Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,000,081	0	T	G	56.2%	9.4 / 17.6	16	L236V (TTG→GTG)	ycbF	fimbrial chaperone
Reads supporting (aligned to +/- strand):  ref base T (2/5);  new base G (9/0);  total (11/5)
Fisher's exact test for biased strand distribution p-value = 4.81e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.80e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

TGTAAATGGTAAAGCGTTAAGTAATGTGGGAGTTGTGCCGCCTAAAAGCCAGCGTCAGACAAGCTGGTGTCAGGCAATCGCACCGTGTCATGTCGCCTGGCGGGCGATAAATGATTACGGCGGGTTGAGTGCAAAGAAGGAGCAAAATCTGCCCTGAAAC‑AGGTTCGGAAAAC‑GTTTGCGTTTTTTTTGCCGCAGGTCAATTCCCTTTTGGTCCGAACTCGCACATAATACGCCCCCGGTTTGCACACCGGGAATCCAGGAG  >  NZ_CP009273/999957‑1000218                                                                                                                             |                                                                                                                                            tgtAAATGGTAAAGCGTTAAGTAATGTGGGAGTTGTGCCGCCTAAAAGCCAGCGTCAGACAAGCTGGTGTCAGGCAATCGCACCGTGTCATGTCGCCTGGCGGGCGATAAATGATTACGGCGGGGTGGGTGGAaaga                                                                                                                                 >  1:306489/1‑137 (MQ=255)             aGCGTTAAGTAATGTGGGAGTTGTGCCGCCTAAAAGCCAGCGTCAGACAAGCTGGTGTCAGGCAATCGCACCGTGTCATGTCGCCTGGCGGGCGATAAATGATTACGGCGGGGTGAGTGGAAAGAAAGAGCAAAAACTg                                                                                                                   >  1:295711/1‑139 (MQ=255)                  tAAGTAATGTGGGAGTTGTGCCGCCTAAAAGCCAGCGTCAGACAAGCTGGTGTCAGGCAATCGCACCGTGTCATGTCGCCTGGCGGGCGATAAATGATTACGGCGGGGTGAGGGGAAAGAAGGAGGAAAAAATGccccg                                                                                                              >  1:56526/1‑137 (MQ=255)                         tgtgGGAGTTGTGCCGCCTAAAAGCCAGCGTCAGACAAGCTGGTGTCAGGCAATCGCACCGTGTCATGTCGCCTGGCGGGCGATAAATGATTACGGCGGGGTGGGGGGAAAGAAAGAGGAAAAACTTCCCTGAAAC‑aag                                                                                                      >  1:253725/1‑137 (MQ=255)                                   gtgCCGCCTAAAAGCCAGCGTCAGACAAGCTGGTGTCAGGCAATCGCACCGTGTCATGTCGCCTGGCGGGCGATAAATGATTACGGCGGGGTTGGTGGCAAAAAGGAGCAAAAACTGCCCTGAAAC‑AAGGCCGGGAAAc                                                                                            >  1:155237/1‑139 (MQ=255)                                                    gCGTCAGACAAGCTGGTGTCAGGCAATCGCACCGTGTCATGTCGCCTGGCGGGCGATAAATGATTACGGCGGGTTTGGGGGAAAAAAGGAGAAAAAAATGCCCCGAAAA‑AAGGTCGGAAAAC‑GATTGCGgttttttttt                                                                          >  1:332594/1‑137 (MQ=255)                                                               gCTGGTGTCAGGCAATCGCACCGTGTCATGTCGCCTGGCGGGCGATAAATGATTACGGCGGGGTGGGGGCAAAGAAGGAGGAAAAACTGCCCCGAAACAAGGTTGGGAAACA‑GTTGGGGTTTTTTTT‑TCGCAGGGCaaa                                                               >  2:434901/1‑138 (MQ=255)                                                                        aGGCAATCGCACCGTGTCATGTCGCCTGGCGGGCGATAAATGATTACGGCGGGGTTGGGGGAAAGAAAGAGGAAAAAACGCCCCGAAAC‑AAGGTTGGAAAACAGTTTCGGTTTTTTTTTCC‑CAGGGCAAATACCttttt                                                      >  1:261122/1‑138 (MQ=255)                                                                         ggCAATCGCACCGTGTCATGTCGCCTGGCGGGCGATAAATGATTACGGCGGGTTGAGTGGAAAGAAAGAGCAAAAACTTCCCTGCAAA‑AAGTTGGGGAAAA‑ATTTGTGGTTTTTTTTTCGCAGGGGAATTCTCtttttg                                                     >  1:351472/1‑137 (MQ=255)                                                                                     gtgtCATGTCGCCTGGCGGGCGATAAATGATTACGGCGGGTTGAGTGCAAAGAAGGAGCAAAATCTGCCCTGAAAC‑AGGTTCGGAAAAC‑GTTTGCGTTTTTTTTGCCGCAGGTCAATTCCCTTTTGGTCCGAACTCGca                                         <  2:401735/139‑1 (MQ=255)                                                                                                ccTGGCGGGCGATAAATGATTACGGCGGGGTGGGTGCAAAGAAGGAGCAAAAACTGCCCTCAAACAAGGTTGGGAAAA‑‑ATTTTCGTTTTTTTTTTCGCAGGGCAAATTCCTTTTTTTCCGCACTCGCACataataagac                              >  2:416650/1‑135 (MQ=255)                                                                                                ccTGGCGGGCGATAAATGATTACGGCGGGGTGAGTGGAAAGAAAGAGGAAAAAATACCCTCAAAA‑AAGGTCGGGGAAC‑GATTGCGTTTTTTTTTTCGCCGGGCAATTCCCTTTTTTTTCGAACTCGCCCATAATACAcc                              >  2:284463/1‑139 (MQ=255)                                                                                                            tAAATGATTACGGCGGGTTGAGTGCAAAGAAGGAGCAAAATCTGCCCTGAAAC‑AGGTTCGGAAAAC‑GTTTGCGTTTTTTTTGCCGCAGGTCAATTCCCTTTTGGTCCGAACTCGCACATAATACGCCCCCGGTTTGcac                  <  2:351472/139‑1 (MQ=255)                                                                                                                  aTTACGGCGGGTTGAGTGCAAAGAAGGAGCAAAATCTGCCCTGAAAC‑AGGTTCGGAAAAC‑GTTTGCGTTTTTTTTGCCGCAGGTCAATTCCCTTTTGGTCCGAACTCGCACATAATACGCCCCCGGTTTGCACACCgg             <  1:284463/138‑1 (MQ=255)                                                                                                                  aTTACGGCGGGTTGAGTGCAAAGAAGGAGCAAAATCTGCCCTGAAAC‑AGGTTCGGAAAAC‑GTTTGCGTTTTTTTTGCCGCAGGTCAATTCCCTTTTGGTCCGAACTCGCACATAATACGCCCCCGGTTTGCACACCgg             <  2:332594/138‑1 (MQ=255)                                                                                                                            gTTGAGTGCAAAGAAGGAGCAAAATCTGCCCTGAAAC‑AGGTTCGGAAAAC‑GTTTGCGTTTTTTTTGCCGCAGGTCAATTCCCTTTTGGTCCGAACTCGCACATAATACGCCCCCGGTTTGCACACCGGGAATCCAGgag  <  2:56526/139‑1 (MQ=255)                                                                                                                             |                                                                                                                                            TGTAAATGGTAAAGCGTTAAGTAATGTGGGAGTTGTGCCGCCTAAAAGCCAGCGTCAGACAAGCTGGTGTCAGGCAATCGCACCGTGTCATGTCGCCTGGCGGGCGATAAATGATTACGGCGGGTTGAGTGCAAAGAAGGAGCAAAATCTGCCCTGAAAC‑AGGTTCGGAAAAC‑GTTTGCGTTTTTTTTGCCGCAGGTCAATTCCCTTTTGGTCCGAACTCGCACATAATACGCCCCCGGTTTGCACACCGGGAATCCAGGAG  >  NZ_CP009273/999957‑1000218

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑