Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,461,863 C→T I132I (ATC→ATT)  gspH → Type II secretion system protein GspH

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,461,8630CT96.4% 177.7 / ‑2.9 56I132I (ATC→ATT) gspHType II secretion system protein GspH
Reads supporting (aligned to +/- strand):  ref base C (1/1);  new base T (23/31);  total (24/32)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

CTGGGTTCCATTACAAGAAGATGCCGCAGACGAGAGCCAAAATGACTGGGATGAAGAACTCTCAATTCATCTTCAGCCATTTAAACCTGATGACAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATCACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGACCGGTGAGCCGCTCCTGACGTTAGTCTGTTCAGGCTCATGGCCCCTGGATCAAACGCTCGCCAGAGATACCCGCCCATGAACAAACAATCAGGGATGACAC  >  NC_000913/3461728‑3461998
                                                                                                                                       |                                                                                                                                       
cTGGGTTCCATTACAAGAAGATGCCGCAGACGAGAGCCAAAATGACTGGGATGAAGAACTCTCAATTCATCTTCAGCCATTTAAACCTGATGACAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGc                                                                                                                                     <  1:556595/140‑1 (MQ=255)
 tGGGTTCCATTACAATAAGATGGCGAAGACGAGAGCCAAAATGACTGGGATGAAGAACTCTCAATTCATCTTCAGCCATTTAAACCTGATGACAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGcc                                                                                                                                    <  1:438637/140‑1 (MQ=255)
   ggTTCCATTACAAGAAGATGCCGCAGACGAGAGCCAAAATGACTGGGATGAAGAACTCTCAATTCATCTTCAGCCATTTAAACCTGATGACGGCAACCAGACACGGGTAGTGATTCTTGCCGACGGACAAATTACGCCCt                                                                                                                                  >  2:417846/1‑140 (MQ=255)
   ggTTCCATTACAAGAAGATGCCGCAGACGAGAGCCAAAATGACTGGGATGAAGAACTCTCAATTCATCTTCAGCCATTTAAACCTGATGACAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGCCCt                                                                                                                                  <  2:221056/140‑1 (MQ=255)
   ggTTCCATTACAAGAAGATGCCGCAGACGAGAGCCAAAATGACTGGGATGAAGAACTCTCAATTCATCTTCAGCCATTTAAACCTGATGACAGCAACCAGCCACAGGTTGTGATTCTAGCCGACGGACAAATTACGCCCt                                                                                                                                  >  2:442921/1‑140 (MQ=255)
             cAAGAAGATGCCGCAGACGAGAGCCAAAATGACTGGGATGAAGAACTCTCAATTCATCTTCAGCCATTTAAACCTGATGACAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGcc                                                                                                                                    >  2:957515/1‑128 (MQ=255)
             cAAGAAGATGCCGCAGACGAGAGCCAAAATGACTGGGATGAAGAACTCTCAATTCATCTTCAGCCATTTAAACCTGATGACAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGcc                                                                                                                                    <  1:957515/128‑1 (MQ=255)
               agaagaTGCCGCAGACGAGAGCCAAAATGACTGGGATGAAGAACTCTCAATTCATCTTCAGCCATTTAAACCTGATGACAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGCCCt                                                                                                                                  <  1:1001598/128‑1 (MQ=255)
               agaagaTGCCGCAGACGAGAGCCAAAATGACTGGGATGAAGAACTCTCAATTCATCTTCAGCCATTTAAACCTGATGACAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGCCCt                                                                                                                                  >  2:1001598/1‑128 (MQ=255)
                    aTGCCGCAGACGAGAGCCAAAATGACTGGGATGAAGAACTCTCAATTCATCTTCAGCCATTTAAACCTGATGACAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGCCCTTCTCTTTGTTGATGGCt                                                                                                                 <  2:966134/140‑1 (MQ=255)
                      gCCGCAGACGAGAGCCAAAATGACTGGGATGAAGAACTCTCAATTCATCTTCAGCCATTTAAACCTGATGACAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGCCCTTCTCTTTGTTGATGGCTaa                                                                                                               >  1:79987/1‑140 (MQ=255)
                       ccGCAGACGAGAGCCCAAATGATTGTGATCAAGAACTCTCAATTCATCTTCAGCCATTTAAACCTGATGACAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGCCCTTCTCTTTGTTGATGGCTAAc                                                                                                              <  1:400679/140‑1 (MQ=255)
                        cGCAGACGAGAGCCAAAATGACTGGGATGAAGAACTCTCAATTCATCTTCAGCCATTTAAACCTGATGACAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGCCCTTCTCTTTGTTGATGGCTAACg                                                                                                             >  2:223983/1‑140 (MQ=255)
                              cGAGAGCCAAAATGACTGGGATGAAGAACTCTCAATTCATCTTCAGCCATTTAAACCTGATGACAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGa                                                                                                       <  1:723986/140‑1 (MQ=255)
                              cGAGAGCCAAAATGACTGGGATGAAGAACTCTCAATTCATCTTCAGCCATTTAAACCTGATGACAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGa                                                                                                       <  1:856295/140‑1 (MQ=255)
                                      aaaaTGACTGGGATGCAGAACTTTCAATTTATCTTCAGCCATTTAAACCTGATGACAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGACCGGTGAg                                                                                               <  1:324967/140‑1 (MQ=255)
                                      aaaaTGACTGGGATGAAGAACTCTCAATTCATCTTCAGCCATTTAAACCTGATGACAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGACCGGTGAg                                                                                               <  1:189089/140‑1 (MQ=255)
                                       aaaTGACTGGGATGAAGAACTCTCAATTCATCTTCAGCCATTTAAACCTGATGACAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGACCGGTGAGc                                                                                              <  1:442921/140‑1 (MQ=255)
                                       aaaTGACTGGGATGAAGAACTCTCAATTCATCTTCAGCCATTTAAACCTGATGACAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGACCGGTGAGc                                                                                              >  2:252123/1‑140 (MQ=255)
                                         aTGACTGGGATGAAGAACTCTCAATTCATCTTCAGCCATTTAAACCTGATGACAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGACCGGTGAGCCg                                                                                            <  1:535175/140‑1 (MQ=255)
                                             cTGGGATGAAGAACTCTCAATTCATCTTCAGCCATTTAAACCTGATGACAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGACCGGTGAGCCGCTcc                                                                                        <  1:121098/140‑1 (MQ=255)
                                                 gATGAAGAACTCTCAATTCATCTTCAGCCATTTAAACCTGATGACAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGACCGGTGAGCCGCTCCTGAc                                                                                    >  2:187869/1‑140 (MQ=255)
                                                       gaaCTCTCAATTCATCTTCAGCCATTTAAACCTGATGACAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGACCGGTGAGCCGCTCCTGACGTTAGt                                                                              <  1:501722/140‑1 (MQ=255)
                                                       gaaCTCTCAATTCATCTTCAGCCATTTAAACCTGATGACAGCAACCAGCCACAGGTTGTGACTCTGGCCGACGGACAAATTACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGACCGGTGAGCCGCTCCTGACGTTAGt                                                                              <  2:616675/140‑1 (MQ=255)
                                                          ctctCAATTCATCTTCAGCCATTTAAACCTGATGACAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATCACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGACCGGTGAGCCGCTCCTGACGTTAGTCTg                                                                           >  1:104723/1‑140 (MQ=255)
                                                           tctcAATTCATCTTCAGCCATTTAAACCTGATGACAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGACCGGTGAGCCGCTCCTGACGTTAGTCTGt                                                                          >  1:593463/1‑140 (MQ=255)
                                                           tctcAATTCATCTTCAGCCATTTAAACCTGATGACAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGACCGGTGAGCCGCTCCTGACGTTAGTCTGt                                                                          >  2:806414/1‑140 (MQ=255)
                                                           tctcAATTCATCTTCAGCCATTTAAACCTGATGACAGCAACCAGCCACAGGTTGGGATTCTGGCCGACGGACAAATTACGCCCTTCTCTTTTTTGATGGCCAACGCAGTGACCGGTGAGCCGCGCCTGACGGTAGTCTGt                                                                          >  2:491828/1‑140 (MQ=255)
                                                            ctcAATTCATCTTCAGCCATTTAAACCTGATGACAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGACCGGTGAGCCGCTCCTGACGTTAGTCTGtt                                                                         >  2:231469/1‑140 (MQ=255)
                                                            ctcAATTCATCTTCAGCCATTTAAACCTGATGACAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGACCGGTGAGCCGCTCCTGACGTTAGTCTGtt                                                                         <  1:187869/140‑1 (MQ=255)
                                                               aaTTCATCTTCAGCCATTTAAACCTGATGACAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGACCGGTGAGCCGCTCCTGACGTTAGTCTGTTCAg                                                                      >  2:19804/1‑140 (MQ=255)
                                                                aTTCATCTTCAGCCATTTAAACCTGATGACAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGACCGGTGAGTCGTTCCTGACGTTAGTCTGTTCAgg                                                                     >  1:264596/1‑140 (MQ=255)
                                                                aTTCATCTTCAGCCATTTAAACCTGATGACAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGACCGGTGAGCCGCTCCTGACGTTAGTCTGTTCAgg                                                                     <  1:252123/140‑1 (MQ=255)
                                                                    aTCTTCAGCCATTTAAACCTGATGACAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGATCGGTGAGCCGCTCCTGACGTTAGTCTGTTCAGGCTCa                                                                 >  1:344073/1‑140 (MQ=255)
                                                                    aTCTTCAGCCATTTAAACCTGATGACAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGACCGGTGAGCCGCTCCTGACGTTAGTCTGTTCAGGCTCa                                                                 >  2:520526/1‑140 (MQ=255)
                                                                     tCTTCAGCCATTTAAACCTGATGACAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGACCGGTGAGCCGCTCCTGACGTTAGTCTGTTCAGGCTCAt                                                                <  1:806414/140‑1 (MQ=255)
                                                                     tCTTCAGCCATTTAAACCTGATGACAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGACCGGTGAGCCGCTCCTGACGTTAGTCTGTTCAGGCTCAt                                                                >  2:788071/1‑140 (MQ=255)
                                                                           gCCATTTAAACCTGATGACAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGACCGGTGAGCCGCTCCTGACGTTAGTCTGTTCAGGCTCATGGcccc                                                          <  1:175798/140‑1 (MQ=255)
                                                                           gCCATTTAAACCTGATGACAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGACCGGTGAGCCGCTCCTGACGTTAGTCTGTTCAGGCTCATGGcccc                                                          <  2:254615/140‑1 (MQ=255)
                                                                            ccATTTAAACCTGATGACAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGACCGGTGAGCCGCTCCTGACGTTAGTCTGTTCAGGCTCATGGCCCCt                                                         <  1:223983/140‑1 (MQ=255)
                                                                                         atgaCAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGACCGGTGAGCCGCTCCTGACGTTAGTCTGTTCAGGCTCATGGCCCCTGGATCAAACGCTc                                            <  2:593463/140‑1 (MQ=255)
                                                                                         atgaCAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGACCGGTGAGCCGCTCCTGACGTTAGTCTGTTCAGGCTCATGGCCCCTGGATCAAACGCTc                                            <  1:19804/140‑1 (MQ=255)
                                                                                         atgaCAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGACCGGTGAGCCGCTCCTGACGTTAGTCTGTTCAGGCTCATGGCCCCTGGATCAAACGCTc                                            >  2:719054/1‑140 (MQ=255)
                                                                                         atgaCAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGACCGGTGAGCCGCTCCTGACGTTAGTCTGTTCAGGCTCATGGCCCCTGGATCAAACGCTc                                            >  2:846241/1‑140 (MQ=255)
                                                                                          tgaCAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGACCGGTGAGCCGCTCCTGACGTTAGTCTGTTCAGGCTCATGGCCCCTGGATCAAACGCTCg                                           <  1:82970/140‑1 (MQ=255)
                                                                                                cAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGACCGGTGAGCCGCTCCTGACGTTAGTCTGTTCAGGCTCATGGCCCCTGGATCAAACGCTCGCCagag                                     >  1:722973/1‑140 (MQ=255)
                                                                                                     aGCCACAGGTTGTGATTCTGGCCGACGGACAAATTACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGACCGGTGAGCCGCTCCTGACGTTAGTCTGTTCAGGCTCATGGCCCCTGGATCAAACGCTCGCCAGAGATAcc                                <  2:79987/140‑1 (MQ=255)
                                                                                                        cacaGGTTGTGATTCTGGCCGACGGACAAATTACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGACCGGTGAGCCGCTCCTGACGTTAGTCTGTTCAGGCTCATGGCCCCTGGATCAAACGCTCGCCAGAGATACCCGc                             >  2:544056/1‑140 (MQ=255)
                                                                                                            ggTTGTGATTCTGGCCGACGGACAAATTACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGACCGGTGAGCCGCTCCTGACGTTAGTCTGTTCAGGCTCATGGCCCCTGGATCAAACGCTCGCCAGAGATACCCGCCCAt                         <  1:833609/140‑1 (MQ=255)
                                                                                                               tgtgATTCTGGCCGACGGACAAATTACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGACCGGTGAGCCGCTCCTGACGTTAGTCTGTTCAGGCTCATGGCCCCTGGATCAAACGCTCGCCAGAGATACCCGCCCATGaa                      >  2:17068/1‑140 (MQ=255)
                                                                                                                        ggCCGACGGACAAATCACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGACCGGTGAGCCGCTCCTGACGTTAGTCTGTTCAGGCTCATGGCCCCTGGATCAAACGCTCGCCAGAGATACCCGCCCATGAACAAACAATc             <  2:104723/140‑1 (MQ=255)
                                                                                                                         gCCGACGGACAAATTACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGACCGGTGAGCCGCTCCTGACGTTAGTCTGTTCAGGCTCATGGCCCCTGGATCAAACGCTCGCCAGAGATACCCGCCCATGAACAAACAATCa            <  1:612473/140‑1 (MQ=255)
                                                                                                                              cGGACAAATTACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGACCGGTGAGCCGCTCCTGACGTTAGTCTGTTCAGGCTCATGGCCCCTGGATCAAACGCTCGTCAGGGATACCCGGCCATGAACAAACAATCAGGGAt       >  2:301526/1‑140 (MQ=255)
                                                                                                                                 aCAAATTACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGACCGGTGAGCCGCTCCTGACGTTAGTCTGTTCAGGCTCATGGCCCCTGGATCAAACGCTCGCCAGAGATACCCGCCCATGAACAAACAATCAGGGATGac    <  2:722973/140‑1 (MQ=255)
                                                                                                                                  cAAATTACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGACCGGTGAGCCGCTCCTGACGTTAGTCTGTTCAGGCTCATGGCCCCTGGATCAAACGCTCGCCAGAGATACCCGCCCATGAACAAACAATCAGGGATGaca   <  1:520526/140‑1 (MQ=255)
                                                                                                                                  cAAATTACGCCCTTCTCTTTGTCGATGGCTACCGCCGGGCCCGGTGAGCCGCTCCTGACGTTAGTCTGTTCAGGCTCATGGCCCCTGGATCAAACGCTCGCCAGAGATACCCGCCCATGAACAAACAATCAGGGATGaca   <  2:404882/140‑1 (MQ=255)
                                                                                                                                   aaaTTACGCCCTTCTCTTTGTTGATGGTTAACGCCGGGACCGGTGAGCCGCTCCTGACGTTAGTCTGTTCAGGCTCATGGCCCCTGGATCAAACGCTCGCCAGAGATACCCGCCCATGAACAAACAATCAGGGATGacac  <  1:895493/140‑1 (MQ=255)
                                                                                                                                       |                                                                                                                                       
CTGGGTTCCATTACAAGAAGATGCCGCAGACGAGAGCCAAAATGACTGGGATGAAGAACTCTCAATTCATCTTCAGCCATTTAAACCTGATGACAGCAACCAGCCACAGGTTGTGATTCTGGCCGACGGACAAATCACGCCCTTCTCTTTGTTGATGGCTAACGCCGGGACCGGTGAGCCGCTCCTGACGTTAGTCTGTTCAGGCTCATGGCCCCTGGATCAAACGCTCGCCAGAGATACCCGCCCATGAACAAACAATCAGGGATGACAC  >  NC_000913/3461728‑3461998

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑