Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,568,5120CA25.6% 97.0 / 14.8 39R3L (CGT→CTT) mdtMmultidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter
Reads supporting (aligned to +/- strand):  ref base C (3/26);  new base A (10/0);  total (13/26)
Fisher's exact test for biased strand distribution p-value = 4.50e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

ACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAGGGCAACGAGACTGCAAATGTACTGAATTTCATGTAATCAACCACACT  >  NC_000913/4568376‑4568649
                                                                                                                                        |                                                                                                                                         
aCTGACATCGGCATTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGGAAAAAAccgg                                                                                                                                        >  2:199266/1‑137 (MQ=255)
 cTGACATCGGCATTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTgg                                                                                                                                       <  1:777246/140‑1 (MQ=255)
   gACATCGGCATTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCa                                                                                                                                     <  1:473477/140‑1 (MQ=255)
   gACATCGGCATTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCa                                                                                                                                     <  1:404825/140‑1 (MQ=255)
         ggCATTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATaacaa                                                                                                                               >  1:225931/1‑140 (MQ=255)
         ggCATTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAAACAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATaacaa                                                                                                                               <  2:835614/140‑1 (MQ=255)
          gCATTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAAAGTGGCATaacaaa                                                                                                                              >  1:169875/1‑140 (MQ=255)
           cATTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATaacaaac                                                                                                                             <  2:824755/140‑1 (MQ=255)
            aTTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAAAGGGGGATaaaaaaaa                                                                                                                            >  2:473477/1‑138 (MQ=255)
            aTTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGGGGCATaaaaaaaa                                                                                                                            >  2:404825/1‑138 (MQ=255)
              tAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGTGGCATAaaaaaaaaa                                                                                                                          >  2:37843/1‑139 (MQ=255)
                aaaTCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAAAGTGGCATAACAAACAACTc                                                                                                                        >  1:805971/1‑140 (MQ=255)
                      cGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAAAGTGGCATAACAAACAACTCCTTGTc                                                                                                                  >  1:289259/1‑140 (MQ=255)
                        tACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGTGGCATAAAAAACAACCCCCTGTCCg                                                                                                                >  2:247501/1‑140 (MQ=255)
                                     aTCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACg                                                                                                   >  1:519068/1‑140 (MQ=255)
                                     aTCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGTGGCATAAAAAAAAACACCTTTTCCGGAGAAACCCCACg                                                                                                   >  2:317036/1‑140 (MQ=255)
                                       cccAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAAATCCTTGTCCGGAGAACCCCCAAggg                                                                                                 >  1:397617/1‑140 (MQ=255)
                                       cccAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGGGGGATAAAAAAAAACACCTTTTCCCGAGGAACCCAACggg                                                                                                 >  1:883496/1‑140 (MQ=255)
                                        ccAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGTGGCATAACAAACAAATCCTTGTCCGGAGAACCCCAACgggg                                                                                                >  1:126843/1‑140 (MQ=255)
                                        ccAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGTGGCATAAAAAAAAACTCCTTGTCCGGAGAACCCCAACgggg                                                                                                >  1:376518/1‑140 (MQ=255)
                                         cAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGa                                                                                               <  1:800855/140‑1 (MQ=255)
                                          aGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGTGGCATAACAAACAACCCCCTGTCCCGGGAACCCCCACggggga                                                                                              >  1:590855/1‑138 (MQ=255)
                                          aGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGTGGCATAAAAAAAAACACCTTGTCCGGAGAACCCCAACggggga                                                                                              >  2:260971/1‑138 (MQ=255)
                                            gCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGCAAAAAAAAGAGGCGTTAAAAAAAACACCTTTTCCCGAGGAACCCCACGGGGaaaa                                                                                            >  2:883805/1‑140 (MQ=255)
                                            gCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAACCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGaaaa                                                                                            <  2:648805/140‑1 (MQ=255)
                                              tGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACg                                                                                          <  1:531321/140‑1 (MQ=255)
                                              tGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACg                                                                                          <  1:662558/140‑1 (MQ=255)
                                              tGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACg                                                                                          <  1:327426/140‑1 (MQ=255)
                                              tGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACg                                                                                          <  2:225931/140‑1 (MQ=255)
                                                gATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAAAGTGGCATAACAAAAAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGaa                                                                                        >  2:721342/1‑140 (MQ=255)
                                                gATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGAGGCATAAAAAAAAACTCCTTTTCCGGAGAACCCCCACGGGGGAAAAGaa                                                                                        >  2:531321/1‑140 (MQ=255)
                                                 aTCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGTGGCATAACAAAAAACTCCTTGTCCGGAGAACCCCAACGGGGAAAAAGaaa                                                                                       >  1:252888/1‑140 (MQ=255)
                                                   cAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAAtt                                                                                     <  2:374337/140‑1 (MQ=255)
                                                      aTCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAAAGTGGCATAAAAAAAAACTCCTTTTCCGGAGAAACCCCACGGGGGAAACGAAAATCaa                                                                                  >  2:523746/1‑140 (MQ=255)
                                                      aTCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGGGGAATAAAAAACAACCCCTTGTCCGGAGAAACCCCACGGGGGAAAAGAAAATCaa                                                                                  >  1:198315/1‑140 (MQ=255)
                                                       tCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAAt                                                                                 <  1:260971/140‑1 (MQ=255)
                                                       tCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAAt                                                                                 <  2:805971/140‑1 (MQ=255)
                                                            cGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGTGGCATAAAAAAAAACTCCTTGTCCGGAGAACCCCAACGGGGAAAAAGAAATTCAATACCGt                                                                            >  1:469068/1‑140 (MQ=255)
                                                                          caAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGaaa                                                              <  1:199266/140‑1 (MQ=255)
                                                                            aaGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAgg                                                            <  1:247501/140‑1 (MQ=255)
                                                                            aaGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAgg                                                            <  1:317036/140‑1 (MQ=255)
                                                                            aaGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAAAGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAAATCAATACCGTCGGTAATGACGaaaag                                                            >  1:133644/1‑138 (MQ=255)
                                                                                     aaaaTCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTgaga                                                   <  1:883805/140‑1 (MQ=255)
                                                                                       aaTCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAg                                                 <  2:169875/140‑1 (MQ=255)
                                                                                         tCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAACGTGGCATAAAAAAAAACTCCCTGTCCGGGGAACCCCCACGGGGGAAAAGAAAATCAATACCGTCGGGAATGACGAAAAGCAGGGGAGAAagg                                               >  2:480210/1‑140 (MQ=255)
                                                                                                  tCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAGGGCAACGAGAc                                      <  2:303273/140‑1 (MQ=255)
                                                                                                  tCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAAACTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCCACGGGGGAAAAGAAATTCAATACCGTCGGGAATGACGAAAAGCAGGGGAGAAAGGCAAAGAGAc                                      >  2:523633/1‑140 (MQ=255)
                                                                                                       aaaaaCAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAGGGCAACGAGACTGCaa                                 <  1:523746/140‑1 (MQ=255)
                                                                                                          aaCAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAGGGCAACGAGACTGCAAATg                              <  1:37843/140‑1 (MQ=255)
                                                                                                                  ggcggcATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAGGGCAACGAGACTGCAAATGTACTGAAt                      <  2:289259/140‑1 (MQ=255)
                                                                                                                                tAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAGGGCAACGAGACTGCAAATGTACTGAATTTCATGTAATCAAc        <  2:252888/140‑1 (MQ=255)
                                                                                                                                tAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGCGAGAAGGGCAACGAGACTGCAAATGTACTGAATTTCATGTAATCAAc        <  2:376518/140‑1 (MQ=255)
                                                                                                                                     aaaCGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAGGGCAACGAGACTGCAAATGTACTGAATTTCATGTAATCAACCacac   <  2:198315/140‑1 (MQ=255)
                                                                                                                                      aaCGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAAATCAATACCGTCGGTAAAAACGAAAAGCAGGTGAGAAGGGCAACGAGACTGCCAAAGTACTGAATTTCATGTAAACAACCCCACt  >  2:507638/1‑140 (MQ=255)
                                                                                                                                        |                                                                                                                                         
ACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAGGGCAACGAGACTGCAAATGTACTGAATTTCATGTAATCAACCACACT  >  NC_000913/4568376‑4568649

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑