Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,659,062	0	C	A	44.0%	33.5 / 14.7	25	A37S (GCG→TCG)	gadX	acid resistance transcriptional activator GadX
Reads supporting (aligned to +/- strand):  ref base C (12/2);  new base A (0/11);  total (12/13)
Fisher's exact test for biased strand distribution p-value = 2.02e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

GAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGC  >  NZ_CP009273/3658973‑3659134                                                                                          |                                                                         gAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGc                                                                          <  2:161148/90‑1 (MQ=255)   gCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaa                                                                        <  2:68070/90‑1 (MQ=255)    cATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaaa                                                                       >  2:309084/1‑90 (MQ=255)     aTCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaaaa                                                                      >  1:34602/1‑90 (MQ=255)                          gtgtCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTaaaa                                                 >  1:389272/1‑90 (MQ=255)                           tgtCCCTTGACACAAATAAAAATTTTTCAACACACTTATCTACTCAATTTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAAt                                                <  1:198460/90‑1 (MQ=255)                            gtCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATa                                               >  1:524488/1‑90 (MQ=255)                              cccTGGACACAAATAAAAATTTTTCAACACCTTTATCTCCTCAATTTTGGTTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGc                                             <  1:293190/90‑1 (MQ=255)                                     cacaAATAAAAATTTTTCAACACATTTTTCTACTCGATTTTGGTTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTc                                      <  1:440380/90‑1 (MQ=255)                                     cacaAATAAAAAATTTTCAACACACTTATCTCCTCGAATTTGGCTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTc                                      <  1:7377/90‑1 (MQ=255)                                         aaTACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCAccc                                  >  2:293190/1‑89 (MQ=255)                                           taaaaatTTTTCAACACACTTATCTACTCGATTTTGGCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCAtt                                <  1:151059/87‑1 (MQ=255)                                             aaaaaTTTCCAACACACTTATCTCCTAAATTTTGGCTTGCACCCAAAAAACCCAGGTCCCCGCCATTAAAATAGCGATATTCACCATTaa                              <  2:102408/89‑1 (MQ=255)                                                aaTTTTCAACACTCTTATCTCCTCGATTTTGGCTTGCACCCGAAAAACCCAGCTCACCGCCATTAAAATAGCGATATTCACCATTAACCa                           <  2:498110/90‑1 (MQ=255)                                                aaTTTTAACCACCCTTATCTCCCCAAATTTGGCTTACACCCCAAAAAACCAGGCCCCCGCCATTAAAATAGCGATATTCACCATTAACCa                           <  1:243940/90‑1 (MQ=255)                                                aaTTTACAACCCACTTCTCTACTGGATTTTGCCTTCCACCCGAAAAAACCAGGTCCCCGCCATTAAGATAGCGATATTCACCATTAACCa                           <  2:335805/90‑1 (MQ=255)                                                  ttttCAACACACTTATCTCCTCAATTTTGGCTTGCACCCGAAAAACCCAGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATg                         <  1:451145/90‑1 (MQ=255)                                                   tttCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATgg                        >  1:225989/1‑90 (MQ=255)                                                     taaaCACCTTTATCTACTCAATTTTGGCTTCCACCAAAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg                      <  2:570178/88‑1 (MQ=255)                                                      cAACACCTTTATCTCCTCAATTTTGGCTTCCATCCCAAAAACCCAGGCCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTga                     <  1:573739/90‑1 (MQ=255)                                                           cacTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAatc                >  1:498110/1‑89 (MQ=255)                                                                    aCTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGt       >  2:97270/1‑90 (MQ=255)                                                                     cTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTc      >  2:123190/1‑90 (MQ=255)                                                                     cTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTc      >  2:462147/1‑90 (MQ=255)                                                                       cGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCtt    >  2:530107/1‑90 (MQ=255)                                                                         aaTTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGc  >  2:468864/1‑90 (MQ=255)                                                                                          |                                                                         GAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGC  >  NZ_CP009273/3658973‑3659134

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑