Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092733,659,0620CA51.6% 10.6 / 36.2 31A37S (GCG→TCG) gadXacid resistance transcriptional activator GadX
Reads supporting (aligned to +/- strand):  ref base C (9/6);  new base A (0/16);  total (9/22)
Fisher's exact test for biased strand distribution p-value = 2.48e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.79e-03
Rejected as consensus: Frequency below/above cutoff threshold.

ATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACAT  >  NZ_CP009273/3658949‑3659189
                                                                                                                  |                                                                                                                               
ataaaGATTAAAGGCCCCCTCCTGGAGCAGGGGAAAAAAAAAGGAAAGCGTGCCCCTGGAAACAAATAAAAAATTTAC‑AACACATTTATCTACTCGAATTTGGCTTGAATCCGAAAAAACCAGGTCACCGCCATTaaaa                                                                                                        <  1:60506/136‑1 (MQ=255)
        ttAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAg                                                                                                     >  2:586691/1‑134 (MQ=255)
        ttAATGCCTCCTCCTTGAGCATCGGGAAAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAg                                                                                                     <  1:586691/134‑1 (MQ=255)
           atccctcctcctTGAGCATCGGGAAAAATAATAAAAGCGTGTCCCTTGACACGAATACAAAATTTCC‑AACACACTTATCTACTCAAATTTGGTTTGCACCCGCAAAACCCAGGTCACCGCCATTAAAATAGCGATAtt                                                                                              <  1:468421/135‑1 (MQ=255)
           aTGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTTGGCTTGCACCCGCAAAAACCAGGCCACCGCCATTAAAATAGCGATAtt                                                                                              <  1:452382/138‑1 (MQ=255)
           aTGCCTCCTCCTTGAGCATCGGAAAAAATAATAAAAGTGTTCCCCTTGACAAAAATAAAAAATTTCC‑AACACCCTTATCTCCTCAAATTTGGCTTACACCCGAAAAAACCAGTTCACCGCCATTAAAATAGCGATAtt                                                                                              <  2:543612/138‑1 (MQ=255)
                  ctcctTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCAtt                                                                                       >  1:441305/1‑138 (MQ=255)
                        gagaATCGGGAAAAATAAAGAAAGCTTGCCCCTTGACACGAATAAAAAATTTTC‑AACACACTTATCTACTCGATTTTGGCTTGCATCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCa                                                                                  <  1:573635/137‑1 (MQ=255)
                         accATCGGGAAAAATAATAAAAGCGTGTCCCTTGACCCAAATAAAAATTTTCC‑AACACACTTATCTCCTCGATTTTGGCTTGCACCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATg                                                                                <  1:360054/136‑1 (MQ=255)
                          gCATCGGAAAAAAAAATGAAAGCGTGTCCCTTGACACAAAAAAAAAATTTTC‑AACACACTTATCTACTCGATTTTGGCTTGCATCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGt                                                                              <  2:362067/139‑1 (MQ=255)
                          ccaccGGGAAAAATAATAAACGCTTTCCCTTTGACACTAATA‑AAAATTTTCAAACACCTTTACCTACTCAATTTTGGTTTGCACCCCAAAAATCCATTACACCGCCATTAAAATATCGATATTCACCATTAACCATGGt                                                                              <  2:593778/135‑1 (MQ=255)
                            aTCGGGAAAAATAATGAAAGCGTTCCCCTTGACACAAATAAAAAATTTTC‑AACACACTTACCTACAAAATTTTGGTTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTga                                                                            <  2:167776/139‑1 (MQ=255)
                              cGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTgag                                                                           >  1:362067/1‑138 (MQ=255)
                              cGGGAAAAAAAATGAAAGCTTCTCCTTTGACAAGAATAAAAATTTTTC‑AACACATTTATCTCCTGGATTTTGGTTTCCATCCCAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTgaga                                                                          <  1:309462/139‑1 (MQ=255)
                                                    tCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACg                                                    >  2:394357/1‑139 (MQ=255)
                                                             acGAATAAAAAATTTCC‑ACCACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGAc                                           <  1:558092/139‑1 (MQ=255)
                                                               gAATACAAAATTTTA‑AACACACTTATCTACCCAAATTTGGCTTCCACCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACaa                                         <  1:550380/139‑1 (MQ=255)
                                                               aaaaaCAAAATTTTC‑AACACACTTATCTCCTCGAATTTGGTTTGCATCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACaa                                         <  1:354994/135‑1 (MQ=255)
                                                               aaaTAAAAAATTTTC‑AACACACTTATCTACTCAAATTTGGCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACaa                                         <  1:459372/138‑1 (MQ=255)
                                                                aaTACAAAATTTTC‑AACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg                                                                             >  2:557029/1‑102 (MQ=255)
                                                                aaTACAAAATTTCC‑AACACACTTATCTACTCGAATTTGGCTTGCATCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg                                                                             <  1:557029/102‑1 (MQ=255)
                                                                 aTACAAAATTTTC‑AACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAAtt                                       >  1:596849/1‑139 (MQ=255)
                                                                             c‑AACACACTTATCTACTCGAATTTGGCTTGCATCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGa                           <  1:394357/139‑1 (MQ=255)
                                                                                        aTCTACTCGAATTTGGCTTACACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGt                  <  2:596849/138‑1 (MQ=255)
                                                                                             cTCGAATTTGGCTTTCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACt             <  2:530980/138‑1 (MQ=255)
                                                                                                gAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGAc                                           >  2:152835/1‑105 (MQ=255)
                                                                                                gAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTaa          >  1:309268/1‑138 (MQ=255)
                                                                                                gAATTTGGCTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGAc                                           <  1:152835/105‑1 (MQ=255)
                                                                                                  aTTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAAt                                                >  2:499920/1‑98 (MQ=255)
                                                                                                  aTTTGGCTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAAt                                                <  1:499920/98‑1 (MQ=255)
                                                                                                       gCTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACAt  <  1:69790/139‑1 (MQ=255)
                                                                                                                  |                                                                                                                               
ATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACAT  >  NZ_CP009273/3658949‑3659189

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑