Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092733,659,0620CA61.1% 4.1 / 23.1 36A37S (GCG→TCG) gadXacid resistance transcriptional activator GadX
Reads supporting (aligned to +/- strand):  ref base C (7/7);  new base A (0/22);  total (7/29)
Fisher's exact test for biased strand distribution p-value = 4.11e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.32e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

TTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGT‑CCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAA  >  NZ_CP009273/3658939‑3659191
                                                                                                                            |                                                                                                                                 
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‑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)
                                                                                                                    tacacccGAAAAAACCGGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATaa  <  2:227767/133‑1 (MQ=255)
                                                                                                                            |                                                                                                                                 
TTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGT‑CCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAA  >  NZ_CP009273/3658939‑3659191

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑