Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	172,772	0	A	G	53.8%	9.1 / 14.8	14	G393G (GGA→GGG)	clcA	H(+)/Cl(‑) exchange transporter ClcA
Reads supporting (aligned to +/- strand):  ref base A (0/6);  new base G (7/0);  total (8/6)
Fisher's exact test for biased strand distribution p-value = 5.83e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.56e-03
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

GGGAACCGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGACGTTTGCTATTGCCGGAATGGGGGCATTACTGGCGGCATCTATTCGCGCGCCGTTAACGGGGATCATTCTGGTTCTGGAG  >  NZ_CP009273/172694‑172835                                                                               |                                                                gggAACCGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGCGTTTTCTTTTTCCGGGATgggggggtt                                                      >  1:436034/1‑86 (MQ=255) gggAACCGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGCGTTTTCTTTTGCCGGGATGGGGGGAtt                                                      >  2:187112/1‑90 (MQ=255)      ccGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGGGGTTGCTTATTTCGGGATGGGGGGCGTACTgg                                                 >  2:332842/1‑90 (MQ=255)      ccGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGCGTTTGCTGTTGTCGGTATGGGGGCTATACTgg                                                 >  2:439294/1‑90 (MQ=255)      ccGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGCGTTTGCTATTGCCGGGATGGGGGCATTACTgg                                                 >  2:183629/1‑90 (MQ=255)      ccGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGACGGTTTCTATTGCCCGGATGGGGGCATTACggg                                                 >  1:253389/1‑90 (MQ=255)         cTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGACGTTTGCTATTGCCGGAATGGGGGCATTACTggcgg                                              <  1:187112/90‑1 (MQ=255)         cTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGACGTTTGCTATTGCCGGAATGGGGGCATTACTggcgg                                              <  1:31183/90‑1 (MQ=255)           ttCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGACGTTTGCTATTGCCGGAATGGGGGCATTACTGGCGGCa                                            <  2:124982/90‑1 (MQ=255)                          gTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGACGTTTGCTATTGCCGGAATGGGGGCATTACTGGCGGCATCTATTCGCGCGCCg                             <  1:413643/90‑1 (MQ=255)                                  gTTTCCGCAATATCACCTTGAGGCGGGGGCGTTTGCTATTGCCGGGATGGGGGGATTACTGGCGGCAGCTTTTTGCGCGCCGGTAAAggg                     >  2:461205/1‑90 (MQ=255)                                     acagCAATATCACCTTGAGGCGGGGACGTTTGCTATTGCCGGAATGGGGGCATTACTGGCGGCATCTATTCGCGCGCCGTTAACGGGGAt                  <  1:319968/87‑1 (MQ=255)                                           atatCACCTTGAGGCGGGGACGTTTGCTATTGCCGGAATGGGGGCATTACTGGCGGCATCTATTCGCGCGCCGTTAACGGGGATCAttct            <  2:181737/90‑1 (MQ=255)                                                     gAGGCGGGGACGTTTGCTATTTCCGGGATGGGGGCATTAATTGGGGCATTTATTCGGGCGGCGGTAACGGGGGTCAgtttggttctgggg  >  1:97725/1‑88 (MQ=255)                                                                               |                                                                GGGAACCGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGACGTTTGCTATTGCCGGAATGGGGGCATTACTGGCGGCATCTATTCGCGCGCCGTTAACGGGGATCATTCTGGTTCTGGAG  >  NZ_CP009273/172694‑172835

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑