Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092733,659,0580TC55.3% 6.9 / 41.5 38D38G (GAT→GGT) gadXacid resistance transcriptional activator GadX
Reads supporting (aligned to +/- strand):  ref base T (10/7);  new base C (0/21);  total (10/28)
Fisher's exact test for biased strand distribution p-value = 4.11e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.83e-04
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

CGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGT‑CCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACAT  >  NZ_CP009273/3658921‑3659189
                                                                                                                                          |                                                                                                                                   
cGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGT‑CCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATc                                                                                                                                    >  1:152446/1‑139 (MQ=255)
   gTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGT‑CCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCg                                                                                                                                  >  2:47787/1‑138 (MQ=255)
   gTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGT‑CCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCg                                                                                                                                  >  1:305749/1‑138 (MQ=255)
                  ttttGTGTACATGGAGATTTCATTCCTCCTCCTTGGCCACCGGGAGAAATAATAAAGCCGGCT‑CCCTTGACACGAATCCAAAATTTTCACCACACTTATCTACTCGAATTTGGCTGGCATCCACAAAAACCAGGTCAc                                                                                                                   <  2:411454/138‑1 (MQ=255)
                                       aTGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGT‑CCCTTGACACAAATAAAAATTTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATAtt                                                                                              <  1:315994/138‑1 (MQ=255)
                                       aTGCCTCCTCCTTGACCATCGGGAAAAATAATGAAAGCGTTT‑CCCTTGACACAAATACAAAATTTTCAACACCCTTATCCACTCAAATTTGGCTTCCATCCGAAAAACCCAGCCCACCGCCATTAAAATAGCGATAtt                                                                                              <  1:264022/138‑1 (MQ=255)
                                       aTGCCTCCCCCTTGAGAATGGGAAAAAATAATAAAAGCGTTC‑CCTTTGACACAAATAAAAAATTTCCAACACACTTACCTACACAATTTTGGTTTCCACCCAAAAAACCCAGGTCACCGCCATTAAAATAGCGATAtt                                                                                              <  2:2103/138‑1 (MQ=255)
                                                     aGCATCGGAAAAAAAAAAAAAAGCGTGT‑CCCTTGACACAAATAAAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATgg                                                                               <  1:425261/139‑1 (MQ=255)
                                                      gCATCGGGAGAAATAATGAAAGCGTGC‑CCCTTGACACAAATAAAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCACCCGCAAAACCAAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGt                                                                              <  1:476249/139‑1 (MQ=255)
                                                       cATCGGGAGAAATAATGAAAGCGTGT‑CCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGt                                                                              >  2:398381/1‑138 (MQ=255)
                                                        atgggaagaAAAAAGGAAAGCGTGT‑CCTTTGACACAAAAACAAAATTTAAAACACGCTTATCTACTCAAATTGGGCTTCCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTga                                                                            <  1:60454/133‑1 (MQ=255)
                                                        aTCGGGAGAAAAAATGAAGGC‑TGTCCCCTGGACACAAATAAAAAATTTTCAACACACTTATCTACTCAAATTTGGCTTGCACCCAAAAAAACCAGTTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTga                                                                            <  2:471741/139‑1 (MQ=255)
                                                          cGGGAGAAATAATGAAAGCGTGT‑CCCTTGACACGAATACAAAATTTTCAACACACTAATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTAACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTgag                                                                           >  2:487392/1‑138 (MQ=255)
                                                           gggAGAAATAATGAAAGCGTGT‑CCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGaa                                                                         >  1:487672/1‑139 (MQ=255)
                                                                      tGAAAGCGTGT‑CCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGt                                                              >  1:109992/1‑139 (MQ=255)
                                                                          aGCGTGT‑CCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCAt                                                                                        >  2:282670/1‑109 (MQ=255)
                                                                          aGCGTGT‑CCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCACCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCAt                                                                                        <  1:282670/109‑1 (MQ=255)
                                                                           cagtct‑CCCTTGACACAAATAAAAAATTTACAACACACTTATCAACGCAAATTTGGCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGc                                                         <  2:263454/134‑1 (MQ=255)
                                                                              tgt‑CCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCAt                                                                                                                                     <  2:467182/60‑1 (MQ=255)
                                                                              tgt‑CCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCAt                                                                                                                                     >  1:467182/1‑60 (MQ=255)
                                                                              tgt‑CCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCAAATTTGGCTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATa                                                      <  1:420042/139‑1 (MQ=255)
                                                                              tgt‑CCCTTGACACGAATACAAAATTTCCAACACACTTATCTACCCAAATTTGGCTTCCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATa                                                      <  1:174531/139‑1 (MQ=255)
                                                                               tgccccTTAACAAAAATAAAAAATTTCCAACACATTTATCTACTCGATTTTGGTTTGCACCCGAAAAACCCGGTTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATa                                                      <  1:222337/136‑1 (MQ=255)
                                                                               tcccctttGACACAAATAAAAAATTTACAACACACTTATCTACAAAAATTTGGTTTGCACCCAAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATa                                                      <  2:152446/133‑1 (MQ=255)
                                                                               gt‑CCCTTAACACAAATAAAAAATTTTCAACCCACTTATCTACAAGATTTTGGCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATa                                                      <  2:305749/138‑1 (MQ=255)
                                                                                         cacaAATACAAAATTATAAACACTCTTATCTCCACAATTTTGCCTACCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGa                                            <  2:450401/139‑1 (MQ=255)
                                                                                         cacaAATAAAAATTTTACACCACTTTTATCATCTAAATTTTGGTTTCCCTCCAAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGa                                            <  2:487672/139‑1 (MQ=255)
                                                                                          acGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTactg                                           >  1:263454/1‑136 (MQ=255)
                                                                                            gAATACAAAATTTTCACCACACTTATCTCCTCGATTTTGGCTTCCCCCCGCAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACaa                                         <  1:47011/139‑1 (MQ=255)
                                                                                            gAATAAAAAATTTTCACCACACTTATCTACTCAAATTTGGCTTGCACCCAAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACaa                                         <  1:219888/139‑1 (MQ=255)
                                                                                            aaaaaaaaaaTTTTAACAACACTTATCTACGCAAATTTGGCTTGCATCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACaa                                         <  1:12046/133‑1 (MQ=255)
                                                                                              aTAAAAAATTTCCACCCCACTTATCTACTCAAATTTGGCTTGCATCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAAtt                                       <  2:109992/139‑1 (MQ=255)
                                                                                                aaaaaaTTTACACCCCCCTTATCTCCTCAAATTTGGCTTCAACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTcc                                     <  2:351935/137‑1 (MQ=255)
                                                                                                         tCAACCCACTTATCTACGCAATTTTGGCTTGCACCCACAAAACCCATGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGt                             <  2:452973/138‑1 (MQ=255)
                                                                                                               cacTTATCTACACGAATTTGGCTTGCACCCGAAAAAACCAGTTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCa                      <  1:476618/139‑1 (MQ=255)
                                                                                                                    aTCTACTCGATTTTGGCTTGCACCCGCAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGt                  <  1:47787/138‑1 (MQ=255)
                                                                                                                              ttttGGCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAatat       <  2:234705/138‑1 (MQ=255)
                                                                                                                              aTTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAatat       >  2:258374/1‑139 (MQ=255)
                                                                                                                                   gCTTTCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACAt  <  1:44746/139‑1 (MQ=255)
                                                                                                                                    cTTGCATCTTCAAAAACCAGTTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACAt  <  2:196658/138‑1 (MQ=255)
                                                                                                                                          |                                                                                                                                   
CGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGT‑CCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACAT  >  NZ_CP009273/3658921‑3659189

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑