Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273595,0320TG51.1% 50.8 / 75.7 47V288G (GTG→GGG) cusACu(+)/Ag(+) efflux RND transporter permease subunit CusA
Reads supporting (aligned to +/- strand):  ref base T (5/18);  new base G (24/0);  total (29/18)
Fisher's exact test for biased strand distribution p-value = 7.37e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.13e-09
Rejected as consensus: Frequency below/above cutoff threshold.

TAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCG  >  NZ_CP009273/594898‑595169
                                                                                                                                      |                                                                                                                                         
tAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGgggggggggggg                                                                                                                                       >  1:1198035/1‑137 (MQ=255)
tAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGggtggt                                                                                                                                        <  2:493499/138‑1 (MQ=255)
       aTCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGCGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGAtgctgc                                                                                                                                >  2:911024/1‑139 (MQ=255)
       aTCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGATCCTGc                                                                                                                                >  1:878957/1‑139 (MQ=255)
                  aGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCaaa                                                                                                                     <  1:1290904/139‑1 (MQ=255)
                    ccAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCaaaaa                                                                                                                   <  1:144708/139‑1 (MQ=255)
                          aaaaTGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGccc                                                                                                              <  1:193510/138‑1 (MQ=255)
                                  gTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGATCCTGCGATCCGGCAAAAAAGCCCGAGAAGGGa                                                                                                     >  2:199349/1‑139 (MQ=255)
                                  gTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCCGCGATCCGGCAAAAAAGCCCGAGAAGGGa                                                                                                     >  2:222569/1‑139 (MQ=255)
                                   gacaggTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGAt                                                                                                    <  1:849276/134‑1 (MQ=255)
                                                 cgcgATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGGGGGGGGGGGGGCCTGCGAGCCGGCAAAAAAAGACGAGAAGGGGTCGCCGCCGTGAggg                                                                                      >  2:9271/1‑139 (MQ=255)
                                                 cgcgATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGGTCCTGCGATCCGGCAAAAACGCCCGGGAAGTGATCGCCGCCGTGAAg                                                                                       >  1:967206/1‑138 (MQ=255)
                                                 cgcgATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGGGATCGCCGCCGTGAAg                                                                                       >  1:989311/1‑138 (MQ=255)
                                                  gcgATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGa                                                                                     <  2:1073670/139‑1 (MQ=255)
                                                  gcgATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGATCCTGCGATCCGGCAAAAACGCCCGGGAAGGGATCGCCGCCGTGAAGGa                                                                                     >  1:1224691/1‑139 (MQ=255)
                                                   cgATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTGCGGTTCGGCAAAAAAGCCCGCGAAGTGATCGCCGCCGTGactgtc                                                                                    >  2:849276/1‑134 (MQ=255)
                                                   cgATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTGCGATCCGGCAAAAACGCCCGGGGAGGGGTCGCCGCCGGGAAggg                                                                                     >  2:845049/1‑137 (MQ=255)
                                                                gTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGGTCCTGCGGTCCGGCAAAAACGCCCGAGGAGAGATCGCCGCCGGGAAGGAGAAAATGGAAACGc                                                                       >  2:825013/1‑139 (MQ=255)
                                                                gTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGATGCTGCGGTCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGGGAAACTGGGAACGc                                                                       >  1:1283130/1‑139 (MQ=255)
                                                                gTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGATCCTGCGGTCCGGCCAAAAAGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGc                                                                       >  1:73332/1‑139 (MQ=255)
                                                                gTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGATACTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGGAAAACTGGGAACGc                                                                       >  1:257352/1‑139 (MQ=255)
                                                                gTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTGCGATCCGGCAAAAACGCCCGGGAAGGGATCGCCGCCGGGAAGGACAAAATGGAAAAGc                                                                       >  2:310986/1‑139 (MQ=255)
                                                                gTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGGTCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAAATGGAAACGc                                                                       >  2:1190246/1‑139 (MQ=255)
                                                                gTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGATCCGGCCAAAACGCCCGAGAAGGGATCGCCGCCGTGAAGGACAAACTGGAAACGc                                                                       >  1:937422/1‑139 (MQ=255)
                                                                gTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGGGAAGGGGCAACTGGAAACGc                                                                       >  2:1073639/1‑139 (MQ=255)
                                                                gTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGATCCGGCAAAAACGCCCGAGAAGGGATCGCCGCCGGGGAGGAAAAACTGGAAACGc                                                                       >  2:1070962/1‑139 (MQ=255)
                                                                       ttGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAag                                                                <  1:9271/139‑1 (MQ=255)
                                                                         ggCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAag                                                                >  1:76587/1‑137 (MQ=255)
                                                                          gCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGGTCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAagtag                                                             >  1:1104335/1‑139 (MQ=255)
                                                                           cccGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAagtagt                                                            >  1:1155106/1‑139 (MQ=255)
                                                                           cccGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGATCCTTCGATCCGGCAAAAACGCCCGAGAAGGGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAagtagt                                                            >  1:126803/1‑139 (MQ=255)
                                                                                   tGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGa                                                    <  2:1155106/139‑1 (MQ=255)
                                                                                     cgcCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGaa                                                   <  1:1070962/138‑1 (MQ=255)
                                                                                     cgcCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGATCCGGCAAAAACGCCCGGGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGGAAAGTAGTCTGCCGGGAg                                                  >  1:9651/1‑139 (MQ=255)
                                                                                        cGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCg                                               <  2:989311/139‑1 (MQ=255)
                                                                                             cATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTTAAAAGTAGTCTGCCGGAAGACGTGgag                                          <  1:2191/139‑1 (MQ=255)
                                                                                                tGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCg                                                                                                             <  2:927721/69‑1 (MQ=255)
                                                                                                tGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCg                                                                                                             >  1:927721/1‑69 (MQ=255)
                                                                                                  ccGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGt                                     <  1:310986/139‑1 (MQ=255)
                                                                                                    gAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTa                                   <  1:998607/139‑1 (MQ=255)
                                                                                                      acaaaaCGGCGAAGGGGAAGTGGCGGGCAGGGTTGTGAACCGGCGATCCGGCAAAGACGCCCGAGAAGTGAGCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTa                                   <  2:412697/134‑1 (MQ=255)
                                                                                                      aCTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCt                                                                      <  2:773706/102‑1 (MQ=255)
                                                                                                      aCTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCt                                                                      >  1:773706/1‑102 (MQ=255)
                                                                                                           aCGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATa                            <  1:911024/139‑1 (MQ=255)
                                                                                                               cgaaggcgaagTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCaaaaa                                                                                                                   <  2:1038792/48‑1 (MQ=255)
                                                                                                               cgaaggcgaagTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCaaaaa                                                                                                                   >  1:1038792/1‑48 (MQ=255)
                                                                                                                       aagTGGCGGGCGGGGGGGGGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAAATGGAAACGCTGGAAAGTAGTCTGCCGGAAGGCGGGGAGATAGTTACAACATACGATCGcagc                  >  2:776492/1‑137 (MQ=255)
                                                                                                                               ggcgggGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGcagcc                 >  1:1123895/1‑130 (MQ=255)
                                                                                                                               ggcgggGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGcagcc                 <  2:1123895/130‑1 (MQ=255)
                                                                                                                                    ggtggtGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGa                                                                                     <  2:881378/57‑1 (MQ=255)
                                                                                                                                    ggtggtGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGa                                                                                     >  1:881378/1‑57 (MQ=255)
                                                                                                                                     gtggtgATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACcgcg  <  1:442070/139‑1 (MQ=255)
                                                                                                                                      |                                                                                                                                         
TAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCG  >  NZ_CP009273/594898‑595169

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑