Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,378,8020AC46.5% 64.9 / 10.8 44V48G (GTA→GGA) ampCpenicillin‑binding protein; beta‑lactamase, intrinsically weak
Reads supporting (aligned to +/- strand):  ref base A (23/0);  new base C (0/20);  total (23/21)
Fisher's exact test for biased strand distribution p-value = 1.04e-12
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCTCGAGCAATAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCCTGATAAATTACCGCCA‑‑CCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCAGAGCGTCGTTTTGAACATAGGGTCTG  >  NC_000913/4378655‑4378952
                                                                                                                                                          |                                                                                                                                                        
ccTCGAGCAATAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCCTGATAAATTacc                                                                                                                                                        >  2:324732/1‑150 (MQ=255)
   cGAGCAATAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCCTGATAAATTaccgcc                                                                                                                                                     <  1:833257/150‑1 (MQ=255)
    gAGCAATAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCCTGATAAATTaccgcca‑‑c                                                                                                                                                 >  2:348276/1‑151 (MQ=255)
    gAGCAATAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCCTGATAAATTaccgcca‑‑c                                                                                                                                                 >  1:98257/1‑151 (MQ=255)
     aGCAATAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCCTGATAAATTaccgcca‑‑cc                                                                                                                                                <  1:137838/151‑1 (MQ=255)
                     ccaAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCCTGATAAATTACCGCCA‑‑CCGCCATACCCGGGATCt                                                                                                                                >  1:226238/1‑151 (MQ=255)
                          cccGCAAGTAATTTTTTTGCTGCCCGAACCTAACTCAAACAACTTTTGTTGTGTGACGGGCTGTTTTTTGGCGATGTCCGCATACCCCCAGGAAAAGTAATAAGTTTTCCCTTAATAAATTCCCGCCA‑‑CCGCCATACCCGGGATCtttt                                                                                                                             <  1:725077/147‑1 (MQ=255)
                           aCGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCCTGATAAATTACCGCCA‑‑CCGCCATACCCGGGATCTTttgtt                                                                                                                          >  2:815626/1‑151 (MQ=255)
                           aCGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCCTGATAAATTACCGCCA‑‑CCGCCATACCCGGGATCTTttgtt                                                                                                                          >  2:520265/1‑151 (MQ=255)
                                            gCTGACCGACCCAACCACAAACACCGTTTGCTGTGTGACGGGCTGTTTTTGGGCGATGCCCGCATACCCCCAGAAAAAGTAAAAAGTTTTCCCCTAAAAAATTCCCGCCA‑‑CCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGt                                                                                                          <  1:658752/150‑1 (MQ=255)
                                               gACCGAACCTAACTCAAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCCTGATAAATCACCGCCA‑‑CCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAAtt                                                                                                      >  2:755746/1‑151 (MQ=255)
                                                    aacaaaacaaaaaCAACTTTGGCTGTGGGGGGGGTTTTTTTTGGGCGTTGCCCGCAACCCCCCAGGAAAAATAATAGGTTTTCCCAGAAAAAATTCCCGCCA‑‑CCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAAtt                                                                                                      <  1:520255/136‑1 (MQ=255)
                                                      ccaaaccaaaaCAAGTTTTGGTGGGTGAGGGGTTGTTTTTGGGGATGGCCCGCAAGCCCCAGGTAAAATTAAAAAGTTTTCCCTTAAAAATTCCCCCCCA‑‑CCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGa                                                                                                <  1:758358/142‑1 (MQ=255)
                                                         accaaaaaCAATGTTGGTGGTGTGGGGGGCTGTTTTTGGGGGATGCCCGCATACCCCAAGTAAAATTAATAAGGTTTACCTTAAAAAATTCCCCCCA‑‑CCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATg                                                                                              <  2:982993/144‑1 (MQ=255)
                                                            tCAAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCCTGATAAATTACCGCCA‑‑CCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGcaca                                                                                          >  1:91137/1‑150 (MQ=255)
                                                              aaaaaaCTTTTGCGGTGGGCCGGGTTGTTTTTGGGGAATGCCCGATTCCCCCCAGAAAAAGTAAAAAGTTTGCCCTAAAAAAATTCCCGCCA‑‑CCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAata                                                                                       <  1:261911/151‑1 (MQ=255)
                                                              aaaCATCTTTGGCTGTGGGAGGGTCTTTTTTTGGGCGTTGCCCGCATCCCCCAAGGTAAAGTAATAGTTTTTCCCCTAATAATTCCCCCCAA‑‑CCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAat                                                                                        <  2:494319/150‑1 (MQ=255)
                                                                acaacGTTTGTTGTGGGACGGGCTTTTTTTGGGCGATGCCCGCATACCCCGAGGAAAATAAAAAGGTTTTCCCTTAAAAATTTCCCGCCA‑‑CCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATc                                                                                     <  1:736618/151‑1 (MQ=255)
                                                                  aacGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCCTGATAAATTACCGCCA‑‑CCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGt                                                                                   >  2:60943/1‑151 (MQ=255)
                                                                    cGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCCTGATAAATTACCGCCA‑‑CCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTg                                                                                 >  2:182684/1‑151 (MQ=255)
                                                                      tttGTTGTGTGGGGGGTTTTTTTTTGGCGATGCCCGCATGCCCCCAGTTAAAGAAAAAGGGTTTCCCCTAAAAATTCCCCGCCA‑‑CCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTg                                                                                 <  1:620548/149‑1 (MQ=255)
                                                                           tgtgtgACGGGTTGTTTTTTGGCGTTGCCCGCATACCCCCAGTAAAATTAAAAATTTTTCCCCTAAAAAATTCCCGCCA‑‑CCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATttg                                                                            <  1:406731/149‑1 (MQ=255)
                                                                            gtgtgACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCCTGATAAATTACCGCCA‑‑CCGCCATACCCGGGATCTTTTGTTGCTCTATAAGAGGGGTAATTGTGCGATGCACAATATCGTTGATttgtt                                                                          >  2:788094/1‑150 (MQ=255)
                                                                             tgtgACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCCTGATAAATTACCGCCA‑‑CCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATttgttg                                                                         >  1:675147/1‑150 (MQ=255)
                                                                               tgACGGGTTTTTTTTTGGCAATGCCCCCACCCCCCCAGATAAAGTAATATTTTTTCCCCTAATAAATTCCCCCCA‑‑CCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGCGCGATGCACAATATCGTTGAttt                                                                             <  2:230613/144‑1 (MQ=255)
                                                                                gtggggTTGTTTTTGGGGGATCCCCGCCTACCCCCAGAAAAAGAAAGAGGTTTTCCAGTAATAATTCCCCGCAA‑‑CCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAg                                                                       <  2:964039/146‑1 (MQ=255)
                                                                                gcggggtttttttttGGCGATGCCCGAACACCCCAAGTAAAATTAAAAGTTTTTCCCCTAATAATTTCCCCCCA‑‑CCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATttg                                                                            <  2:1015578/134‑1 (MQ=255)
                                                                                gaggggTTGTTTTTTGGCGATGCCCGAATCCCCCCAGGAAAAGTAATAAGTTTTCCCATAAAAAATTCCCGCCA‑‑CCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATttgttg                                                                         <  1:1111064/144‑1 (MQ=255)
                                                                                         ctTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCCTGATAAATTACCGCCA‑‑CCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAAt                                                            >  2:573839/1‑151 (MQ=255)
                                                                                         ctTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCCTGATAAATTACCGCCA‑‑CCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAAt                                                            >  2:591202/1‑151 (MQ=255)
                                                                                           ttttGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCCTGATAAATTACCGCCA‑‑CCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAAtg                                                           >  2:557534/1‑150 (MQ=255)
                                                                                                        ccacacacccccGGGTAAAGAAATAGGTTTTTCCATGAAAATTCCCCGCCA‑‑CCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCaa                                                   <  2:286908/138‑1 (MQ=255)
                                                                                                         cGCATAGCCCCAGGTAAAGTAATAAGGTTTACCCTGATAAATTACCGCCA‑‑CCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCCCAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCg                                             >  2:777782/1‑151 (MQ=255)
                                                                                                            aTAGCCCAAGTAAAAGAAAAAGGTTTTACCTTAAAAAATTCCCGCCA‑‑CCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCg                                             <  1:451856/148‑1 (MQ=255)
                                                                                                             tAGCCCCAGGTAAAGTAATAAGGTTTACCCTGATAAATTACCGCCA‑‑CCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGta                                          >  1:786856/1‑150 (MQ=255)
                                                                                                             tAGCCCCAGGTAAAGTAATAAGGTTTACCCTGATAAATTACCGCCA‑‑CCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGt                                           >  2:798151/1‑149 (MQ=255)
                                                                                                             ataccccAAGAAAAATTAAAAGGTTTTCCCCTAAAAATTTCCCCCCA‑‑CCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGt                                           <  2:655950/147‑1 (MQ=255)
                                                                                                               gCCCCAGGTAAAGTAATAAGGTTTACCCTGATAAATTACCGCCA‑‑CCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGtaatt                                       >  1:992242/1‑151 (MQ=255)
                                                                                                                ccccAGGAAAAGTAATAAGTTTTCCCTTGATAATTTCCCGCCA‑‑CCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGtaat                                        <  1:843935/149‑1 (MQ=255)
                                                                                                                       tAAAGTAATAAGGTTTACCCTGATAAATTACCGCCA‑‑CCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAgg                                >  1:852816/1‑150 (MQ=255)
                                                                                                                        aaaGTAATAAGGTTTACCCTGATAAATTACCGCCA‑‑CCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGgcg                              >  2:542334/1‑151 (MQ=255)
                                                                                                                        aaaGTAATAATTTCACCCTATAAATTTCCCCCCCCCCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAggt                               <  1:312340/150‑2 (MQ=255)
                                                                                                                              ataaGGTTTACCCTGATAAATTACCGCCA‑‑CCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCAGAGc                        >  1:687028/1‑151 (MQ=255)
                                                                                                                                aaGGTTTACCCTGATAAATTACCGCCA‑‑CCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCAGAGcg                       >  1:610640/1‑150 (MQ=255)
                                                                                                                                    gttttCCCCTAATAATTCCCCCCCA‑‑CCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCAGAGcgtc                     <  1:815601/148‑1 (MQ=255)
                                                                                                                                    gttttCCCCTAAAAAATTCCCGCCA‑‑CCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCAGAGcgtcg                    <  1:348268/149‑1 (MQ=255)
                                                                                                                                        tACCCTGATAAATTACCGCCA‑‑CCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCAGAGCGTCGtttt                >  1:493055/1‑151 (MQ=255)
                                                                                                                                            cTGCTAAATTACCGCCA‑‑CCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGCGCGATGCACAAAATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGAAATTAATAAGGGGCAGAGCGATGTTTTg               >  2:889832/1‑148 (MQ=255)
                                                                                                                                                    aaTTACCGCCA‑‑CCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCAGAGCGTCGTTTTGAACATAggg      >  2:287998/1‑151 (MQ=255)
                                                                                                                                                     aaagaaccgccg‑‑ccgccATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCAGAGCGTCGTTTTGAACATAg        <  1:324728/145‑1 (MQ=255)
                                                                                                                                                          accgcca‑‑ccgccATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCAGAGCGTCGTTTTGAACATAGGGTCTg  >  1:717717/1‑151 (MQ=255)
                                                                                                                                                          |                                                                                                                                                        
CCTCGAGCAATAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCCTGATAAATTACCGCCA‑‑CCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCAGAGCGTCGTTTTGAACATAGGGTCTG  >  NC_000913/4378655‑4378952

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: