Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,568,5120CA33.3% 63.3 / 12.1 27R3L (CGT→CTT) mdtMmultidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter
Reads supporting (aligned to +/- strand):  ref base C (2/16);  new base A (9/0);  total (11/16)
Fisher's exact test for biased strand distribution p-value = 1.17e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

CATCGGCATTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAGGGCAACGAGACTGCAAATGTACTGAATTTCATGTAATCAACCACACTGC  >  NC_000913/4568381‑4568651
                                                                                                                                   |                                                                                                                                           
cATCGGCATTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGTGGCATa                                                                                                                                     >  2:219935/1‑140 (MQ=255)
    ggCATTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATaacaa                                                                                                                                 <  2:33499/140‑1 (MQ=255)
     gCATTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGTGGCATaacaaa                                                                                                                                >  1:260196/1‑140 (MQ=255)
      cATTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATaacaaac                                                                                                                               <  2:480013/140‑1 (MQ=255)
         tAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAAAAAGGCATAaaaaaaaaa                                                                                                                            >  2:343420/1‑139 (MQ=255)
                 cGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAGCTCCTTGTc                                                                                                                    <  2:228911/140‑1 (MQ=255)
                              tGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAAAGTGGCATAAAAAAAAAACCCTTGTCCGGAGAAACCCaa                                                                                                       >  2:274380/1‑140 (MQ=255)
                                aTCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACg                                                                                                     >  1:237538/1‑140 (MQ=255)
                                aTCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCAGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACg                                                                                                     >  2:699700/1‑140 (MQ=255)
                                  cccAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACggg                                                                                                   <  1:205005/140‑1 (MQ=255)
                                   ccAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGGGGCATAAAAAACAACTCCCTGTCCGGAGAACCCCAACgggg                                                                                                  >  1:658639/1‑140 (MQ=255)
                                   ccAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAACGTGGCATAACAAACAACCCCTTGTCCGGAGAACCCCAACgggg                                                                                                  >  1:265965/1‑140 (MQ=255)
                                   ccAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGGGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACgggg                                                                                                  >  1:700714/1‑140 (MQ=255)
                                   ccAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGAGGCATAAAAAACAACACCTTGTCCGGGGAACCCCAACgggg                                                                                                  >  2:661316/1‑140 (MQ=255)
                                    cAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGa                                                                                                 <  1:583385/140‑1 (MQ=255)
                                     aGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGTGGGATAACAAAAAACTCCTTGTCCGGAGAACCCCAACGGGGaa                                                                                                >  1:159589/1‑140 (MQ=255)
                                      ggCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGTGGCATAACAAAAAACTCCTTGTCCGGAGAACCCCCACGGGGaaa                                                                                               >  2:226989/1‑140 (MQ=255)
                                      ggCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGGGGCATAAAAAACAACACCTTTTCCCGAGAACCCCAACGGGGgaa                                                                                               >  2:355086/1‑140 (MQ=255)
                                       gCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAAAGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGaaaa                                                                                              >  1:723650/1‑140 (MQ=255)
                                       gCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGGGGCATAACAAAAAACCCCTTGTCCCGAGAACCCCCACCGGGgaaa                                                                                              >  2:766523/1‑140 (MQ=255)
                                       gCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGCAAAAAAAAGTGGCAAAAAAAAAAACCCCTTTTCCGGAGAAACCCAACGGGGgaaa                                                                                              >  1:139941/1‑140 (MQ=255)
                                           gATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGaa                                                                                          <  1:274380/140‑1 (MQ=255)
                                           gATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAAAAGGGCATAAAAAAAAAACCCTTTTCCGGAGAACCCCAACGGGGAAAAAGaa                                                                                          >  2:510714/1‑140 (MQ=255)
                                            aTCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGTGGCATAACAAACAACCCCCTGTCCGGGGAACCCCAACCGGGAgaaagaaa                                                                                         >  2:781081/1‑140 (MQ=255)
                                                                cGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGTGGCATAAAAAAAAACTCCTTGTCCCGAGAACCCCCACAGGGAAAAAGAAAATCAAAACCGTCGGGAATGa                                                                     >  2:708994/1‑140 (MQ=255)
                                                                    gcaAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAAAGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAAATCAATACCGTCGGTAATGACGaa                                                                 >  1:461181/1‑140 (MQ=255)
                                                                          tCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAg                                                           <  2:88030/140‑1 (MQ=255)
                                                                            aTACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGt                                                         <  1:13508/140‑1 (MQ=255)
                                                                               cAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAAGGGGATAAAAAAAAACACCCTGTCCGGAGAAACCCCACGGGGGAAAAGAAAATCAATACCGTCGGGAATGACGAAAAGCAgggggg                                                      >  2:559207/1‑136 (MQ=255)
                                                                                aaaaTCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCAGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTgaga                                                     <  1:699700/140‑1 (MQ=255)
                                                                                       aCGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAACGTGGCATAAAAAAAAACTCCTTGTCCGGAGAAACCCAACGGGGAAAACGAAAATCAATACCGTCGGTAATGACGAAAAGCAGGGGAGAAGGGCaa                                              >  2:628058/1‑140 (MQ=255)
                                                                                             tCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAGGGCAACGAGAc                                        <  1:766523/140‑1 (MQ=255)
                                                                                                        aGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAGGGCAACGAGACTGCAAATGTAc                             <  2:658639/140‑1 (MQ=255)
                                                                                                        aGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAGGGCAACGAGACTGCAAATGTAc                             <  2:700714/140‑1 (MQ=255)
                                                                                                           gTGGCGGCATGGCGGGGAAAAAAACGGGGCATAACAAACAACCCCTTGTCCGGGGAACCCCCACGGGGAAAAAGAAAATCAATACCGTCGGTAATGAAGAAAAGCAGGGGGGAAGGGGAACGAGACTGCAAATGTACTGa                          >  2:457651/1‑140 (MQ=255)
                                                                                                           gTGGCGGCATGGCCGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAGGGCAACGAGACTGCAAATGTACTGa                          >  1:210798/1‑140 (MQ=255)
                                                                                                                     ggCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAGGGCAACGAGACTGCAAATGTACTGAATTTCATGTa                <  1:457651/140‑1 (MQ=255)
                                                                                                                             aaaaaaCGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAGGGCAACGAGACTGCAAATGTACTGAATTTCATGTAATCAACca        <  1:559207/140‑1 (MQ=255)
                                                                                                                                aaaCGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAGGGCAACGAGACTGCAAATGTACTGAATTTCATGTAATCAACCacac     <  2:139941/140‑1 (MQ=255)
                                                                                                                                aaaCGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAGGGCAACGAGACTACAAATGTACTGAATTTCATGTAATCAACCacac     <  1:337575/140‑1 (MQ=255)
                                                                                                                                   cGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAGGGCAACGAGACTGCAAATGTACTGAATTTCATGTAATCAACCACACTGc  >  1:767919/1‑140 (MQ=255)
                                                                                                                                   |                                                                                                                                           
CATCGGCATTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAGGGCAACGAGACTGCAAATGTACTGAATTTCATGTAATCAACCACACTGC  >  NC_000913/4568381‑4568651

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: ‑