Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,791,121	0	G	T	57.1%	2.6 / 20.0	14	D272Y (GAC→TAC)	waaL	O‑antigen ligase
Reads supporting (aligned to +/- strand):  ref base G (3/3);  new base T (4/4);  total (7/7)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

ATATTAGCTAGCATTGTTATTATATTTAATAAACCAATACAGAATCGCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTACGAAATTGGTTT  >  NZ_CP009273/3791055‑3791194                                                                   |                                                                          atatTAGCTAGCATTGTTATTATATTTAATAAACCAATACAGAATCGCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCt                                                    >  2:347958/1‑90 (MQ=255)                           taataaACCAATACAGAATCGCTATAATGAAGCATTAAATGACTTaaa                                                                    <  1:91785/48‑1 (MQ=255)                           taataaACCAATACAGAATCGCTATAATGAAGCATTAAATGACTTaaa                                                                    >  2:91785/1‑48 (MQ=255)                                   cAATACAGAATCGCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCaa                  <  1:347958/90‑1 (MQ=255)                                                            aTTAAATTACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTACGAAATTGGttt  >  1:234671/1‑81 (MQ=255)                                                            aTTAAATTACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTACGAAATTGGttt  >  1:267064/1‑81 (MQ=255)                                                            aTTAAATTACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTACGAAATTGGttt  >  1:309791/1‑81 (MQ=255)                                                            aTTAAATTACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTACGAAATTGGttt  >  1:393034/1‑81 (MQ=255)                                                            aTTAAATTACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTACGAAATTGGttt  <  2:234671/81‑1 (MQ=255)                                                            aTTAAATTACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTACGAAATTGGttt  <  2:267064/81‑1 (MQ=255)                                                            aTTAAATTACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTACGAAATTGGttt  <  2:309791/81‑1 (MQ=255)                                                            aTTAAATTACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTACGAAATTGGttt  <  2:393034/81‑1 (MQ=255)                                                            aTTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTACGAAAtt       <  1:27343/76‑1 (MQ=255)                                                            aTTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTACGAAAtt       >  2:27343/1‑76 (MQ=255)                                                                   |                                                                          ATATTAGCTAGCATTGTTATTATATTTAATAAACCAATACAGAATCGCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTACGAAATTGGTTT  >  NZ_CP009273/3791055‑3791194

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑