Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 4,142,512 C→A 8.8% intergenic (‑291/‑18) frwA ← / → frwC putative PTS enzyme: Hpr, enzyme I and II components/putative enzyme IIC component of PTS

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,142,5120CA 8.8% 185.3 / 8.6 57intergenic (‑291/‑18)frwA/frwCputative PTS enzyme: Hpr, enzyme I and II components/putative enzyme IIC component of PTS
Reads supporting (aligned to +/- strand):  ref base C (22/30);  new base A (3/2);  total (25/32)
Fisher's exact test for biased strand distribution p-value = 6.45e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.68e-01

CGGTTTATCGCAAGTTATGAGGCGGATCGCATTTTTGTACTGATATTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTCCCTTCGTGGTATCGGGCGGTATTTTGCTGGCGGTTTCCGTCATGTTGTATGGCAAAGGCGC  >  NC_000913/4142371‑4142660
                                                                                                                                             |                                                                                                                                                    
cGGTTTAGCGCAAGTTATGAGGCAGATCGCATTTTTGTACTGATATTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCg                                                                                                                                               >  4:441787/1‑149 (MQ=255)
   tttATCGCAAGTTATGAGGCGGATCGCATTTTTGTACTGATATTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGa                                                                                                                                            <  3:37924/149‑1 (MQ=255)
   tttATCGCAAGTTATGAGGCGGATCGCATTTTTGTACTGATATTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGa                                                                                                                                            <  3:91707/149‑1 (MQ=255)
       tCGCAAGTTATGAGGCGGATCGCATTTTTGTACTGATATTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGagcag                                                                                                                                        <  1:216317/149‑1 (MQ=255)
         gCAAGTTATGAGGCGGATCGCATTTTTGTACTGATATTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCt                                                                                                                                      <  3:306174/149‑1 (MQ=255)
              ttATGAGGCGGATCGCATTTTTGTACTGATATTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTatga                                                                                                                                 <  1:446433/149‑1 (MQ=255)
                aTGAGGCGGATCGCATTTTTGTACTGATATTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTatgaat                                                                                                                               <  2:102746/149‑1 (MQ=255)
                  gAGGCGGATCGCATTTTTGTACTGATATTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTatgaatga                                                                                                                             <  1:120413/149‑1 (MQ=255)
                   aGGCGGATCGCATTTTTGTACTGATATTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAg                                                                                                                            <  3:188497/149‑1 (MQ=255)
                   aGGCGGATCGCATTTTTGTACTGATATTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAg                                                                                                                            <  3:271665/149‑1 (MQ=255)
                        gATCGCATTTTTGTACTGATATTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGt                                                                                                                       >  1:361593/1‑149 (MQ=255)
                            gCATTTTTGTACTGATATTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAg                                                                                                                   >  2:150773/1‑149 (MQ=255)
                                     tACTGATATTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGaaa                                                                                                          >  4:240954/1‑149 (MQ=255)
                                       cTGATATTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGa                                                                                                                                            <  3:167983/113‑1 (MQ=255)
                                       cTGATATTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGa                                                                                                                                            >  4:167983/1‑113 (MQ=255)
                                            atTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATAccc                                                                                                   <  4:401109/149‑1 (MQ=255)
                                            atTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGACCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATAccc                                                                                                   >  2:365514/1‑149 (MQ=255)
                                                        cAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTaa                                                                                       <  3:441787/149‑1 (MQ=255)
                                                        cAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTaa                                                                                       <  3:240954/149‑1 (MQ=255)
                                                                   cTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGtt                                                                            <  3:220736/149‑1 (MQ=255)
                                                                    tttttATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGttt                                                                           >  2:60763/1‑149 (MQ=255)
                                                                      tttATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATTCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTca                                                                         >  4:383286/1‑149 (MQ=255)
                                                                          tCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGa                                                                                                            <  4:28687/110‑1 (MQ=255)
                                                                          tCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGa                                                                                                            >  3:28687/1‑110 (MQ=255)
                                                                           ccACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACAt                                                                    <  4:299817/149‑1 (MQ=255)
                                                                            cACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATg                                                                   >  2:319350/1‑149 (MQ=255)
                                                                             aCTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGa                                                                  >  3:369203/1‑149 (MQ=255)
                                                                              cTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGAt                                                                 >  3:459188/1‑149 (MQ=255)
                                                                                 tttGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCAttt                                                                                         >  4:80698/1‑122 (MQ=255)
                                                                                 tttGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCAttt                                                                                         <  3:80698/122‑1 (MQ=255)
                                                                                 tttGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTcc                                                              >  1:190683/1‑149 (MQ=255)
                                                                                  ttGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTccc                                                             <  2:361593/149‑1 (MQ=255)
                                                                                      tCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTca                                                                         <  3:101889/133‑1 (MQ=255)
                                                                                      tCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTca                                                                         >  4:101889/1‑133 (MQ=255)
                                                                                      tCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTCCCTTCg                                                         <  1:319350/149‑1 (MQ=255)
                                                                                            tGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTCCCTTCGTGGTAt                                                   <  1:60763/149‑1 (MQ=255)
                                                                                                aTTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTCCCTTCGTGGTATCggg                                               <  1:54670/149‑1 (MQ=255)
                                                                                                     cTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTCCCTTCGTGGTATCGGGCGGTa                                          >  2:222600/1‑149 (MQ=255)
                                                                                                           tttCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTCCCTTCGTGGTATCGGGCGGTATTTTGc                                    <  1:222600/149‑1 (MQ=255)
                                                                                                                tccATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTCCCTTCGTGGTATCGGGCGGTATTTTGCTGGCg                               >  1:78110/1‑149 (MQ=255)
                                                                                                                  cATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTCCCTTCGTGGTATCGGGCGGTATTTTGCTGGCGGt                             >  3:401099/1‑149 (MQ=255)
                                                                                                                   aTCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTCCCTTCGTGGTATCGGGCGGTATTTTGCTGGCGGtt                            <  3:383286/149‑1 (MQ=255)
                                                                                                                    tCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTCCCTTCGTGGTATCGGGCGGTATTTTGCTGGCGGttt                           >  2:284170/1‑149 (MQ=255)
                                                                                                                         aaTATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTCCCTTCGTGGTATCGGGCGGTATTTTGCTGGCGGTTTCCGTc                      <  1:150773/149‑1 (MQ=255)
                                                                                                                              ggACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTCCCTTCGTGGTATCGGGCGGTATTTTGCTGGCGGTTTCCGTCAtgtt                 <  1:296229/149‑1 (MQ=255)
                                                                                                                                tcccgggCTTGCGAAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGa                                                                  >  4:169094/5‑98 (MQ=255)
                                                                                                                                tcccgggCTTGCGAAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGa                                                                  <  3:169094/94‑1 (MQ=255)
                                                                                                                                tcccgggCTTGCGAAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTCCCTTCGTGGTATCGGGCGGTATTTTGCTGGCGGTTTCCGTCAtgttgt               >  3:145863/5‑149 (MQ=255)
                                                                                                                                  aTGGGCTTTCGCAAGCCCGGGAGCAGCGTATGAATGAGTTGGTGCGAAGCCTGAAAAATACCCGTCAGCATTTAATGACGGTCGTTTCACACATGATTCCCTTCGTGGTATCGGGCGGTATTTTGCTGGCGGTTTCCGTCATGTTGTAt             <  4:401099/149‑1 (MQ=255)
                                                                                                                                   cgggCTTGCGAAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGAtt                                                                >  2:17581/2‑97 (MQ=255)
                                                                                                                                   cgggCTTGCGAAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGAtt                                                                <  1:17581/96‑1 (MQ=255)
                                                                                                                                      gCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTCCCTTCGTGGTATCGGGCGGTATTTTGCTGGCGGTTTCCGTCATGTTGTATGGCa         >  2:423217/1‑149 (MQ=255)
                                                                                                                                       cTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTCCCTTCGTGGTATCGGGCGGTATTTTGCTGGCGGTTTCCGTCATGTTGTATGGCaa        <  2:78110/149‑1 (MQ=255)
                                                                                                                                        tttCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTCCCTTCGTGGTATCGGGCGGTATTTTGCTGGCGGTTTCCGTCATGTTGTATGGCaaa       >  2:278499/1‑149 (MQ=255)
                                                                                                                                        tttCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTCCCTTCGTGGTATCGGGCGGTATTTTGCTGGCGGTTTCCGTCATGTTGTATGGCaaa       >  1:49500/1‑149 (MQ=255)
                                                                                                                                         ttCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTCCCTTCGTGGTATCGGGCGGTATTTTGCTGGCGGTTTCCGTCATGTTGTATGGCAAAg      <  2:190683/149‑1 (MQ=255)
                                                                                                                                         ttCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTCCCTTCGTGGTATCGGGCGGTATTTTGCTGGCGGTTTCCGTCATGTTGTATGGCAAAg      <  4:369203/149‑1 (MQ=255)
                                                                                                                                             cAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTCCCTTCGTGGTATCGGGCGGTATTTTGCTGGCGGTTTCCGTCATGTTGTATGGCAAAGgcgc  >  4:320812/1‑149 (MQ=255)
                                                                                                                                             |                                                                                                                                                    
CGGTTTATCGCAAGTTATGAGGCGGATCGCATTTTTGTACTGATATTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTCCCTTCGTGGTATCGGGCGGTATTTTGCTGGCGGTTTCCGTCATGTTGTATGGCAAAGGCGC  >  NC_000913/4142371‑4142660

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑