Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,815,986 G→A pseudogene (564/669 nt) rph ← ribonuclease PH (defective),enzyme, Degradation of RNA, RNase PH

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,815,9860GA100.0% 220.3 / NA 65pseudogene (564/669 nt)rphribonuclease PH (defective),enzyme, Degradation of RNA, RNase PH
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (34/31);  total (34/31)

CTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCATCCCTTTCATCGGATTGGTTTTCAGCTTGCCGTTTTCCACCAGC  >  NC_000913/3815863‑3816121
                                                                                                                           |                                                                                                                                       
cTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTACACTTCAATGATGCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTctct                                                                                                                          >  2:500915/1‑139 (MQ=255)
       ggATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTACACTTCAATGATGCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCag                                                                                                                   <  2:1006570/139‑1 (MQ=255)
        gattcgattcCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTACACTTCAATGATGCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCaga                                                                                                                  <  1:944268/139‑1 (MQ=255)
           tcgattcCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTACACTTCAATGATGCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTc                                                                                                               >  2:1314651/1‑139 (MQ=255)
             gattcCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTACACTTCAATGATGCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCtt                                                                                                             <  1:874930/139‑1 (MQ=255)
             gattcCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTACACTTCAATGATGCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCtt                                                                                                             <  1:500915/139‑1 (MQ=255)
               ttcCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTACACTTCAATGATGCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCa                                                                                                           <  2:1287082/139‑1 (MQ=255)
                       gggCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTACACTTCAATGATGCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTc                                                                                                   >  1:383389/1‑139 (MQ=255)
                                   acaaGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTACACTTCAATGATGCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAAc                                                                                       >  2:226190/1‑139 (MQ=255)
                                        aTGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTACACTTCAATGATGCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCtt                                                                                                             >  2:795326/1‑112 (MQ=255)
                                        aTGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTACACTTCAATGATGCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCtt                                                                                                             <  1:795326/112‑1 (MQ=255)
                                        aTGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTACACTTCAATGATGCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCtt                                                                                  >  2:306266/1‑139 (MQ=255)
                                         tGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTACACTTCAATGATGCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTc                                                                                 <  2:169473/139‑1 (MQ=255)
                                               gCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTACACTTCAATGATGCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCAAc                                                                                                         <  2:1239171/109‑1 (MQ=255)
                                               gCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTACACTTCAATGATGCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCAAc                                                                                                         >  1:1239171/1‑109 (MQ=255)
                                                ctctTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTACACTTCAATGATGCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTc                                                                          >  2:18424/1‑139 (MQ=255)
                                                 tctTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTACACTTCAATGATGCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTca                                                                         >  2:917022/1‑139 (MQ=255)
                                                 tctTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTACACTTCAATGATGCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTca                                                                         <  1:306266/139‑1 (MQ=255)
                                                  ctTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTACACTTCAATGATGCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCag                                                                                                                   <  2:324835/96‑1 (MQ=255)
                                                  ctTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTACACTTCAATGATGCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCag                                                                                                                   >  1:324835/1‑96 (MQ=255)
                                                  ctTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTACACTTCAATGATGCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCaaa                                                                                        <  2:425496/123‑1 (MQ=255)
                                                  ctTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTACACTTCAATGATGCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCaaa                                                                                        >  1:425496/1‑123 (MQ=255)
                                                     cATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTACACTTCAATGATGCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAAt                                                                     >  2:477016/1‑139 (MQ=255)
                                                             aaCGGCTCGCCTTCTGCCGTCCCCTACACTTCAATGATGCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAg                                                             >  1:794037/1‑139 (MQ=255)
                                                               cGGCTCGCCTTCTGCCGTCCCCTACACTTCAATGATGCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGaa                                                           >  2:1330891/1‑139 (MQ=255)
                                                                  cTCGCCTTCTGCCGTCCCCTACACTTCAATGATGCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAAtt                                                                    <  1:153275/127‑1 (MQ=255)
                                                                  cTCGCCTTCTGCCGTCCCCTACACTTCAATGATGCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAAtt                                                                    >  2:153275/1‑127 (MQ=255)
                                                                  cTCGCCTTCTGCCGTCCCCTACACTTCAATGATGCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACt                                                        >  1:485910/1‑139 (MQ=255)
                                                                  cTCGCCTTCTGCCGTCCCCTACACTTCAATGATGCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACt                                                        <  1:917022/139‑1 (MQ=255)
                                                                         tCTGCCGTCCCCTACACTTCAATGATGCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTa                                                 <  2:1430943/139‑1 (MQ=255)
                                                                         tCTGCCGTCCCCTACACTTCAATGATGCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTa                                                 >  1:543343/1‑139 (MQ=255)
                                                                            gCCGTCCCCTACACTTCAATGATGCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCa                                                                                                           <  1:946608/78‑1 (MQ=255)
                                                                            gCCGTCCCCTACACTTCAATGATGCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCa                                                                                                           >  2:946608/1‑78 (MQ=255)
                                                                                           tCAATGATGCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCATCCCTTTCATCGGAt                               <  2:858643/139‑1 (MQ=255)
                                                                                            cAATGATTCGCCCGTCTTCGGTCAGCACTACATTCATGTCCGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCATCCCTTTCATCGGAtt                              >  1:895323/1‑139 (MQ=255)
                                                                                            cAATGATGCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCaga                                                                                                                  >  1:1102114/1‑55 (MQ=255)
                                                                                            cAATGATGCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCaga                                                                                                                  <  2:1102114/55‑1 (MQ=255)
                                                                                                 atgCGCCCGTCTTCGGTCATCACTACATTCATGTCGGtct                                                                                                                            <  2:1411780/40‑1 (MQ=255)
                                                                                                 atgCGCCCGTCTTCGGTCATCACTACATTCATGTCGGtct                                                                                                                            >  1:1411780/1‑40 (MQ=255)
                                                                                                 atgCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTc                                                                          <  2:833426/90‑1 (MQ=255)
                                                                                                 atgCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTc                                                                          >  1:1357147/1‑90 (MQ=255)
                                                                                                 atgCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTc                                                                          >  1:833426/1‑90 (MQ=255)
                                                                                                 atgCGCCCGCCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTc                                                                          <  2:1357147/90‑1 (MQ=255)
                                                                                                  tgCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCa                                                                                                           >  2:987783/1‑56 (MQ=255)
                                                                                                  tgCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCa                                                                                                           >  2:1132561/1‑56 (MQ=255)
                                                                                                  tgCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCa                                                                                                           <  1:1132561/56‑1 (MQ=255)
                                                                                                  tgCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCa                                                                                                           <  1:987783/56‑1 (MQ=255)
                                                                                                  tgCGCCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCATCCCTTTCATCGGATTGGtttt                        >  2:504081/1‑139 (MQ=255)
                                                                                                    cgcCCGTCTTCGGTCATCACTACATTCATGTCGGtct                                                                                                                            >  2:1380369/1‑37 (MQ=255)
                                                                                                    cgcCCGTCTTCGGTCATCACTACATTCATGTCGGtct                                                                                                                            <  1:1380369/37‑1 (MQ=255)
                                                                                                    cgcCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCtt                                                                                  >  1:1063401/1‑79 (MQ=255)
                                                                                                    cgcCCGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCtt                                                                                  <  2:1063401/79‑1 (MQ=255)
                                                                                                      cccGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCtt                                                                                                             >  1:1442449/1‑50 (MQ=255)
                                                                                                      cccGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCtt                                                                                                             <  2:1442449/50‑1 (MQ=255)
                                                                                                      cccGTCTTCGGTCATCACTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCATCCCTTTCATCGGATTGGTTTTCAGc                    >  2:322696/1‑139 (MQ=255)
                                                                                                                 tcatcaCTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGcc                                                                              >  1:922287/1‑70 (MQ=255)
                                                                                                                 tcatcaCTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGcc                                                                              <  2:922287/70‑1 (MQ=255)
                                                                                                                   atcaCTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCATCCCTTTCATCGGATTGGTTTTCAGCTTGCCGTTTTcca       >  1:436833/1‑139 (MQ=255)
                                                                                                                   atcaCTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCATCCCTTTCATCGGATTGGTTTTCAGCTTGCCGTTTTcca       <  2:1405356/139‑1 (MQ=255)
                                                                                                                    tcaCTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCa                                                                                                           <  2:733496/38‑1 (MQ=255)
                                                                                                                    tcaCTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCa                                                                                                           >  1:733496/1‑38 (MQ=255)
                                                                                                                     caCTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCATCCCTTTCATCGGATTGGTTTTCAGCTTGCCGTTTTccacc     <  2:140193/139‑1 (MQ=255)
                                                                                                                     caCTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCATCCCTTCCATCGGATTGGTTTTCAGCTTGCCGTTTTccacc     <  1:18424/139‑1 (MQ=255)
                                                                                                                      aCTACATTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCATCCCTTTCATCGGATTGGTTTTCAGCTTGCCGTTTTccacca    >  1:1173189/1‑139 (MQ=255)
                                                                                                                        tACATTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCATCCCTTTCATCGGAGTGGTTTTCAGCTTGCCGTTTTCCACCAGc  <  2:895323/139‑1 (MQ=255)
                                                                                                                           |                                                                                                                                       
CTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCATCCCTTTCATCGGATTGGTTTTCAGCTTGCCGTTTTCCACCAGC  >  NC_000913/3815863‑3816121

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑