Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,435,7210TA32.3% 60.6 / 10.3 31intergenic (‑102/+39)uspF/ompNuniversal stress protein F/outer membrane porin N
Reads supporting (aligned to +/- strand):  ref base T (19/2);  new base A (0/10);  total (19/12)
Fisher's exact test for biased strand distribution p-value = 1.49e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

AGAGGCATAGTAGGGCAGTGAAGGTATTACCGTCAGGAAATGAACCTCTGCATCATCAATCTTTGCCTCTTCCTCAACGTGGCTAA‑TCACGCGTTGAGTTAATTCTGAATCGGAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAG‑ATGACACTTTTTG‑TGTAATGACGGAGTT‑CACATTTTTAATTTAGATCAAAGGA‑GGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGACATGTTTTTATTGAAATAGTAAGTCGCGCCAATATCGGCGTATTTAACCAGATCTTTATCATCAACACCTGCCGGGTTGTCT  >  NC_000913/1435473‑1435955
                                                                                                                                                                                                                                                             |                                                                                                                                                                                                                                          
agagGCATAGTAGGGCAGTGAAGGTATTACCGTCAGGAAATGAACCTCTGCATCATCAATCTTTGCCTCTTCCTCAACGTGGCTAA‑TCACGCGTTGAGTTAATTCTGAATCGGAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAG‑ATGACACTTTTTG‑TGTAATGACGGAGTT‑CACATTTTTAATTTAGATCAAAGGA‑GGAAGAATaa                                                                                                                                                                                                                                          <  1:116131/251‑1 (MQ=255)
         gtagGGCAGTGAAGGTATTACCGTCAGGAAATGAACCTCTGCATCATCAATCTTTGCCTCTTCCTCAACGTGGCTAA‑TCACGCGTTGAGTTAATTCTGAATCGGAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAG‑ATGACACTTTTTG‑TGTAATGACGGAGTT‑CACATTTTTAATTTAGATCAAAGGA‑GGAAGAATAAGCAGaaaa                                                                                                                                                                                                                                  >  1:55220/1‑250 (MQ=255)
                         aTTACCGTCAGGAAATGAACCTCTGCATCATCAATCTTTGCCTCTTCCTCAACGTGGCTAA‑TCACGCGTTGAGTTAATTCTGAATCGGAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAG‑ATGACACTTTTTG‑TGTAATGACGGAGTT‑CACATTTTTAATTTAGATCAAAGGA‑GGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCg                                                                                                                                                                                                                 >  1:527055/1‑251 (MQ=255)
                                tCAGGAAATGAACCTCTGCATCATCAATCTTTGCCTCTTCCTCAACGTGGCTAA‑TCACGCGTTGAGTTAATTCTGAATCGGAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAG‑ATGACACTTTTTG‑TGTAATGACGGAGTT‑CACATTTTTAATTTAGATCAAAGGA‑GGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCagg                                                                                                                                                                                                           >  2:197017/1‑250 (MQ=255)
                                       aTGAACCTCTGCATCATCAATCTTTGCCTCTTCCTCAACGTGGCTAA‑TCACGCGTTGAGTTAATTCTGAATCGGAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAG‑ATGACACTTTTTG‑TGTAATGACGGAGTT‑CACATTTTTAATTTAGATCAAAGGA‑GGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGAttt                                                                                                                                                                                                    >  1:327952/1‑250 (MQ=255)
                                         gAACCTCTGCATCATCAATCTTTGCCTCTTCCTCAACGTGGCTAA‑TCACGCGTTGAGTTAATTCTGAATCGGAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAG‑ATGACACTTTTTG‑TGTAATGACGGAGTT‑CACATTTTTAATTTAGATCAAAGGA‑GGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGAttt                                                                                                                                                                                                    >  1:283394/1‑248 (MQ=255)
                                          aaCCTCTGCATCATCAATCTTTGCCTCTTCCTCAACGTGGCTAA‑TCACGCGTTGAGTTAATTCTGAATCGGAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAG‑ATGACACTTTTCG‑TGTAATGACGGAGTT‑CACATTTTTAATTTAGATCAAAGGA‑GGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGa                                                                                                                                                                                                 >  1:15005/1‑250 (MQ=255)
                                            ccTCTGCATCATCAATCTTTGCCTCTTCCTCAACGTGGCTAA‑TCACGCGTTGAGTTAATTCTGAATCGGAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAG‑ATGACACTTTTTG‑TGTAATGACGGAGTT‑CACATTTTTAATTTAGATCAAAGGA‑GGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACt                                                                                                                                                                                              >  1:84809/1‑251 (MQ=255)
                                                  aataatataTCTTTCCCTCTCCCTCAAGGTG‑CTAAATCGCGTGTTGAGTAAATTCTGAATGGAAAATAGGGAGGGGAAAAAGAATCTTTTTGTTAAAAAACCCTCTTTTTTTAGTACCCGAAAAAAGTGAACCGCAAG‑AT‑ACCTTTTTTGGTGAAATGGCGGATTT‑CACATTTTTAATTTAGAAAAAAGGA‑GGAAAAAAAAGCAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATaan                                                                                                                                                                                        <  2:241726/243‑2 (MQ=255)
                                                                    cgtCCTCAACGTGGCTAA‑TCAGGTGTTGATTTATTTAAAAATCGGAAATATCGTAAGGAAAAAAAATCTTTCTGTTAATAAACCCTCTTTTTTTAGTACCCGAATAAAGTGTACCGCAAG‑ATGACTTTTTTTG‑TGTAATGGGGGAGTT‑CTATTTTTTAATTTAGAGAAAGGGA‑GAAAGAAAAAGAAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACa                                                                                                                                                                       <  2:312881/248‑1 (MQ=255)
                                                                                   tAA‑TCACGCGTTGAGTTAATTCTGAATCGGAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAG‑ATGACACTTTTTG‑TGTAATGACGGAGTT‑CACATTTTTAATTTAGATCAAAGGA‑GGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTag                                                                                                                                                          >  2:162658/1‑248 (MQ=255)
                                                                                           gtgtgtagttatttcgaaaTCGAAAATATAGATGGGAACAAGATTCTTTTTGTTCAAAAACCCTCTTTTTTTAGTACCCGCATAAAGTGTAACGCAAA‑ATGACTTTTTTTG‑TGTAA‑GGCGGATTTTCACTTTTTAAATTTAGAAAAAAGGA‑GAAAAAAAAAAAAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCAtt                                                                                                                                                <  2:359455/234‑1 (MQ=255)
                                                                                                         ntGAATCGGAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAG‑ATGACACTTTTTG‑TGTAATGACGGAGTT‑CACATTTTTAATTTAGATCAAAGGA‑GGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGc                                                                                                                                  >  2:251002/2‑251 (MQ=255)
                                                                                                          tGAATCGGAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAG‑ATGACACTTTTTG‑TGTAATGACGGAGTT‑CACATTTTTAATTTAGATCAAAGGA‑GGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCt                                                                                                                                 >  2:58334/1‑251 (MQ=255)
                                                                                                              tCGGAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAG‑ATGACACTTTTTG‑TGTAATGACGGAGTT‑CACATTTTTAATTTAGATCAAAGGA‑GGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTc                                                                                                                              >  1:551346/1‑250 (MQ=255)
                                                                                                                  aaaTATCGATAGGGACAAAAATCGTTCTTTTCATAAACCCTCTTTTTTTAGTATCCGCATAAAGTGAAACGCCAG‑AGGACTTTTTTTG‑TGTAATGCCGAATTT‑CACATTTTAAATTTAGAACAAAGGA‑GAAAGAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCtt                                                                                                                         <  1:373393/251‑1 (MQ=255)
                                                                                                                                         gTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAG‑ATGACACTTTTTG‑TGTAATGACGGAGTT‑CACATTTTTAATTTAGATCAAAGGA‑GGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTtat                                                                                                    >  1:182843/1‑249 (MQ=255)
                                                                                                                                            gtGTTCATAAATCCTCCTTTTTAAGTTCCCTTAAAAAGTGTAACCCCAGTAT‑ACTCTTTTTG‑TTTAAGGACGGATTC‑CACTTTTTTAATTTAGATAAAAGGG‑GAAAAAAAAAGAAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGTCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTc                                                                                                <  1:490463/249‑1 (MQ=255)
                                                                                                                                                  aTAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAG‑ATGACACTTTTTG‑TGTAATGACGGAGTT‑CACATTTTTAATTTAGATCAAAGGA‑GGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGt                                                                                           >  2:148999/1‑249 (MQ=255)
                                                                                                                                                         ctcctGTTTTAGTATCCGCATAAAGTGTAACGCCAG‑ATGACACTTTTTG‑TGTAATGACGGAGTT‑CACATTTTTAATTTAGATCAAAGGA‑GGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGAc                                                                                   >  1:323920/1‑250 (MQ=255)
                                                                                                                                                          tcctGTTTTAGTATCCGCATAAAGTGTAACGCCAG‑ATGACACTTTTTG‑TGTAATGACGGAGTT‑CACATTTTTAATTTAGATCAAAGGA‑GGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGACAt                                                                                 >  1:256787/1‑251 (MQ=255)
                                                                                                                                                           ccttttttATTATCCGCAAAAATTGTACCGCCAA‑ATGACTTTTTTTG‑TGAAATGACGGAGTT‑CATATTTTAAATTAAGAAAAAAGGA‑GGAAGAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGACATg                                                                                <  1:251002/247‑1 (MQ=255)
                                                                                                                                                              gttttggaatcagaaTAAAGTGTAACGCCAG‑ATGACTTTTTTTG‑TGTAATGGCGAATTT‑CATTTTTTTATTATAGA‑AAAAGGAAGAAAGAAAAAGAAGAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGACATGtt                                                                              <  1:465257/236‑1 (MQ=255)
                                                                                                                                                                   agtgtCCGCATAAAGTGTAACGCCAG‑ATGACACTTTTTG‑TGTAATGACGGAGTT‑CACATTTTTAATTTAGATCAAAGGA‑GGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGACATGTTTTTAtt                                                                        >  2:125379/5‑251 (MQ=255)
                                                                                                                                                                        ccgaaTAAAGTGTAACACCAG‑ATGATATTTTTGG‑TATAATGAGGGATTT‑CACTTTTTTAATTAAGAAAAAAGGA‑GAAAGAATAAGAAAAAAAGGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGACATGTTTTTATTGAAAt                                                                   <  2:182843/247‑1 (MQ=255)
                                                                                                                                                                                     gtaaccccagttaattttttttttatAATGACGGTGTT‑CACATTTTTAATTAAAAAAAAAGAA‑GAAAGAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGACATGTTTTTATTGAAATAGTAAGTcgc                                                         <  1:197996/225‑1 (MQ=255)
                                                                                                                                                                                          caggatgattcTTTTTG‑TGTAGTGGCGGACTG‑CAATTTTTTAATTTAAATAAAGGGA‑GAAAAAAAAAAAAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGACATGTTTTTATTGAAATAGTAAGTCGCGCCAata                                                  <  2:75549/241‑1 (MQ=255)
                                                                                                                                                                                                                       aGTT‑CACATTTTTAATTTAGATCAAAGGA‑GGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGACATGTTTTTATTGAAATAGTAAGTCGCGCCAATATCGGCGTATTTAACCa                                  >  2:482999/1‑239 (MQ=255)
                                                                                                                                                                                                                        atttccattttttAATTAAGATAAAAGGA‑GGAAAAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGACATGTTTTTATTGAAATAGTAAGTCGCGCCAATATCGGCGTATTTAACCa                                  <  1:482999/231‑1 (MQ=255)
                                                                                                                                                                                                                          t‑CACATTTTTAATTTAGATCAAAGGA‑GGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGACATg                                                                                >  1:273668/1‑190 (MQ=255)
                                                                                                                                                                                                                                            aTCAAAGGA‑GGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGACATGTTTTTATTGAAATAGTAAGTCGCGCCAATATCGGCGTATTTAACCAGATCTTTATCATCAACACCTGCCGGGTTGTCt  >  1:78942/1‑251 (MQ=255)
                                                                                                                                                                                                                                                             |                                                                                                                                                                                                                                          
AGAGGCATAGTAGGGCAGTGAAGGTATTACCGTCAGGAAATGAACCTCTGCATCATCAATCTTTGCCTCTTCCTCAACGTGGCTAA‑TCACGCGTTGAGTTAATTCTGAATCGGAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAG‑ATGACACTTTTTG‑TGTAATGACGGAGTT‑CACATTTTTAATTTAGATCAAAGGA‑GGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGACATGTTTTTATTGAAATAGTAAGTCGCGCCAATATCGGCGTATTTAACCAGATCTTTATCATCAACACCTGCCGGGTTGTCT  >  NC_000913/1435473‑1435955

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑