Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	4,091,435	0	T	G	53.8%	11.4 / 13.5	13	intergenic (+77/‑183)	sodA/kdgT	superoxide dismutase [Mn]/2‑keto‑3‑deoxygluconate transporter
Reads supporting (aligned to +/- strand):  ref base T (1/5);  new base G (7/0);  total (8/5)
Fisher's exact test for biased strand distribution p-value = 4.66e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.13e-02
Rejected as consensus: Frequency below/above cutoff threshold.

GCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATCAATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGC  >  NZ_CP009273/4091368‑4091489                                                                    |                                                       gccTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATCAATTTCaaaa                                  <  2:238103/90‑1 (MQ=255)               ggCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATCAATTTCAAAATAAAAACAATGATc                    <  2:153359/90‑1 (MQ=255)               ggCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCACCAACGGCGGTGGGTTTTTTGTAATCAATTTTAAAAAAAAAAAAATGATc                    >  2:454143/1‑90 (MQ=255)                gCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGGTTTTTTTTGATCAATTTTAAAATAAAAAAAAAGATcc                   >  2:326241/1‑90 (MQ=255)                    ataGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATCAATTTCAAAATAAAAACAATGATCCGata               <  2:128634/90‑1 (MQ=255)                         ccGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTTTGATCAATTTTAAAATAAAAAAAATGATCCGataaaaat          >  2:320088/1‑90 (MQ=255)                         ccGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGGGGGTTTTTTTTGATCAATTTTAAAAAAAAAAAAAAGATCCCataaaaat          >  1:13740/1‑90 (MQ=255)                         ccGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGGGGGTTTTTTTTGATCAAATTTAAAAAAAAAAAAAAGATCCGaaaaaaaa          >  1:300335/1‑89 (MQ=255)                            cATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGGTTTTTTTTGGTCAATTTTAAAATAAAAAAAAAGATCCGataaaaaaaaa       >  2:247927/1‑90 (MQ=255)                            cATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGGTTTTTTTTGATCAATTTTAAAAAAAAAAAAAAGATCCGataaaaataaa       >  2:391823/1‑90 (MQ=255)                            cATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGGGGGTTTTTTTTGGTTAATTTTAAAAAAAAAAAAAAGATCCGataaaaataaa       >  1:272477/1‑90 (MQ=255)                               atCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATCAATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACa    <  2:481203/90‑1 (MQ=255)                                 cAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATCAATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGc  <  2:100772/90‑1 (MQ=255)                                                                    |                                                       GCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATCAATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGC  >  NZ_CP009273/4091368‑4091489

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑