Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092733,902,4800TA40.0% 58.3 / 15.9 40Y107F (TAT→TTT) pstAphosphate ABC transporter permease PstA
Reads supporting (aligned to +/- strand):  ref base T (19/5);  new base A (0/16);  total (19/21)
Fisher's exact test for biased strand distribution p-value = 3.39e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

AGTGCTCCATCTGCGCCACCACAATGGTGTAAACAAACAGACCAACCACAATCGACGGCGCAGAGAGCAGAATGTCGTTAATGAAGCGAATCACTTCTGCCAGCCAGGATTTA‑CGACCATATTCCGCCAGATAAATCCCCGCCATAATGCCCAGCGGCGTACCGAATACCGTGGCCCACAAAATTAACAGCCCGCTACCCGCCAGAGCGTTCGCCAGACCACCACCTTCCGTATTGGGCGGCGGCGTCATTTCAGTGAACAGCGCCAGC  >  NZ_CP009273/3902349‑3902617
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aGTCCTCCATCGGCGCCACCACAATGGTGTAAACAAACAGACCACCCACAACCGACGGCGCAGAGAGAAGAATGTCGTTAAGGAAGCAAATCACTTCTGCCAGCCAGGATTTC‑CGACCATTTTCCCCCAAATAAAcccc                                                                                                                                    <  2:263878/139‑1 (MQ=255)
  tGCTCCATCTGCGCCACCACAATGGTGTAAACAAACAGACCAACCACAATCGACGGCGCAGAGAGCAGAATGTCGTTAATGAAGCGAATCACTTCTGCCAGCCAGGATTTA‑CGACCATATTCCGCCAGATAAATCCCCg                                                                                                                                  >  1:461663/1‑139 (MQ=255)
   gCTCCATCTGCGCCACCACAATGGTGTAAACAAACAGACCAACCACAATCGACGGCGCAGAGAGCAGAATGTCGTTAATGAAGCGAATCACTTCTGCCAGCCAGGATTTA‑CGACCATATTCCGCCAGATAAATCCCCGc                                                                                                                                 >  2:498049/1‑139 (MQ=255)
    cTCCATCTGCGCCACCACAATGGTGTAAACAAACAGACCAACCACAATCGACGGCGCAGAGAGCAGAATGTCGTTAATGAAGCGAATCACTTCTGCCAGCCAGGATTTA‑CGACCATATTCCGCCAGATAAATCCCCGc                                                                                                                                 >  1:108594/1‑138 (MQ=255)
       cATCTGCGCCACCACAATGGTGTAAACAAACAGACCAACCACAATCGACGGCGCAGAGAGCAGAATGTCGTTAATGAAGCGAATCACTTCTGCCAGCCAGGATTTA‑CGACCATATTCCGCCAGATAAATCCCCGCCAt                                                                                                                              >  1:155624/1‑138 (MQ=255)
            gcgcCACCACAATGGTGTAAACAAACAGACCAACCACAATCGACGGCGCAGAGAGCAGAATGTCGTTAATGAAGCGAATCACTTCTGCCAGCCAGGATTTA‑CGACCATATTCCGCCAGATAAATCCCCGCCATAATGcc                                                                                                                        >  1:679015/1‑139 (MQ=255)
             cgcCACCACAATGGTGTAAACAAACAGACCAACCACAATCGACGGCGCAGAGAGCAGAATGTCGTTAATGAAGCGAATCACTTCTGCCAGCCAGGATTTA‑CGACCATATTCCGCCAGATAAATCCCCGCCATAATGcc                                                                                                                        >  2:218384/1‑138 (MQ=255)
             ccccaccaAAAGGGGGAAAACAAAAAGCCCAACCACAACGGAGGGCGCAGAGAGCAGATTGTCGTAAATAAGGCGAATCACTCCCCCCAGCCAGGTTTTA‑CGACCATATTCCGCCAGATAAATCCCCGCCATAATGcc                                                                                                                        <  1:378252/136‑1 (MQ=255)
                 cccaaAATGGTGTAAACAACCAACCCCCCCACAACCGCCGGCGAAGAGAGCAGAATGTCGTTAATGAAGCGAATCACTTCTGCCAGCCAGGATTTC‑CGCCCATATCCCGCCAGATAATTCCCCGCCATAATGCCCAgcg                                                                                                                   <  1:275841/138‑1 (MQ=255)
                 accacAATGGTTAAAACAAACAAACCAACCACAAGCGACGGCGCAGAGAGCAAAATGCCGTTAATGAAGCAAACCCCTTCGGCCAGCCAGGATTTA‑CGCCCATATTCCCCAAAAAAAATCCCCGCCATAATGCCCAgcg                                                                                                                   <  1:884824/139‑1 (MQ=255)
                   cacaAGGGTGAAAAAAAACAGACCAACCACAATCGACGGCGCAGAGAGCAGAATGTCTTAAATGAAGCAAATCACTTCTGCCAGCAAGGATTTA‑CGACCATATCCCGCCAGAAAAATCCCCGCCATAATGCCCAgcggc                                                                                                                 <  1:733465/139‑1 (MQ=255)
                   caaaagggTGAAAACAAACAACCCACCCACAACCGCCGGCGCGGAGAGAAAAATGTCGTAAATGAAGCAAATCCCTCCTGCCAGCCAGGATTTC‑CGACAATTTCCCGCCAAAAAAACCCCCGCCATAATGCCCAgcggc                                                                                                                 <  2:679015/133‑1 (MQ=255)
                   caaaaTGGTGTAAACAAACAAACCACCCACAACCGCCGGCGCAGAGAGCAGAATGTCTTTAATGAAGCAAATCCCTCCTGCCAGCCAGGATTTC‑CGCCCATATCCCGCCAGATAAACCCCCGCCATAATGCCCAgcggc                                                                                                                 <  2:131493/136‑1 (MQ=255)
                   caaaaTGGTGAAAACAAACAACCCAACCAAAACCGACGGCGCAGAGAGAAGAATGTCGTAAAAGAAGCAAATCCCTTCGGCCAGCCAGGATTTA‑CGACCATATCCCGCAAGAAAAATCCCCGCCATAATGCCCAgcggc                                                                                                                 <  1:18947/136‑1 (MQ=255)
                   aacaATGGAGTAAACAAAAAGCCCAACCACAATCGACGGCGCAGAGAGCAGAATGTCGTAAATGAAGCAAATCTCTTCGGCCAGCCAGGATTGA‑CGACCATATTCCGCAAGAAAAATCCCCGCCATAATGCCCAgcggc                                                                                                                 <  2:363614/138‑1 (MQ=255)
                      aaTGGTGTAAAAAAACAGCCCAACCACAATCGCCGGCGAAGAGAGAAGAATGTCGTTAATGAAGCGATTCCCTTCTGCCGGCCAGGTTTTA‑CGACCATTTTCCGCCAGATAAATCCCCGCCATAATGCCCAGCGGCGTa                                                                                                              <  1:605701/139‑1 (MQ=255)
                      aaTGGTGAAAAAAAAAAGACCACCCACAATCGACGGCGCAGAAAGAAAAATGTCGTAAATGAAGCAAATCACTTCGGCAAGCAAGGATTTA‑CGACAATATTCCGCAAGAAAAACCCCCGCCATAATGCCCAGCGGCGTa                                                                                                              <  1:539922/139‑1 (MQ=255)
                        gggtaaaaacaaacAGACCAACCAAAACCGCGGGCGCAGAGGGCAAAATGTCGTAAAAGAAGCAAAACCCTGCTGCCGGCGGGGTTTGG‑CGCCCATATCCCGCAAAAAAAGCCCCCGCCATAATGCCCAGCGGCGTAcc                                                                                                            <  2:362457/133‑1 (MQ=255)
                        gggTATAAACAAACAGCCCACCCACAAGCGCGGGGGCAGAGAGCAGAGTGTCGTAAAGGAACGAAATCCCTTCCGCCAG‑CAGGTTTTACCGCCCATTTCCCGCCAAAAAACCCCCCGCCATAATGCCCAGCGGCGTAcc                                                                                                            <  2:455212/138‑1 (MQ=255)
                          gtgtAAACAAACAGACCAACCACAATCGACGGCGCAGAGAGCAGAATGTCGTTAATGAAGCGAATCACTTCTGCCAGCCAGGATTTA‑CGACCATATTCCGCCAGATAAATCCCCGCCATAATGCCCAGCGGCGTACCg                                                                                                           >  2:18947/1‑138 (MQ=255)
                             tAAACAAACAGACCAACCACAATCGACGGCGCAGAGAGCAGAATGTCGTTAATGAAGCGAATCACTTCTGCCAGCCAGGATTTA‑CGACCATATTCCGCCAGATAAATCCCCGCCATAATGCCCAGCGGCGTACCGAATa                                                                                                       >  2:239852/1‑139 (MQ=255)
                                    acaGACCAACCACAATCGACGGCGCAGAGAGCAGAATGTCGTTAATGCAGCGAATCACTTCTGCCAGCCAGGATTTA‑CGACCATATTCCGCCAGATAACTCCCCGCCATAATGCCCAGCGGCGTACCGAATACCGTGGc                                                                                                >  2:156473/1‑139 (MQ=255)
                                    acaGACCAACCACAATCGACGGCGCAGAGAGCAGAATGTCGTTAATGAAGCGAATCACTTCTGCCAGCCAGGATTTA‑CGACCATATTCCGCCAGATAAATCCCCGCCATAATGCCCAGCGGCGTACCGAATAcctgtct                                                                                                >  1:868183/1‑134 (MQ=255)
                                            accaCAATCGACGGCGCAGAGAGCAGAATGTCGTTAATGAAGCGAATCACTTCTGCCAGCCAGGATTTA‑CGACCATATTCCGCCAGATAAATCCCCGCCATAATGCCCAGCGGCGTACCGAATACCGTGGCCCACaaaa                                                                                        >  2:216900/1‑139 (MQ=255)
                                                  atcgcgggCGGAGAGAGCAGAATCTCTTAAATGAAGCAAATCCCTTCTGCCAGCCAGTTTTAC‑CGCCCTTATCCCGCCATAAAAACCCCCGCCATAATGCCCAGCGGCGTACCGAATACCGTGGCCCACAAAATTAACa                                                                                  <  2:514297/133‑1 (MQ=255)
                                                         gcgcAGAGAGAAAAATGTCGTAAAGGAAGCAAATCCCTCCGCCCAGCCGGGTTTAC‑CGACCTTTCCCCGCCAAAAAAACCCCCGCCATAATGCCCAGCGGCGTACCGAATACCGTGGCCCACAAAATTAACAGCCCGCt                                                                           <  2:514159/139‑1 (MQ=255)
                                                                 agaaGAATGTCTTAAAGGAAGCAAACCCCTCCCCCCACACAGTATTTC‑CGACATTATCCCCCAAAAAAACCCCCCGCCATAATGCCCAGCGGCGTACCGAATACCGTGGCCCACAAAATTAACAGCCCGCTACCCGCCa                                                                   <  2:624838/136‑1 (MQ=255)
                                                                      aaTGTCGTTAATGAAGCGAATCACTTCTGCCGGCCGGGATTCA‑CGCCCATTTCCCGCCAGAAAAACCCCCGCCATAATGCCCAGCGGCGTACCGAATACCGTGGCCCACAAAATTAACAGCCCGCTACCCGCCAGAGCg                                                              <  2:528626/139‑1 (MQ=255)
                                                                      aaTGTCGTTAATGAAGCGAATCACTTCTGCCAGCCAGGATTTA‑CGACCATATTCCGCCAGATAAATCCCCGCCATAATGCCCAGCGGCGTACCGAATACCGTGGCCCACAAAATTAACAGCCCGCTACCCGCCAGAGCg                                                              >  1:624838/1‑139 (MQ=255)
                                                                           cataaaTGAAGCAATCCCCTTCGCCCCGCCGGGATTCC‑CGACCATATTCCCCCAGAAAAACCCCCGCCATAATGCCCAGCGGCGTACCGAATACCGTGGCCCACAAAATTAACAGCCCGCTACCCGCCAGAGCGTTCGc                                                         <  2:377721/135‑1 (MQ=255)
                                                                           cGTTAATGAAGCGAATCACTTCTGCCAGCCAGGATTTA‑CGACCATATTCCGCCAGATAAATCCCCGCCATAATGCCCAGCGGCGTACCGAATACCGTGGCCCACAAAATTAACAGCCCGCTACCCGCCAGAGCGTTCGc                                                         >  1:616657/1‑139 (MQ=255)
                                                                                  gAAGCAAATCCCTTCCCCCAGCCGGGATTTA‑CGCCAATATCCCCCCAAAAAAACCCCCGCCATAATGCCCAGCGGCGTACCGAATACCGTGGCCCACAAAATTAACAGCCCGCTACCCGCCAGAGCGTTCGCCAGacca                                                  <  1:556749/139‑1 (MQ=255)
                                                                                         ctCACTCCGGCAACCCGGGATGTA‑CGACCATATCCCGCCAAAAAAACCCCCGCCATAATGCCCAGCGGCGTACCGAATACCGTGGCCCACAAAATTAACAGCCCGCTACCCGCCAGAGCGTTCGCCAGACCACCACCtt                                           <  2:842331/138‑1 (MQ=255)
                                                                                                       ccagGATTTA‑CGACCATATTCCGCCAGATAAATCCCCGCCATAATGCCCAGCGGCGTACCGAATACCGTGGCCCACAAAATTAACAGCCCGCTACCCGCCAGAGCGTTCGCCAGACCACCACCTTCCGTATTGggcggc                             >  1:258823/1‑139 (MQ=255)
                                                                                                                tacacccATATCCCGCAAAAAAACCCCCCGCCATAATGCCCAGCGGCGTACCGAATACCGTGGCCCACAAAATTAACAGCCCGCTACCCGCCAGAGCGTTCGCCAGACCACCACCTTCCGTATTGGGCGGCGGCGTCa                      <  2:129104/133‑1 (MQ=255)
                                                                                                                      cATATTCCGCCAGATAAATCCCCGCCATAATGCCCAGCGGCGTACCGAATACCGTGGCCCACAAAATTAACAGCCCGCTACCCGCCAGAGCGTTCGCCAGACCACCACCTTCCGTATTGGGCGGCGGCGTCATTTCAGt               >  1:582442/1‑139 (MQ=255)
                                                                                                                       atatTCCGCCAGATAAATCCCCGCCATAATGCCCAGCGGCGTACCGAATACCGTGGCCCACAAAATTAACAGCCCGCTACCCGCCAGAGCGTTCGCCAGACCACCACCTTCCGTATTGGGCGGCGGCGTCATTTCAGt               >  1:728333/1‑138 (MQ=255)
                                                                                                                               ccAGATAAATCCCCGCCATAATGCCCAGCGGCGTACCGAATACCGTGGCCCACAAAATTAACAGCCCGCTACCCGCCAGAGCGTTCGCCAGACCACCACCTTCCGTATTGGGCGGCGGCGTCATTTCAGTGAACAgcgc      >  2:559385/1‑139 (MQ=255)
                                                                                                                               ccAGATAAATCCCCGCCATAATGCCCAGCGGCGTACCGAATACCGTGGCCCACAAAATTAACAGCCCGCTACCCGCCAGAGCGTTCGCCAGACCACCACCTTCCGTATTGGGCGGCGGCGCCATTTCAGTGAACAgcgc      >  2:401818/1‑139 (MQ=255)
                                                                                                                                   aTAAATCCCCGCCATAATGCCCAGCGGCGTACCGAATACCGTGGCCCACAAAATTAACAGCCCGCTACCCGCCAGAGCGTTCGCCAGACCACCACCTTCCGTATTGGGCGGCGGCGTCATTTCAGTGAACAGCGCCAGc  >  1:453129/1‑139 (MQ=255)
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AGTGCTCCATCTGCGCCACCACAATGGTGTAAACAAACAGACCAACCACAATCGACGGCGCAGAGAGCAGAATGTCGTTAATGAAGCGAATCACTTCTGCCAGCCAGGATTTA‑CGACCATATTCCGCCAGATAAATCCCCGCCATAATGCCCAGCGGCGTACCGAATACCGTGGCCCACAAAATTAACAGCCCGCTACCCGCCAGAGCGTTCGCCAGACCACCACCTTCCGTATTGGGCGGCGGCGTCATTTCAGTGAACAGCGCCAGC  >  NZ_CP009273/3902349‑3902617

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑