Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092733,659,0580TC40.6% 31.0 / 12.2 32D38G (GAT→GGT) gadXacid resistance transcriptional activator GadX
Reads supporting (aligned to +/- strand):  ref base T (10/9);  new base C (0/13);  total (10/22)
Fisher's exact test for biased strand distribution p-value = 1.65e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

GTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACAT  >  NZ_CP009273/3658924‑3659189
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gTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTTGGCTTGCATCCg                                                                                                                                  >  2:404021/1‑138 (MQ=255)
                         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)
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GTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACAT  >  NZ_CP009273/3658924‑3659189

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑