Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092733,659,0620CA54.8% 8.2 / 46.7 42A37S (GCG→TCG) gadXacid resistance transcriptional activator GadX
Reads supporting (aligned to +/- strand):  ref base C (11/8);  new base A (0/23);  total (11/31)
Fisher's exact test for biased strand distribution p-value = 1.77e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.88e-05
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

TAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAA‑TTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACA  >  NZ_CP009273/3658925‑3659194
                                                                                                                                          |                                                                                                                                    
tAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAA‑TTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCa                                                                                                                                     <  2:862999/139‑1 (MQ=255)
tAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAA‑TTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCa                                                                                                                                     <  2:210578/139‑1 (MQ=255)
                   tgtgCATGAAGATTTAATGCCCCCTCCTGGAGCATCGGGAGAAAAAATAAAAGCGTGCCCCTGGACACGAAAACAAAA‑TTTTCAACACACTTATCTACTCAAATTTGGCTTGCACCCGAAAAAACCAGGTCACCGCCAt                                                                                                                  <  2:590885/139‑1 (MQ=255)
                      gCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAA‑TTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTa                                                                                                                >  1:731870/1‑138 (MQ=255)
                             gATTTAATCCCCCCCCCTTGAGCATCGGGAAAAATAATGAAAGCGTGCCCCTGGACACGAATACAAAA‑TTTCCAACACCTTTATCTCCACGAATTTGGCTTCCATCCGAAAAAACCAGGTCACCGCCATTAAAATAGCg                                                                                                        <  2:648752/139‑1 (MQ=255)
                                  aaTCCCTCCTCCTTGAGCATCGGGAAAAAAAATAAAAGCGTGTCCCTTGACACAAAAACAAAA‑TTTTCAACACACTTTTCTACTCAATTTTGGCTTGCACCCAAAAAAACCAGGTCACCGCCATTAAAATAGCGatat                                                                                                    <  2:296477/138‑1 (MQ=255)
                                   atccctcctcttTGAGCAGCGGGAAAAATAATGAAGGCGTGTCCCTTAACACAAAAAAAAAA‑TTTCCAACCCACTTATCTACGCAATTTTGGTTTGCATCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATAtt                                                                                                   <  2:712616/135‑1 (MQ=255)
                                   aTGCCTCCTCCTTGAGCATCGGGAAAAATAATGAAAGCGTGTCCCTTGACACGAATAAAAAA‑TTTTCACCACACTTATCTACTCGAATTTGGCTTGCATCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATAtt                                                                                                   <  1:372362/138‑1 (MQ=255)
                                   aTGCCTCCTCCTTGAGCATCGGGAAAAATAATGAAAGCGTGTCCCTTGACACAAATACAAAA‑TTTTCAACACATTTATCTACTCGAATTTGGCTTGCATCCGCAAAACCCAGGTCACCGCCATTAAAATAGCGATAtt                                                                                                   <  1:454373/138‑1 (MQ=255)
                                   aTGCCTCCCCCTTGAGCATCGGGAAAAATAATGAAAGCGTGTCCCTTGACACGAAAACAAAA‑TTTTCAACACCCTTATCTTCTCGATTTTGGCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATAtt                                                                                                   <  2:702061/138‑1 (MQ=255)
                                        tcctcctTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAA‑TTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCAt                                                                                             >  2:141146/1‑139 (MQ=255)
                                        ccctcctTGAGCATCGGGAAAAAAAATAAAGGCGTGCCCCTTGACACAAATAAAAAA‑TTTCCAACACCCTTATCTCCTCGAATTTGGCTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCAt                                                                                             <  1:141146/138‑1 (MQ=255)
                                             ctTGAGCACCGGGAAAAATAATGAAGGCGTGTCCCTTGACACGAATAAAAAA‑TTTTCAACACACTTATCTACGCGATTTTGGCTTGCATCCGCAAAACCCAGGCCACCGCCATTAAAATAGCGATATTCACCATTAAcc                                                                                        <  1:118332/139‑1 (MQ=255)
                                                  gCATGGGGAAAAATAAGGAAAGCGTGTCCCTTGACACAAATACAAAA‑TTTCAAACACACTTATCTACTAAATTTTGGCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGt                                                                                   <  2:77776/139‑1 (MQ=255)
                                                   taTCGGGAAAAATAATCAGTGCGTCTCCCTTGACAAGAATAAAAAA‑TTTTCACCACTCTTATCTACCCGAATTTGGCTTGCATCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg                                                                                  <  1:672657/138‑1 (MQ=255)
                                                     tCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAA‑TTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGt                                                                                   >  1:341568/1‑136 (MQ=255)
                                                      cGGGAAAAATAATGAAGGCGTGTCCCTTGACACAAAAAAAAAA‑TTTTCAACCCCCTTATCTCCTAAAATTTGGCTTGCACCCCAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTgaga                                                                               <  2:455387/139‑1 (MQ=255)
                                                       gggAAAAATAATGAAAGCGTGTCCTTGGACAAGAAAAAAAAA‑TTTCCAACACTCTTATTTTCTAAATTTGGGCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGaa                                                                              <  2:537591/139‑1 (MQ=255)
                                                       gggAAAAATAATAAAGGCGT‑TCCCTTTGCAAAAAAAAAAAATTTTTAAACACACTTATCTCCTCAAATTTGGCTTGCATCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGaa                                                                              <  2:434608/139‑1 (MQ=255)
                                                         gaaaaaTAATGAAAGCGTGTCCCTGAACACAAATAAAAAA‑TTTTCAACACACTTATCTACTAAAATTTGGCTTGCATCCGAAAAAACCAGGTCACCGCCATTAAAAGAGCGATATTCACCATTAACCATGGTGAGAata                                                                            <  1:754880/136‑1 (MQ=255)
                                                             aataatGAAAGCGTGTCCCTTGACACGAATACAAAA‑TTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATAtt                                                                        >  1:537591/1‑139 (MQ=255)
                                                                                  gacaaaaaTAAAAAA‑TTTTCAACACACTTATCTACTCGATTTTGGCTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAAt                                                     <  1:90391/131‑1 (MQ=255)
                                                                                  aacagaaaTAAAAAA‑TTTTCACCACCCTTATCTACTCGATTTTGGCTTGCATCCAAAAAAACAAGGTAACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAAt                                                     <  2:341568/131‑1 (MQ=255)
                                                                                       gAATAAAAAA‑TTTTAAACACTTTTATCTACTAAAATTGGGTTTGCACCCGAAAAAACCGGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACaa                                              <  1:426980/139‑1 (MQ=255)
                                                                                        aaTACAAAA‑TTTTCAACACTCTTATCTACTCGAATTTGGCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATAtt                                                                                                   <  1:494609/85‑1 (MQ=255)
                                                                                        aaTACAAAA‑TTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATAtt                                                                                                   >  2:494609/1‑85 (MQ=255)
                                                                                        aaTACAAAA‑TTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAAt                                             >  1:308001/1‑139 (MQ=255)
                                                                                         aataaaaa‑TTCTAAAGACACTCATCTCCAAGATTTTGGATTGTACCTTAAAAAACAAGGGAACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAAtt                                            <  2:263739/135‑1 (MQ=255)
                                                                                         aTACAAAA‑TTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAAtt                                            >  2:322284/1‑139 (MQ=255)
                                                                                            aaaaa‑TTTTCAACCCCCTTATCTACTCGATTTTGGCTTGCACCCAAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTccc                                         <  1:312646/138‑1 (MQ=255)
                                                                                               aa‑TTTCCAACACTCTTATCTACACAAATTTGGCTGCCCCCCAAAAAACCCAGGCCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATg                                      <  2:711646/139‑1 (MQ=255)
                                                                                                           ctcTTATCTACTCAAATTTGGCTTGCATCCACAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCa                           <  2:308001/137‑1 (MQ=255)
                                                                                                                accTACTCAAATTTGGCTTCCATCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGt                       <  2:771825/136‑1 (MQ=255)
                                                                                                                aTCTACTCGATTTTGGCTTCCATCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGt                       <  1:516080/138‑1 (MQ=255)
                                                                                                                      tCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACtt                 >  1:480356/1‑138 (MQ=255)
                                                                                                                        gAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTaa               >  1:740026/1‑138 (MQ=255)
                                                                                                                          aTTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAatat            <  1:322284/139‑1 (MQ=255)
                                                                                                                           tttGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAatat            >  1:811135/1‑138 (MQ=255)
                                                                                                                               gCTTGCACCCGAAAAAACCAGTTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACAt       <  1:317993/139‑1 (MQ=255)
                                                                                                                               gCTTCCACCCGCAAAACCCGGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACAt       <  2:690698/139‑1 (MQ=255)
                                                                                                                                   gCATCCGCAAAAACCAGTTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATaaa    <  1:535941/138‑1 (MQ=255)
                                                                                                                                    cATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACa  >  2:464679/1‑139 (MQ=255)
                                                                                                                                          |                                                                                                                                    
TAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAA‑TTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACA  >  NZ_CP009273/3658925‑3659194

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑