Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 269,159 C→T intergenic (‑199/+130) ykfA ← / ← perR CP4‑6 prophage; putative GTP‑binding protein YkfA/putative transcriptional regulator PerR

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913269,1590CT96.2% 175.0 / ‑1.7 53intergenic (‑199/+130)ykfA/perRCP4‑6 prophage; putative GTP‑binding protein YkfA/putative transcriptional regulator PerR
Reads supporting (aligned to +/- strand):  ref base C (1/1);  new base T (29/22);  total (30/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.48e-01

AGAGTGATGATATATATCTGAAGATTTTTTCAATCCTCTGCGCTTGAGGCAGCTGCGCGACTGCTGGCTCAGGCAATGAATGAGTTATAATAGCAGCATTTACTAACAGGGATTTATTGAGAGTATGAGCCGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAGCAAAAGTGAGAGCCTTCACAAAATAATGCTTAGTAATAAAGTTACTTTGAATTCAGAGCCCCGATTAATGTGAACATGATCA  >  NC_000913/269029‑269291
                                                                                                                                  |                                                                                                                                    
agagTGATGATATATATCTGAAGATTTTTTCAATCCTCTGCGCTTGAGGCAGCTGCGCGACTGCTGGCTCAGGCAATGAATGAGTTATAATAGCAGCATTTACTAACAGGGATTTATTGAGAGTATGAGCTGCCGTGATa                                                                                                                             <  1:241457/140‑1 (MQ=255)
 gagTGATGATATATATCTGAAGATTTTTTCAATCCTCTGCGCTTGAGGCAGCTGCGCGACTGCTGGCTCAGGCAATGAATGAGTTATAATAGCAGCATTTACTAACAGGGATTTATTGAGAGTATGAGCTGCCGTGATac                                                                                                                            >  1:714065/1‑140 (MQ=255)
  agTGATGATATATATCTGAAGATTTTTTCAATCCTCTGCGCTTGAGGCAGCTGCGCGACTGCTGGCTCAGGCAATGAATGAGTTATAATAGCAGCATTTACTAACAGGGATTTATTGAGAGTATGAGCTGCCGTGATaca                                                                                                                           >  1:244840/1‑140 (MQ=255)
      atgatATATATCTGAAGATTTTTTCAATCCTCTGCGCTTGAGGCAGCTGCGCGACTGCTGGCTCAGGCAATGAATGAGTTATAATAGCAGCATTTACTAACAGGGATTTATTGAGAGTATGAGCTGCCGTGATACACCtt                                                                                                                       >  2:974874/1‑140 (MQ=255)
      atgatATATATCTGAAGATTTTTTCAATCCTCTGCGCTTGAGGCAGCTGCGCGACTGCTGGCTCAGGCAATGAATGAGTTATAATAGCAGCATTTACTAACAGGGATTTATTGAGAGTATGAGCTGCCGTGATACACCtt                                                                                                                       >  1:776200/1‑140 (MQ=255)
        gatATATATCTGAAGATTTTTTCAATCCTCTGCGCTTGAGGCAGCTGCGCGACTGCTGGCTCAGGCAATGAATGAGTTATAATAGCAGCATTTACTAACAGGGATTTATTGAGAGTATGAGCTGCCGTGATACACCTTaa                                                                                                                     <  2:714065/140‑1 (MQ=255)
          tatatatCTGAAGATTTTTTCAATCCTCTGCGCTTGAGGCAGCTGCGCGACTGCTGGCTCAGGCAATGAATGAGTTATAATAGCAGCATTTACTAACAGGGATTTATTGAGAGTATGAGCTGCCGTGa                                                                                                                               <  2:662056/128‑1 (MQ=255)
          tatatatCTGAAGATTTTTTCAATCCTCTGCGCTTGAGGCAGCTGCGCGACTGCTGGCTCAGGCAATGAATGAGTTATAATAGCAGCATTTACTAACAGGGATTTATTGAGAGTATGAGCTGCCGTGa                                                                                                                               >  1:662056/1‑128 (MQ=255)
            tatatCTGAAGATTTTTTCAATCCTCTGCGCTTGAGGCAGCTGCGCGACTGCTGGCTCAGGCAATGAATGAGTTATAATAGCAGCATTTACTAACAGGGATTTATTGAGAGTATGAGCTGCCGTGATACACCTTAAAAtc                                                                                                                 >  1:1010731/1‑140 (MQ=255)
            tatatCTGAAGATTTTTTCAATCCTCTGCGCTTGAGGCAGCTGCGCGACTGCTGGCTCAGGCAATGAATGAGTTATAATAGCAGCATTTACTAACAGGGATTTATTGAGAGTATGAGCTGCCGTGATACACCTTAAAAtc                                                                                                                 >  2:1022866/1‑140 (MQ=255)
            tatatCTGAAGATTTTTTCAATCCTCTGCGCTTGAGGCAGCTGCGCGACTGCTGGCTCAGGCAATGAATGAGTTATAATAGCAGCATTTACTAACAGGGATTTATTGAGAGTATGAGCCGCCGTGATACACCTTAAAAtc                                                                                                                 >  2:974288/1‑140 (MQ=255)
             atatCTGAAGATTTTTTCAATCCTCTGCGCTTGAGGCAGCTGCGCGACTGCTGGCTCAGGCAATGAATGAGTTATAATAGCAGCATTTACTAACAGGGATTTATTGAGAGTATGAGCTGCCGTGATACACCTTAAAAtct                                                                                                                <  2:244840/140‑1 (MQ=255)
                tCTGAAGATTTCTTCAATCCTCTGCGCTTGAGGCAGCTGCGCGACTGCTGGCTCAGGCAATGAATGAGTTATAATAGCAGCATTTACTAACAGGGATTTATTGAGAGTATGAGCTGCCGTGATACACCTTAAAATCTCaa                                                                                                             <  2:478181/140‑1 (MQ=255)
                 cTGAAGATTTTTTCAATCCTCTGCGCTTGAGGCAGCTGCGCGACTGCTGGCTCAGGCAATGAATGAGTTATAATAGCAGCATTTACTAACAGGGATTTATTGAGAGTATGAGCTGCCGTGATa                                                                                                                             <  2:1037868/123‑1 (MQ=255)
                 cTGAAGATTTTTTCAATCCTCTGCGCTTGAGGCAGCTGCGCGACTGCTGGCTCAGGCAATGAATGAGTTATAATAGCAGCATTTACTAACAGGGATTTATTGAGAGTATGAGCTGCCGTGATa                                                                                                                             >  1:1037868/1‑123 (MQ=255)
                    aaGATTTTTTCAATCCTCTGCGCTTGAGGCAGCTGCGCGACTGCTGGCTCAGGCAATGAATGAGTTATAATAGCAGCATTTACTAACAGGGATTTATTGAGAGTATGAGCTGCCGTGATACACCTTAAAATCTCAACCCa                                                                                                         >  2:488344/1‑140 (MQ=255)
                                         gcTTGAGGCAGCTGCGCGACTGCTGGCTCAGGCAATGAATGAGTTATAATAGCAGCATTTACTAACAGGGATTTATTGAGAGTATGAGCTGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAg                                                                                    <  2:165369/140‑1 (MQ=255)
                                         gcTTGAGGCAGCTGCGCGACTGCTGGCTCAGGCAATGAATGAGTTATAATAGCAGCATTTACTAACAGGGATTTATTGAGAGTATGAGCCGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAg                                                                                    <  1:974288/140‑1 (MQ=255)
                                               ggCAGCTGCGCGACTGCTGGCTCAGGCAATGAATGAGTTATAATAGCAGCATTTACTAACAGGGATTTATTGAGAGTATGAGCTGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAGCAAAAg                                                                              >  1:1018387/1‑140 (MQ=255)
                                                  aGCTGCGCGACTGCTGGCTCAGGCAATGAATGAGTTATAATAGCAGCATTTACTAACAGGGATTTATTGAGAGTATGAGCTGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAGCAAAAGTga                                                                           <  1:488344/140‑1 (MQ=255)
                                                    cTGCGCGACTGCTGGCTCAGGCAATGAATGAGTTATAATAGCAGCATTTACTAACAGGGATTTATTGAGAGTATGAGCTGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAGCAAAAGTgaga                                                                         <  2:1010731/140‑1 (MQ=255)
                                                          gACTGCTGGCTCAGGCAATGAATGAGTTATAATAGCAGCATTTACTAACAGGGATTTATTGAGAGTATGAGCTGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAGCAAAAGTGAGAGCCTTc                                                                   >  1:699029/1‑140 (MQ=255)
                                                              gctgGCTCAGGCAATGAATGAGTTATAATAGCAGCATTTACTAACAGGGATTTATTGAGAGTATGAGCTGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAGCAAAAGTGAGAGCCTTCACaa                                                               >  2:94031/1‑140 (MQ=255)
                                                               ctgGCTCAGGCAATGAATGAGTTATAATAGCAGCATTTACTAACAGGGATTTATTGAGAGTATGAGCTGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAGCAAAAGTGAGAGCCTTCACaaa                                                              >  2:865186/1‑140 (MQ=255)
                                                                     cAGGCAATGAATGAGTTATAATAGCAGCATTTACTAACAGGGATTTATTGAGAGTATGAGCTGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAGCAAAAGTGAGAGCCTTCACAAAATAATg                                                        <  2:1018387/140‑1 (MQ=255)
                                                                     cAGGCAATGAATGAGTTATAATAGCAGCATTTACTAACAGGGATTTATTGAGAGTATGAGCTGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAGCAAAAGTGAGAGCCTTCACAAAATAATg                                                        <  2:1041242/140‑1 (MQ=255)
                                                                       ggCAATGAATGAGTTATAATAGCAGCATTTACTAACAGGGATTTATTGAGAGTATGAGCTGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAGCAAAAGTGAGAGCCTTCACAAAATAATGCt                                                      <  2:17168/140‑1 (MQ=255)
                                                                            tgaatgaGTTATAATAGCAGCATTTACTAACAGGGATTTATTGAGAGTATGAGCTGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAGCAAAAGTGAGAGCCTTCACAAAATAATGCTTAGta                                                 >  1:464573/1‑140 (MQ=255)
                                                                                  aGTTATAATAGCAGCATTTACTAACAGGGATTTATTGAGAGTATGAGCTGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAGCAAAAGTGAGAGCCTTCACAAAATAATGCTTAGTAATAAAg                                           >  2:522474/1‑140 (MQ=255)
                                                                                    ttATAATAGCAGCATTTACTAACAGGGATTTATTGAGAGTATGAGCTGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAGCAAAAGTGAGAGCCTTCACAAAATAATGCTTAGTAATAAAGtt                                         >  2:525903/1‑140 (MQ=255)
                                                                                        aataGCAGCATTTACTAACAGGGATTTATTGAGAGTATGAGCTGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAGCAAAAGTGAGAGCCTTCACAAAATAATGCTTAGTAATAAAGTTACtt                                     >  2:776825/1‑140 (MQ=255)
                                                                                             cagcaTTTACTAACAGGGATTTATTGAGAGTATGAGCTGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAGCAAAAGTGAGAGCCTTCACAAAATAATGCTTAGtaa                                                <  1:35403/124‑1 (MQ=255)
                                                                                             cagcaTTTACTAACAGGGATTTATTGAGAGTATGAGCTGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAGCAAAAGTGAGAGCCTTCACAAAATAATGCTTAGtaa                                                >  2:35403/1‑124 (MQ=255)
                                                                                             cagcaTTTACTAACAGGGATTTATTGAGAGTATGAGCTGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAGCAAAAGTGAGAGCCTTCACAAAATAATGCTTAGTAATAAAGTTACTTTGAAt                                >  2:956693/1‑140 (MQ=255)
                                                                                             cagcaTTTACTAACAGGGATTTATTGAGAGTATGAGCTGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAGCAAAAGTGAGAGCCTTCACAAAATAATGCTTAGTAATAAAGTTACTTTGAAt                                >  2:289220/1‑140 (MQ=255)
                                                                                             cagcaTTTACTAACAGGGATTTATTGAGAGTATGAGCTGCCGTGATACACCTTAAAATCTCAACCAAGCAAAGTTTCGGAGCCGCGAGCAAAAGTGAGAGCCTTCACAAAATAATGCTTAGTAATAAAGTTACTTTGAAt                                >  2:1066162/1‑140 (MQ=255)
                                                                                              agcaTTTACTAACAGGGATTTATTGAGAGTATGAGCTGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAGCAAAAGTGAGAGCCTTCACAAAATAATGCTTAGTAATAAAGTTACTTTGAAtt                               >  1:933333/1‑140 (MQ=255)
                                                                                              agcaTTTACTAACAGGGATTTATTGAGAGTATGAGCTGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAGCAAAAGTGAGAGCCTTCACAAAATAATGCTTAGTAATAAAGTTACTTTGAAtt                               >  1:26776/1‑140 (MQ=255)
                                                                                                 aTTTACTAACAGGGATTTATTGAGAGTATGAGCTGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAGCAAAAGTGAGAGCCTTCACAAAATAATGCTTAGTAATAAAGTTGCt                                      <  1:561970/130‑1 (MQ=255)
                                                                                                 aTTTACTAACAGGGATTTATTGAGAGTATGAGCTGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAGCAAAAGTGAGAGCCTTCACAAAATAATGCTTAGTAATAAAGTTACt                                      >  2:561970/1‑130 (MQ=255)
                                                                                                 aTTTACTAACAGGGATTTATTGAGAGTATGAGCTGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAGCAAAAGTGAGAGCCTTCACAAAATAATGCTTAGTAATAAAGTTACTTTGAATTCag                            >  2:634888/1‑140 (MQ=255)
                                                                                                    tACTAACAGGGATTTATTGAGAGTATGAGCTGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAGCAAAAGTGAGAGCCTTCACAAAATAATGCTTAGTAATAAAGTTACTTTGAATTCAGAGc                         >  2:274900/1‑140 (MQ=255)
                                                                                                    tACTAACAGGGATTTATTGAGAGTATGAGCTGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAGCAAAAGTGAGAGCCTTCACAAAATAATGCTTAGTAATAAAGTTACTTTGAATTCAGAGc                         <  2:26776/140‑1 (MQ=255)
                                                                                                          cAGGGATTTATTGAGAGTATGAGCTGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAGCAAAAGTGAGAGCCTTCACAAAATAATGCTTAGTAATAAAGTTACTTTGAATTCAGAGCCCCGAt                   <  1:94031/140‑1 (MQ=255)
                                                                                                          cAGGGATTTATTGAGAGTATGAGCTGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAGCAAAAGTGAGAGCCTTCACAAAATAATGCTTAGTAATAAAGTTACTTTGAATTCAGAGCCCCGAt                   <  1:776825/140‑1 (MQ=255)
                                                                                                            gggATTTATTGAGAGTATGAGCTGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAGCAAAAGTGAGAGCCTTCACAAAATAATGCTTAGTAATAAAGTTACTTTGAATTCAGAGCCCCGATTa                 <  2:189190/140‑1 (MQ=255)
                                                                                                             ggATTTATTGAGAGTATGAGCTGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAGCAAAAGTGAGAGCCTTCACAAAATAATGCTTAGTAATAAAGTTACTTTGAATTCAGAGCCCCGATTaa                >  2:728372/1‑140 (MQ=255)
                                                                                                              gATTTATTGAGAGTATGAGCTGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAGCAAAAGTGAGAGCCTTCACAAAATAATGCTTAGTAATAAAGTTACTTTGAATTCAGAGCCCCGATTAAt               <  1:269505/140‑1 (MQ=255)
                                                                                                              gATTTATTGAGAGTATGAGCTGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAGCAAAAGTGAGAGCCTTCACAAAATAATGCTTAGTAATAAAGTTACTTTGAATTCAGAGCCCCGATTAAt               <  1:634888/140‑1 (MQ=255)
                                                                                                              gATTTATTGAGAGTATGAGCTGCCGTGATACACCTTAAAATCTCAACCAAGCAAAGTTTCGGAGCCGCGAGCAAAAGTGAGAGCCTTCACAAAATAATGCTTAGTAATAAAGTTACTTTGAATTCAGAGCCCCGATTAAt               <  1:1066162/140‑1 (MQ=255)
                                                                                                               aTTTATTGAGAGTATGAGCTGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAGCAAAAGTGAGAGCCTTCACAAAATAATGCTTAGTAATAAAGTTACTTTGAATTCAGAGCCCCGATTAAtg              <  1:956693/140‑1 (MQ=255)
                                                                                                                   aTTGAGAGTATGAGCTGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAGCAAAAGTGAGAGCCTTCACAAAATAATGCTTAGTAATAAAGTTACTTTGAATTCAGAGCCCCGATTAATGTGaa          >  2:124958/1‑140 (MQ=255)
                                                                                                                           tATGAGCTGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAGCAAAAGTGAGAGCCTTCACAAAATAATGCTTAGTAATAAAGTTACTTTGAATTCAGAGCCCCGATTAATGTGAACATGATCa  >  1:324546/1‑140 (MQ=255)
                                                                                                                                  |                                                                                                                                    
AGAGTGATGATATATATCTGAAGATTTTTTCAATCCTCTGCGCTTGAGGCAGCTGCGCGACTGCTGGCTCAGGCAATGAATGAGTTATAATAGCAGCATTTACTAACAGGGATTTATTGAGAGTATGAGCCGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAGCAAAAGTGAGAGCCTTCACAAAATAATGCTTAGTAATAAAGTTACTTTGAATTCAGAGCCCCGATTAATGTGAACATGATCA  >  NC_000913/269029‑269291

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑