Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,676,1060CA40.0% 74.8 / 21.7 50L240F (TTG→TTTyphDputative sugar ABC transporter permease
Reads supporting (aligned to +/- strand):  ref base C (27/3);  new base A (0/20);  total (27/23)
Fisher's exact test for biased strand distribution p-value = 3.76e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGTAATCACCAGCACACCAAGCAATGTACCGAACAGGGAACCGCGACCGCCGGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGTTTTGCGGCTGATGAAC  >  NC_000913/2675959‑2676256
                                                                                                                                                     |                                                                                                                                                        
cGTAATCCCCAGCACCCCAAGCAATGTACCGAACAGGGAACCGCGACCGCCGGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCcaaca                                                                                                                                                         <  1:678253/149‑1 (MQ=255)
 gTAATCACCAGCACACCAAGCAATGTACCGAACAGGGAACCGCGACCGCCGGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACaaa                                                                                                                                                       >  2:745669/1‑150 (MQ=255)
      cACCAGCACACCAAGCAATGTACCGAACAGGGAACCGCGACCGCCGGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCg                                                                                                                                                >  1:455326/1‑151 (MQ=255)
       aCCAGCACACCAAGCAATGTACCGAACAGGGAACCGCGACCGCCGGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCgg                                                                                                                                               >  2:799442/1‑151 (MQ=255)
         cAGCACACCAAGCAATGTACCGAACAGGGAACCGCGACCGCCGGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTc                                                                                                                                            <  2:687522/151‑1 (MQ=255)
                 cAAGCAATGTACCGAACAGGGAACCGCGACCGCCGGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACcgccgc                                                                                                                                    >  2:296085/1‑151 (MQ=255)
                            ccGAACAGGGAACCGCGACCGCCGGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCg                                                                                                                         >  1:446648/1‑151 (MQ=255)
                               aaCAGGGAACCGCGACCGCCGGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGaa                                                                                                                       >  1:702167/1‑150 (MQ=255)
                                aCAGGGAACCCGCGCCCGCCGAAAGGTGCCTTACCGCCGACCACGCCCGCGGCGATGACGTCAACCTCCAGCCCGTTTGCGGCCCCTGCGTTCCCAGACCCGAGGCGCGCGGCAAACAAAATGCCGGTCACCGCCGCTAATAATCCCGa                                                                                                                        <  2:622849/149‑1 (MQ=255)
                                aCAGGGAACCGCGACCGCCGGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGaa                                                                                                                       >  1:98949/1‑149 (MQ=255)
                                    ggaacccgcccccgcggGAAAGTGCCGTCCCGCCGCCCACGACCGCGGCGACGCGGTCAACCCCCAGCCCGTTTGCGCCCCCTGCGTTACCAGACCGGAGGCGCGCCGCAAAAAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAgg                                                                                                                    <  2:446661/138‑1 (MQ=255)
                                    ggAACCGCGACCGCCGGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGt                                                                                                                  >  2:195104/1‑150 (MQ=255)
                                      ggacccggACCCCCGGAAAAGGGCCGAACCGCCGCCCACGCCCGCGGCGATGACGCAAAACCCAAGACGTTTGGCGCCACCTGTGTCCCCAGACCCGAGGCGCCCCCCAAAAAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTa                                                                                                                 <  2:716828/144‑1 (MQ=255)
                                       aCCGCGACCGCCGGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTaa                                                                                                                >  1:407628/1‑149 (MQ=255)
                                         ccGCGACCGCGGAAAGGTGCCTTCCCGCCGACCCCGCCCGCGGCGATGCCGTAAAACTCCAGCCCTTTTCCGCCCCCTGCGTCCCAAGAACCGGGGCGCCCCGCCAAAAAAATCCCGGCCACCGCCGCTAATAATCCCGAAAGGGTAAAGa                                                                                                             <  2:1202183/151‑1 (MQ=255)
                                          cgcgACCGCCGGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTaa                                                                                                                >  2:238810/1‑147 (MQ=255)
                                             gACCGCCGGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATa                                                                                                           >  1:480187/1‑149 (MQ=255)
                                              aCCGCCGGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATa                                                                                                           >  1:912577/1‑148 (MQ=255)
                                               ccgccgAAAAGTGCCGTCCCGCCGACCCCGCCCGCGGCGATGACGTCAACCCCCAGACGTTTGGCGGCCCCTGCGTTACCAGACCCGAGGCGCGCCGCAAAAAAAAGGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATa                                                                                                           <  2:187429/147‑1 (MQ=255)
                                                cgcggGAAAGTGCCGTCCCGCCGACCACGCCCGCGGCGATGACGTAAAACTCCAGACCGTTTGCGGCCCCTGCGTTACCAGAACCGAGGCGCGCCGCAAAAAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAAt                                                                                                      <  2:692795/151‑1 (MQ=255)
                                                cgccgGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGAAAAGATAAGaa                                                                                                       >  1:1134359/1‑150 (MQ=255)
                                                       aaaGTGCCGTCCCGCCGCCCACGCCCGCGGCGATGACGAAAACCCCCAGACCTTTGGCGGCACCTGCGTCCCAAAACCCGAGGCGCGCCGCAAAAAAAAGGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCAc                                                                                                <  1:5996/151‑1 (MQ=255)
                                                       aaaGGGCCGTCCCGCCGACCACGCCCGCGGCGATGACGCCAAACTCCAGACCGTTTGCGGCCCCTGCGTTACCAGACCCGAGGCGCGCCGCAAAAAAAAGGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATgcgc                                                                                                  <  2:767267/149‑1 (MQ=255)
                                                        aaGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCAcc                                                                                               >  1:557550/1‑151 (MQ=255)
                                                          gTGCCGTCCCGCCGCCCACGCCCGCGGCGATGACGTAAAACCCCAGACCGTTTGCGGCCCCTGCGTTCCCAGACCCGAGGCGCGCCGCCAAAAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCcg                                                                                             <  2:707998/151‑1 (MQ=255)
                                                             ccGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCcgacg                                                                                          >  2:1126331/1‑151 (MQ=255)
                                                                tACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAAc                                                                                       >  1:361166/1‑151 (MQ=255)
                                                                   cgccgcCCCCGACCGGGGCGATGACGTAAACCTCCAGCCCTTTTGCGCCCCCTGCGTTCCCAGACCGGGGGCGCGCCCCAAAAAAAAGGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGtt                                                                                    <  2:606424/151‑1 (MQ=255)
                                                                     ccgACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTg                                                                                   >  1:528073/1‑150 (MQ=255)
                                                                         ccACGCCCGGGGCGAGGACTTCAAACCCCAGACGTTTTGCGGCCCCTGCTTTCCAAGACCCGAGGCGCGCCCCAAAAAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGcc                                                                              <  2:1064628/151‑1 (MQ=255)
                                                                          cACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCg                                                                             >  1:263528/1‑151 (MQ=255)
                                                                                 gcggcgATGCCGTCAACCCCCAGCCCGTTCGCGGCCCCTGCTTTCCCAGACCCGGGGCGCGCCGCAAAAAAAATCCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACt                                                                      <  2:860231/151‑1 (MQ=255)
                                                                                 gcggcgATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAAc                                                                       >  1:471894/1‑150 (MQ=255)
                                                                                    gcgATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTgcg                                                                   >  2:476522/1‑151 (MQ=255)
                                                                                           cGTCAATCTCCACACGGTTAGCGGCCCCTGGGTTCCAAAACCCGCGGCGCGCCGCAAAAAAAATCCCGCCCTCCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGccgccg                                                             <  2:996857/150‑1 (MQ=255)
                                                                                           cGTAAAACTCCAGCCGGTTTGCGCCCCCTGCGTTCCCAGACCCGGGGCGCGCCGCCAAAAAAATGCGGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCgccgcc                                                              <  2:383431/149‑1 (MQ=255)
                                                                                                   tCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTAc                                                    >  2:493173/1‑151 (MQ=255)
                                                                                                     cAGACTTTTTGCGCCCCCTGCTTTCCAAGACCCGGGGCGCCCCCCCAAAAAAATGCCGTTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTAcc                                                   <  1:578729/150‑1 (MQ=255)
                                                                                                     cAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCg                                                  >  1:1081564/1‑151 (MQ=255)
                                                                                                         cgttttGCGGCACGGGAGTTACCACAGCCGGGGCGGGCGGCAAACAAAAGCCCGGTAACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTAc                                                    <  2:554171/142‑1 (MQ=255)
                                                                                                                cGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCaa                                        >  1:1203997/1‑150 (MQ=255)
                                                                                                                   ctcctgttttACCAGACCGGAGGCGCGCTCCCAAAAAAAGGCCGCTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCaaaa                                      <  2:698586/141‑1 (MQ=255)
                                                                                                                    aCCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAAcc                                   >  2:1108581/1‑151 (MQ=255)
                                                                                                                        gCGTTCCCAAACCCGAGGCGCGCCCACAAAAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGa                                 <  2:41849/149‑1 (MQ=255)
                                                                                                                           ttACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGcc                            >  2:853422/1‑151 (MQ=255)
                                                                                                                                aGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGa                         >  1:774858/1‑149 (MQ=255)
                                                                                                                                   aCCGGGGGGCCCCGCAAAAAAAAGTGCGGCTCCCCGCCGCTAATAACCCCGAAAGGTTAAAGATAAGAATCCGCGCCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAgg                      <  1:949637/150‑1 (MQ=255)
                                                                                                                                    ccGAGGCGCCCCCCAAAAAAAAAGCCGGTCCCCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTCCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAg                       <  2:111449/147‑1 (MQ=255)
                                                                                                                                      ggggCGCGCGCCAAAAAAAAGGCCGGCCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCCCCCGACGAACGTTGAGGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGc                     <  1:639121/145‑1 (MQ=255)
                                                                                                                                          cgcgcCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGTTTTGc             >  2:1167473/1‑151 (MQ=255)
                                                                                                                                              ccgcaAAAAAAAGCCCGTCCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGTTTTGCGGc          <  2:544227/150‑1 (MQ=255)
                                                                                                                                              caccaaacaaAGGGCCGCGCACCGCCGCTAATAACCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGTTTTg              <  1:514459/141‑1 (MQ=255)
                                                                                                                                                  caaaaaAAAGCCCGTCCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGTTTTGCGGCtg        <  1:641841/149‑1 (MQ=255)
                                                                                                                                                   aacaaAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGTTTTGCGGCtgatg     >  1:114398/1‑150 (MQ=255)
                                                                                                                                                     caaAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGTTTTGCGGCTGATGAac  >  2:522189/1‑151 (MQ=255)
                                                                                                                                                     |                                                                                                                                                        
CGTAATCACCAGCACACCAAGCAATGTACCGAACAGGGAACCGCGACCGCCGGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGTTTTGCGGCTGATGAAC  >  NC_000913/2675959‑2676256

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: