Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,497,835 A→G pseudogene (1086/1191 nt) intB → KpLE2 phage‑like element; putative integrase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,497,8350AG98.3% 205.4 / ‑4.3 59pseudogene (1086/1191 nt)intBKpLE2 phage‑like element; putative integrase
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base G (25/33);  total (25/34)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.79e-01

GGCTTTCGAACAATGGCCTGTAGTTCATTGGTCGAATCAGGTCTGTGGTCTCGTGATGCTGTTGAACGTCAGATGAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAACGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCCCGGGAATT  >  NC_000913/4497698‑4497966
                                                                                                                                         |                                                                                                                                   
ggCTTTCGAACAATGGCCTGTAGTTCATTGGTCGAATCAGGTCTGTGGTCTCGTGATGCTGTTGAACGTCAGATGAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCg                                                                                                                                   <  1:438459/140‑1 (MQ=255)
ggCTTTCGAACAATGGCCTGTAGTTCATTGGTCGAATCAGGTCTGTGGTCTCGTGATGCTGTTGAACGTCAGATGAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCg                                                                                                                                   >  1:286437/1‑140 (MQ=255)
     tCGAACAATGGCCTGTAGTTCATTGGTCGAATCAGGTCTGTGGTCTCGTGATGCTGTTGAACGTCAGATGAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGAt                                                                                                                              <  1:420968/140‑1 (MQ=255)
     tCGAACAATGGCCTGTAGTTCATTGGTCGAATCAGGTCTGTGGTCTCGTGATGCTGTTGAACGTCAGATGAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGAt                                                                                                                              <  2:214802/140‑1 (MQ=255)
     tCGAACAATGGCCTGTAGTTCATTGGTCGAATCAGGTCTGTGGTCTCGTGATGCTGTTGAACGTCAGATGAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGAt                                                                                                                              <  1:162693/140‑1 (MQ=255)
     tCGAACAATGGCCTGTAGTTCATTGGTCGAATCAGGTCTGTGGTCTCGTGATGCTGTTGAACGTCAGATGAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGAt                                                                                                                              >  2:162693/1‑140 (MQ=255)
     tCGAACAATGGCCTGTAGTTCATTGGTCGAATCAGGTCTGTGGTCTCGTGATGCTGTTGAACGTCAGATGAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGAt                                                                                                                              <  2:286437/140‑1 (MQ=255)
        aaCAATGGCCTGTAGTTCATTGGTCGAATCAGGTCTGTGGTCTCGTGATGCTGTTGAACGTCAGATGAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGATTGa                                                                                                                           <  2:106914/140‑1 (MQ=255)
          cAATGGCCTGTAGTTCATTGGTCGAATCAGGTCTGTGGTCTCGTGATGCTGTTGAACGTCAGATGAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGATTGATg                                                                                                                         <  2:277439/140‑1 (MQ=255)
                  tGTAGTTCATTGGTCGAATCAGGTCTGTGGTCTCGTGATGCTGTTGAACGTCAGATGAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGATTGATGCTACAgtg                                                                                                                 >  1:150044/1‑140 (MQ=255)
                   gTAGTTCATTGGTCGAATCAGGTCTGTGGTCTCGTGATGCTGTTGAACGTCAGATGAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGATTGATGCTACAgtgg                                                                                                                <  1:163003/140‑1 (MQ=255)
                         cATTGGTCGAATCAGGTCTGTGGTCTCGTGATGCTGTTGAACGTCAGATGAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGATTGa                                                                                                                           <  1:421622/123‑1 (MQ=255)
                         cATTGGTCGAATCAGGTCTGTGGTCTCGTGATGCTGTTGAACGTCAGATGAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGATTGa                                                                                                                           >  2:421622/1‑123 (MQ=255)
                         cATTGGTCGAATCAGGTCTGTGGTCTCGTGATGCTGTTGAACGTCAGATGAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGcc                                                                                                          >  1:323832/1‑140 (MQ=255)
                           ttGGTCGAATCAGGTCTGTGGTCTCGTGATGCTGTTGAACGTCAGATGAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGATTGATGCTa                                                                                                                      >  1:221887/1‑126 (MQ=255)
                           ttGGTCGAATCAGGTCTGTGGTCTCGTGATGCTGTTGAACGTCAGATGAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGATTGATGCTa                                                                                                                      <  2:221887/126‑1 (MQ=255)
                           ttGGTCGAATCAGGTCTGTGGTCTCGTGATGCTGTTGAACGTCAGATGAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGCCGa                                                                                                        >  1:95431/1‑140 (MQ=255)
                                         tCTGTGGTCTCGTGATGCTGTTGAACGTCAGATGAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTaa                                                                                          <  2:46355/140‑1 (MQ=255)
                                         tCTGTGGTCTCGTGATGCTGTTGAACGTCAGATGAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTaa                                                                                          <  2:323832/140‑1 (MQ=255)
                                         tCTGTGGTCTCGTGATGCTGTTGAACGTCAGATGAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTaa                                                                                          <  2:187748/140‑1 (MQ=255)
                                                 ctcGTGATGCTGTTGAACGTCAGATGAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGaa                                                                                  <  2:95431/140‑1 (MQ=255)
                                                  tcGTGATGCTGTTGAACGTCAGATGAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGaaa                                                                                 >  2:24004/1‑140 (MQ=255)
                                                  tcGTGATGCTGTTGAACGTCAGATGAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGaaa                                                                                 >  2:263287/1‑140 (MQ=255)
                                                   cGTGATGCTGTTGAACGTCAGATGAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAg                                                                                <  1:24004/140‑1 (MQ=255)
                                                     tGATGCTGTTGAACGTCAGATGAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGt                                                                              >  2:373805/1‑140 (MQ=255)
                                                          cTGTTGAACGTCAGATGAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATc                                                                         >  1:241370/1‑140 (MQ=255)
                                                          cTGTTGAACGTCAGATGAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATc                                                                         >  1:349003/1‑140 (MQ=255)
                                                            gTTGAACGTCAGATGAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAg                                                                       >  1:309583/1‑140 (MQ=255)
                                                            gTTGAACGTCAGATGAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAg                                                                       <  2:449978/140‑1 (MQ=255)
                                                              tGAACGTCAGATGAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTc                                                                     >  2:155382/1‑140 (MQ=255)
                                                                 aCGTCAGATGAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCAt                                                                  >  1:513925/1‑140 (MQ=255)
                                                                  cGTCAGATGAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGTTGTAAACAGAGAAAGGTTTATCAGTCCAtt                                                                 <  2:418126/140‑1 (MQ=255)
                                                                  cGTCAGATGAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCAtt                                                                 <  2:211334/140‑1 (MQ=255)
                                                                  cGTCAGATGAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGCATATCCATAAAGCAGGGCATCTGGAAGAGCGGCGATTGATGCTACAGTGGTAGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCAtt                                                                 <  2:508500/140‑1 (MQ=255)
                                                                     cAGATGAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGa                                                              >  2:358950/1‑140 (MQ=255)
                                                                     cAGATGAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGa                                                              <  1:319223/140‑1 (MQ=255)
                                                                      aGATGAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGaa                                                             <  2:520727/140‑1 (MQ=255)
                                                                       gATGAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAat                                                            >  2:495069/1‑140 (MQ=255)
                                                                          gAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATg                                                         <  1:127951/140‑1 (MQ=255)
                                                                          gAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATg                                                         <  1:495069/140‑1 (MQ=255)
                                                                            gCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCa                                                       <  2:150044/140‑1 (MQ=255)
                                                                                    gcgcGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATtaa                                               <  1:155382/140‑1 (MQ=255)
                                                                                       cgAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATtaataa                                            <  2:128022/140‑1 (MQ=255)
                                                                                            ttCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCAt                                       <  2:268642/140‑1 (MQ=255)
                                                                                                     ggCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGt                              >  1:379086/1‑140 (MQ=255)
                                                                                                      gCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTa                             >  2:74789/1‑140 (MQ=255)
                                                                                                        cgcgTATATCCATAAAGCAGAGCATCTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAat                           <  2:379086/140‑1 (MQ=255)
                                                                                                              tatCCATAAAGCAGAGCATCTGGAAGAACGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATccc                     <  1:223806/140‑1 (MQ=255)
                                                                                                                         cAGAGCATCTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGcc          >  2:172270/1‑140 (MQ=255)
                                                                                                                          agagCATCTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGccc         <  1:150091/140‑1 (MQ=255)
                                                                                                                          agagCATCTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGccc         <  1:263287/140‑1 (MQ=255)
                                                                                                                          agagCATCTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGccc         >  2:64480/1‑140 (MQ=255)
                                                                                                                          agagCATCTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGccc         <  1:532097/140‑1 (MQ=255)
                                                                                                                           gagCATCTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCCCg        >  1:259161/1‑140 (MQ=255)
                                                                                                                            agCATCTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCCCgg       >  1:115113/1‑140 (MQ=255)
                                                                                                                            agCATCTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCCCgg       >  1:454651/1‑140 (MQ=255)
                                                                                                                             gCATCTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCCCggg      <  2:241370/140‑1 (MQ=255)
                                                                                                                               aTCTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCCCGGGaa    <  2:250260/140‑1 (MQ=255)
                                                                                                                                 cTGGAAGAGCGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCCCGGGAatt  >  1:497549/1‑140 (MQ=255)
                                                                                                                                         |                                                                                                                                   
GGCTTTCGAACAATGGCCTGTAGTTCATTGGTCGAATCAGGTCTGTGGTCTCGTGATGCTGTTGAACGTCAGATGAGCCACATGGCGCGAAATTCAGTGAGGGCCGCGTATATCCATAAAGCAGAGCATCTGGAAGAACGGCGATTGATGCTACAGTGGTGGGCCGATTTTCTGGATGTAAACAGAGAAAGGTTTATCAGTCCATTTGAATATGCAAAGATTAATAATCCATTAAAACAGTAATCATCCCGGGCAAATGCCCGGGAATT  >  NC_000913/4497698‑4497966

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑