Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,273,830	0	A	C	55.0%	17.8 / 23.5	20	T85T (ACA→ACC)	agaV	PTS N‑acetylgalactosamine transporter subunit IIB
Reads supporting (aligned to +/- strand):  ref base A (8/1);  new base C (0/11);  total (8/12)
Fisher's exact test for biased strand distribution p-value = 7.14e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.01e-04
Rejected as consensus: Frequency below/above cutoff threshold.

ATCGCCGTACGTTTCTGGACGCTGCAAAAAGTTATCGACAACATTCATCGCGCCGCCGATCGACAGAAAATCCTGCTGGTTTGTAAAACACCCGCCGATTTCCTGACGCTGGTGAAAGGTGGCGTTCCGGTGAATCGCATTAACGTTGGCAATATGCACTACGCCAATGGCAAACAAC  >  NZ_CP009273/3273741‑3273918                                                                                          |                                                                                         aTCGCCGTACGTTTCTGGACGCTGCAAAAAGTTATCGACAACATTCATCGCGCCGCCGATCGACAGAAAATCCTGCTGGTTTGTAAAaca                                                                                          >  1:271117/1‑90 (MQ=255) aTCGCCGTACGTTTCTGGACGCTGCAAAAAGTTATCGACAACATTCATCGCGCCGCCGATCGACAGAAAATCCTGCTGGTTTGTAAAaca                                                                                          >  1:756002/1‑90 (MQ=255) aTCGCCGTACGTTTCTGGACGCTGCAAAAAGTTATCGACAACATTCATCGCGCCGCCGATCGACAGAAAATCCTGCTGGTTTGTAAAaca                                                                                          >  1:791853/1‑90 (MQ=255)   cGCCGTACGTTTCTGGACGCTGCAAAAAGTTATCGACAACATTCATCGCGCCGCCGATCGACAGAAAATCCTGCTGGTTTGTAAAACAcc                                                                                        >  1:539034/1‑90 (MQ=255)          cttttCGGGACGCTAAAAAAATTTATCAACAACTTTCACCGCCCCGCCGATCGACAGAAAATCCTGCTGTTTTGAAAAACCCCCGCCGAt                                                                                 <  1:198913/88‑1 (MQ=255)              tCTGGACGCTGCAAAAAGTTATCGACAACATTCATCGCGCCGCCGATCGACAGAAAATCCTGCTGGTTTGTAAAACACCCGCCGATTTcc                                                                             >  2:836750/1‑90 (MQ=255)                      cTGCAAAAAGTTATCGACAACATTCATCGCGCCGCCGATCGACAGAAAATCCTGCTGGTTTGTAAAACACCCGCCGATTTCCTGACGCTg                                                                     >  2:501279/1‑90 (MQ=255)                      cTGCAAAAAGTTATCGACAACATTCATCGCGCCGCCGATCGACAGAAAATCCTGCTGGTTTGTAAAACACCCGCCGATTTCCTGACGCTg                                                                     >  1:683004/1‑90 (MQ=255)                                    cGAAAACATCCACCCCCCCGCCGACCGAAAAAAAACCCTGTTGTTTTGAAAAACCCCCGCCGATTTCCTGACGCTGGTGAAAGGTGGCGt                                                       <  1:372734/90‑1 (MQ=255)                                       caacaTTCATCGCGCCGCCGATCGACAGAAAATCCTGCTGGTTTGTAAAACACCCGCCGATTTCCTGACGCTGGTGAAAGGTGGCGTTcc                                                    >  1:238293/1‑90 (MQ=255)                                            ttCATCGCGCCGCCGATCGACAGAAAATCCTGCTGGTTTGTAAAACACCCGCCGATTTCCTGACGCTGGTGAAAGGTGGCGTTCCGGTGa                                               >  1:200605/1‑90 (MQ=255)                                              caccgcgCCGCCGATCGACAGAAAATCCTGCTGGTTTGTAAAACCCCCGCCGATTTCCTGACGCTGGTGAAAGGTGGCGTTCCGGTGAAt                                             <  2:257998/87‑1 (MQ=255)                                              caccgccCCGCCGATCGACAAAAAATCCTGTTGGTTTGAAAAACCCCCGCCGATTTCCTGACGCTGGTGAAAGGTGGCGTTCCGGTGAAt                                             <  2:808537/87‑1 (MQ=255)                                              caccgccCCGCCGATCGACAAAAAATCCTGCTGGTTTGTAAAACCCCCGCCGATTTCCTGACGCTGGTGAAAGGTGGCGTTCCGGTGAAt                                             <  2:271117/87‑1 (MQ=255)                                                   cgccgcCGATCGACAAAAAATCCTGCTGGTTTGTAAAACCCCCGCCGATTTCCTGACGCTGGTGAAAGGTGGCGTTCCGGTGAATCGCAt                                        <  2:125703/90‑1 (MQ=255)                                                         cgATCGACAGAAAATCCTGCTGTTTTGAAAAACCCCCGCCGATTTCCTGACGCTGGTGAAAGGTGGCGTTCCGGTGAATCGCATTAACGt                                  <  2:1038/90‑1 (MQ=255)                                                         cgATCGACAAAAAATCCTGCTGGTTTGTAAAACACCCGCCGATTTCCTGACGCTGGTGAAAGGTGGCGTTCCGGTGAATCGCATTAACGt                                  <  2:238293/90‑1 (MQ=255)                                                          gATCGAAAAAAAATCCTGCTGTTTTGAAAAACCCCCGCCGATTTCCTGACGCTGGTGAAAGGTGGCGTTCCGGTGAATCGCATTAACGtt                                 <  2:756002/90‑1 (MQ=255)                                                          gATCGAAAAAAAACCCTTCGGGTTTGAAAACCCCCCGCCGATTTCCTGACGCTGGTGAAAGGTGGCGTTCCGGTGAATCGCATTAACGtt                                 <  2:818285/90‑1 (MQ=255)                                                            tCGACAAAAAATCCTGCTGTTTTGAAAACCCCCCGCCGATTTCCTGACGCTGGTGAAAGGTGGCGTTCCGGTGAATCGCATTAACGTTgg                               <  1:6645/90‑1 (MQ=255)                                                            tCGACAAAAAATCCTGCTGGTTTGTAAAACCCCCGCCGATTTCCTGACGCTGGTGAAAGGTGGCGTTCCGGTGAATCGCATTAACGTTgg                               <  2:212993/90‑1 (MQ=255)                                                                            ctgGTTTGTAAAACACCCGCCGATTTCCTGACGCTGGTGAAAGGTGGCGTTCCGGTGAATCGCATTAACGTTGGCAATATGCACTACGcc               >  1:880413/1‑90 (MQ=255)                                                                                tttGTAAAACACCCGCCGATTTCCTGACGCTGGTGAAAGGTGGCGTTCCGGTGAATCGCATTAACGTTGGCAATATGCACTACGCCAATg           >  1:301349/1‑90 (MQ=255)                                                                                        acacCCGCCGATTTCCTGACGCTGGTGAAAGGTGGCGTTCCGGTGAATCGCATTAACGTTGGCAATATGCACTACGCCAATGGCAaacaa   >  2:785220/1‑90 (MQ=255)                                                                                         cacCCGCCGATTTCCTGACGCTGGTGAAAGGTGGCGTTCCGGTGAATCGCATTAACGTTGGCAATATGCACTACGCCAATGGCAaacaac  >  2:407388/1‑90 (MQ=255)                                                                                          |                                                                                         ATCGCCGTACGTTTCTGGACGCTGCAAAAAGTTATCGACAACATTCATCGCGCCGCCGATCGACAGAAAATCCTGCTGGTTTGTAAAACACCCGCCGATTTCCTGACGCTGGTGAAAGGTGGCGTTCCGGTGAATCGCATTAACGTTGGCAATATGCACTACGCCAATGGCAAACAAC  >  NZ_CP009273/3273741‑3273918

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑