Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	997,447	0	T	G	58.3%	2.1 / 10.4	13	V62G (GTA→GGA)	elfG	fimbrial protein
Reads supporting (aligned to +/- strand):  ref base T (1/4);  new base G (7/0);  total (8/5)
Fisher's exact test for biased strand distribution p-value = 1.01e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.39e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

ACTCAGGGGAATCCGTATATTGGCGTCAATTTTGGCGTTAAAACCCTGGAGGAAGAAGCAAATACGGCAGGGGTAGTTAAAGACAAATTTTATCAGTGGAACGAATCGAATGATTATTATGTTTCCTGTGATTGCGATAAAGACAATGTCAGAAGT  >  NZ_CP009273/997374‑997529                                                                          |                                                                                   actCAGGGGAATCCGTATATTGGCGTCAATTTTGGCGTTAAAACCCTGGAGGAAGAAGCAAATACGGCAGGGGGAGTTAAAGACAAAttt                                                                    >  1:293095/1‑90 (MQ=255) actCAGGGGAATCCGTATATTGGCGTCAATTTTGGCGTTAAAACCCTGGAGGAAGAAGCAAATACGGCAGGGGGAGTTAAAAAAAAAatt                                                                    >  2:485524/1‑90 (MQ=255)    cAGGGGAATCCGTATATTGGCGTCAATTTTGGCGTTAAAACCCTGGAGGAAGAAGCAAATACGGCAGGGGGTGGTAAAGAAAAAattttt                                                                 >  2:557482/1‑88 (MQ=255)           aTCCGTATATTGGCGTCAATTTTGGCGTTAAAACCCTGGAGGAAGAAGCAAATACGGCAGGGGTAGTTAAAGACAAATTTTATCAGTGGa                                                          >  1:134050/1‑90 (MQ=255)                      ggCGTCAATTTTGGCGTTAAAACCCTGGAGGAAGAAGCAAATACGGCAGGGGTAGTTAAAGACAAATTTTATCAGTGGAAcgaatcgaat                                               <  1:484925/90‑1 (MQ=255)                      ggCGTCAATTTTGGCGTTAAAACCCTGGAGGAAGAAGCAAATACGGCAGGGGGAGTTAAAGAAAAATTTTTTTAGTGGAAcgaaacgaat                                               >  2:406919/1‑90 (MQ=255)                                             ccTGGAGGAAGAAGCAAATACGGCAGGGGTAGTTAAAGACAAATTTTATCAGTGGAACGAATCGAATGATTATTATGTTTCCTGTGATTg                        <  2:134050/90‑1 (MQ=255)                                             ccTGGAGGAAGAAGCAAATACGGCAGGGGAAGTTAAAGACAAATTTTATCAGTGGAACGAATCGAATGATTATTATGTTTCCTGTGATTg                        <  2:293095/90‑1 (MQ=255)                                                        aagCAAATACGGCAGGGGTAGTTAAAGACAAATTTTATCAGTGGAACGAATCGAATGATTATTATGTTTCCTGTGATTGCGATAAAGACa             <  1:447593/90‑1 (MQ=255)                                                         agCAAATACGGCAGGGGTAGTTAAAGACAAATTTTATCAGTGGAACGAATCGAATGATTATTATGTTTCCTGTGATTGCGATAAAGACaa            <  1:406919/90‑1 (MQ=255)                                                              aTACGGCAGGGGGAGGTAAAGACAAATTTTTTCAGTGGAACGAAACGAATGATTATTATGTTTCCTGTGATTGCGATAAAAACAAAGTCa       >  2:327697/1‑90 (MQ=255)                                                                  ggCAGGGGGAGTTAAAGACAAATTTTTTCAGTGGGACGAATCGAATGATTATTTTGTTTCCTGTGTTTTCGATAAAAACAATGTCAGAAg   >  2:379178/1‑90 (MQ=255)                                                                   gCAGGGGGAGTTAAAGACAAATTTTTTCAGTGGAACGAATCGAATGATTATTATGTTTTCTGTGATTGCGATAAAGACAATGTCAGAAGt  >  2:495231/1‑90 (MQ=255)                                                                          |                                                                                   ACTCAGGGGAATCCGTATATTGGCGTCAATTTTGGCGTTAAAACCCTGGAGGAAGAAGCAAATACGGCAGGGGTAGTTAAAGACAAATTTTATCAGTGGAACGAATCGAATGATTATTATGTTTCCTGTGATTGCGATAAAGACAATGTCAGAAGT  >  NZ_CP009273/997374‑997529

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑