Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,435,7270GA41.9% 62.6 / 18.9 43intergenic (‑108/+33)uspF/ompNstress‑induced protein, ATP‑binding protein/outer membrane pore protein N, non‑specific
Reads supporting (aligned to +/- strand):  ref base G (23/2);  new base A (0/18);  total (23/20)
Fisher's exact test for biased strand distribution p-value = 3.12e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AATCGGAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGACAT  >  NC_000913/1435580‑1435876
                                                                                                                                                   |                                                                                                                                                     
aaTCGGAAATATCGATAGGGACAAGAATCGCTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGaa                                                                                                                                                     >  2:524609/1‑150 (MQ=255)
   cGGAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAg                                                                                                                                                 <  1:281404/151‑1 (MQ=255)
            cGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCAt                                                                                                                                         >  2:16501/1‑150 (MQ=255)
                aGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAAc                                                                                                                                      >  2:590965/1‑149 (MQ=255)
                         aaTCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCagg                                                                                                                            >  1:620793/1‑150 (MQ=255)
                              ttctttaaaaaaacCCTCCTTTTTTAGTATCCGAAAAAAGTTTAACGCAAGAGGACCTTTTTTGTAAAATGAGGGAGTACACTTTTTAAATTAAGATAAAAGGGGAAAAAAAAAGAAAAAAACGCCCGCCATAACAGCGGGCAGGAGGAt                                                                                                                       <  2:69232/140‑1 (MQ=255)
                              ttatGTTGATAAAAATTAATGTTTTAGTATACGTATAAAGTGTAACGAAAGATGACACTTTTTGTGTAATGATGGAGTTAACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGTAGAAAAAGACTGCTATAATAGAGGGAAGGAGGAtt                                                                                                                      >  2:394295/4‑151 (MQ=255)
                                  ttaaaTAAACCCCCTTTTTTTATTACCCGAAAAAAGTGTAACGCCAGAGAACTTTTTTTGTGAAAGGAGGGAGTTCACATTTTTAATTAAGAGAAAAGAGGAAAAAATAAGCAAAAAAGGCCCGCCATAACAGCGGGCAGGAGGATTTa                                                                                                                    <  2:413136/145‑1 (MQ=255)
                                   ttCAAAAACCCCCCTTTTTTAGTATCCGCAAAAAGTTTAACGCCAGATGACATTTTTTGTTTAATGACGGAGTTCACATTTTTAATTTAGAAAAAAGGAGGAAAAATAAGAAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGa                                                                                                                  <  1:585073/150‑1 (MQ=255)
                                      aTAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTg                                                                                                              >  1:338393/1‑151 (MQ=255)
                                               cctTTTTTAGTATCCGCAAAAAGTGTAACGCCAGATGACTTTTTTTGTGTAATGACGGATTTCACTTTTTTAATTTAGATAAAAGGAGGAAGAAAAAGAAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAAcc                                                                                                       <  1:734770/149‑1 (MQ=255)
                                                 tttttttttttCCACATAAAGTGTAACGCCAGATGCCTTTTTTTGTGTAATGCCGGATTTCACTTTTTTAATTTAGATCAAAGGAGAAAAAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAAcc                                                                                                       <  1:582604/137‑1 (MQ=255)
                                                        gTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGc                                                                                            >  2:513152/1‑151 (MQ=255)
                                                          aTCCGCAAAAAGTTTACCCCCAGATGACACTTTTTGTGTAAGGAGGGAGTTCACATTTTAAATTAAAAAAAAAGAGGAAAAAAAAAGAAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGa                                                                                          <  2:498260/151‑1 (MQ=255)
                                                                  aaaGTATAACCCCAGATGACACTTTTTGGAAAAGGAGGGAGTCCCCTTTTTTAATTTAGAACAAAGGAGAAAAAAAAAAAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCg                                                                                           <  2:462932/142‑1 (MQ=255)
                                                                   aaGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATatcat                                                                                 >  2:395924/1‑151 (MQ=255)
                                                                        tAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGt                                                                             >  1:733725/1‑150 (MQ=255)
                                                                          acgcaagagaatattttttGAGTAATGGCGGAGTTAACTTTTTTAATTAAGAACAAGGGGGGAAAAAAAAGAAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGt                                                                             <  2:606124/134‑1 (MQ=255)
                                                                           cGCCAGATGACTTTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGAAAAAAAAAGCAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTagag                                                                         <  1:776238/151‑1 (MQ=255)
                                                                                  tGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCAt                                                                  >  2:219467/1‑151 (MQ=255)
                                                                                   gACATTTTTTGTGTAATGAGGGATTCCACTTTTTTAATTAAAAAAAAAGGAGGAAAAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCAtt                                                                 <  1:749019/151‑1 (MQ=255)
                                                                                     cattttttGTGTAATGAGGGATTTCACTTTTTTAATTTAAATAAAAGGAGAAAAAATAAGCAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTg                                                                <  1:692295/147‑1 (MQ=255)
                                                                                       cTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGc                                                              >  2:320349/1‑150 (MQ=255)
                                                                                        tttttGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGc                                                              >  1:717204/1‑149 (MQ=255)
                                                                                          tttGTGAAAGGGCGGGGTTAAATTTTTTAATTGAAATAAAGGGAAAAAAAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGc                                                           <  1:54103/150‑1 (MQ=255)
                                                                                           ttGTGTAATGAGGGAGTCCACTTTTTTAATTAAGACAAAGGGAGAAAAAAAAAGCAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCg                                                          <  2:481906/150‑1 (MQ=255)
                                                                                           ttGTGTAATGACGAAGTTACCATTTTAAATTAAGATAAAAGAAGAAAAAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCg                                                          <  1:697364/150‑1 (MQ=255)
                                                                                            tgtgTAATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGt                                                         >  2:616057/1‑150 (MQ=255)
                                                                                                  aTGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCTTAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCt                                                  <  1:381894/151‑1 (MQ=255)
                                                                                                   tGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTg                                                 >  2:558117/1‑151 (MQ=255)
                                                                                                    gACGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGt                                                >  2:240289/1‑151 (MQ=255)
                                                                                                       ggAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCAt                                             >  1:324477/1‑151 (MQ=255)
                                                                                                         aGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCt                                           >  1:219000/1‑151 (MQ=255)
                                                                                                            tCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTc                                         >  1:57557/1‑150 (MQ=255)
                                                                                                                 ttttaaataaaaaacAAAGGAGAAAAAAAAAAAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCAt                                       <  2:221012/133‑1 (MQ=255)
                                                                                                                   tttAATTAAGAAAAAAGGAGAAAAAATAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAAc                                  <  2:222155/150‑1 (MQ=255)
                                                                                                                      aattaaaaaaaaaGGGGGAAAAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAgg                               <  2:728902/140‑1 (MQ=255)
                                                                                                                      aaTTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGt                              >  1:671434/1‑151 (MQ=255)
                                                                                                                        tttAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGtt                             >  2:402238/1‑150 (MQ=255)
                                                                                                                         ttAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTg                            >  1:599204/1‑150 (MQ=255)
                                                                                                                                aaaGGAGGAAGAATAAGCAGAAAAAGCCCGCCACAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATGATCGGTAGAGATGACATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACCGGTTGATTTtat                     >  2:420148/1‑150 (MQ=255)
                                                                                                                                 aaGGGGAAAAAATAAGAAAAAAAGGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTtat                     <  1:419073/149‑1 (MQ=255)
                                                                                                                                           aaTAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAgg         >  2:226583/1‑151 (MQ=255)
                                                                                                                                                  cgAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGACAt  >  2:219003/2‑151 (MQ=255)
                                                                                                                                                   |                                                                                                                                                     
AATCGGAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGACAT  >  NC_000913/1435580‑1435876

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑