTTAACAGCCATCTCGCCACGCTTCCCGTACCACCGCCAATAAAAACTGCTAAAAGAAGTTGTAACACTGCAAAATCCTGCTATTTGATTTGTATGAGTGATA  >  NZ_CP009273/653310‑653429

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑