Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 4,142,512 C→A 5.6% 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 5.6% 260.1 / 4.9 72intergenic (‑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 (34/34);  new base A (2/2);  total (36/36)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.85e-01

TCCGGTTTATCGCAAGTTATGAGGCGGATCGCATTTTTGTACTGATATTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTCCCTTCG  >  NC_000913/4142369‑4142605
                                                                                                                                               |                                                                                             
tCCGGTTTATCGCAAGTTATGAGGCGGATCGCATTTTTGTACTGATATTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAg                                                                                            <  4:163173/147‑1 (MQ=255)
tCCGGTTTATCGCAAGTTATGAGGCGGATCGCATTTTTGTACTGATATTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAg                                                                                            >  3:163173/1‑147 (MQ=255)
                   tGAGGCGGATCGCATTTTTGTACTGATATTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTGCGAAAGcccat                                                                                       <  2:859518/133‑3 (MQ=255)
                   tGAGGCGGATCGCATTTTTGTACTGATATTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTGCGAAAGcccat                                                                                       >  1:859518/1‑131 (MQ=255)
                             cGCATTTTTGTACTGATATTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGc                                                              >  3:857627/1‑148 (MQ=255)
                               cATTTTTGTACTGATATTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAg                                                                     >  2:267969/1‑139 (MQ=255)
                               cATTTTTGTACTGATATTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAg                                                                     <  1:267969/139‑1 (MQ=255)
                                        aCTGATATTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTatgaa                                                                         <  3:360268/126‑1 (MQ=255)
                                        aCTGATATTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTatgaa                                                                         >  4:360268/1‑126 (MQ=255)
                                             tatTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTgg                                                                 <  1:5266/129‑1 (MQ=255)
                                             tatTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTgg                                                                 >  2:5266/1‑129 (MQ=255)
                                             tatTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATAc                                              <  4:857627/148‑1 (MQ=255)
                                                 aCAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGt                                          >  3:628810/1‑148 (MQ=255)
                                                             tAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATc                                                         >  3:28369/1‑121 (MQ=255)
                                                             tAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATc                                                         <  4:28369/121‑1 (MQ=255)
                                                                    ccTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCtt                                                                              >  1:540043/1‑93 (MQ=255)
                                                                    ccTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCtt                                                                              <  2:540043/93‑1 (MQ=255)
                                                                      tttttATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATa                                               <  4:1111567/122‑1 (MQ=255)
                                                                      tttttATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATa                                               >  3:1111567/1‑122 (MQ=255)
                                                                       ttttATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGagcagc                                                                                >  2:875512/1‑88 (MQ=255)
                                                                       ttttATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGagcagc                                                                                <  1:875512/88‑1 (MQ=255)
                                                                             ccACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATg                              <  1:157330/132‑1 (MQ=255)
                                                                             ccACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATg                              >  2:157330/1‑132 (MQ=255)
                                                                             ccACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTGCGAAAGccc                                                                                         >  2:970403/1‑73 (MQ=255)
                                                                             ccACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTGGCGAAAGccc                                                                                         <  1:970403/73‑1 (MQ=255)
                                                                               aCTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGAt                                                          >  3:197449/1‑102 (MQ=255)
                                                                               aCTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGAt                                                          <  4:197449/102‑1 (MQ=255)
                                                                                cTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTatga                                                                          >  4:691857/1‑85 (MQ=255)
                                                                                cTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTatga                                                                          <  3:691857/85‑1 (MQ=255)
                                                                                 tGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCGGCATTTAATGACGGGCGTTTCACACATGAt          <  4:628810/148‑1 (MQ=255)
                                                                                  gTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGtt                     >  2:245192/1‑136 (MQ=255)
                                                                                  gTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGtt                     <  1:245192/136‑1 (MQ=255)
                                                                                    ctGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCg                                                                                        >  4:878705/2‑67 (MQ=255)
                                                                                    ctGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCg                                                                                        <  3:878705/66‑1 (MQ=255)
                                                                                         ccGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGt                                                                >  4:553878/1‑86 (MQ=255)
                                                                                         ccGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGt                                                                <  3:553878/86‑1 (MQ=255)
                                                                                           gCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGt                                          <  4:614320/106‑1 (MQ=255)
                                                                                           gCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGt                                          >  3:614320/1‑106 (MQ=255)
                                                                                                   ttGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTatgaatg                                                                       >  4:942387/1‑69 (MQ=255)
                                                                                                   ttGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTatgaatg                                                                       <  3:942387/69‑1 (MQ=255)
                                                                                                         aTTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGt                                                                <  2:795416/70‑1 (MQ=255)
                                                                                                         aTTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGt                                                                >  1:795416/1‑70 (MQ=255)
                                                                                                         aTTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTa                                 <  2:753820/101‑1 (MQ=255)
                                                                                                         aTTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTa                                 >  1:753820/1‑101 (MQ=255)
                                                                                                         aTTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGAc                            <  1:543815/106‑1 (MQ=255)
                                                                                                         aTTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGAc                            >  2:543815/1‑106 (MQ=255)
                                                                                                         aTTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCg                       <  2:368801/111‑1 (MQ=255)
                                                                                                         aTTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCg                       >  1:368801/1‑111 (MQ=255)
                                                                                                           tGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGt                      >  1:1084351/1‑110 (MQ=255)
                                                                                                           tGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGt                      <  2:1084351/110‑1 (MQ=255)
                                                                                                              ttCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACg                           <  1:484365/102‑1 (MQ=255)
                                                                                                              ttCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACg                           >  2:484365/1‑102 (MQ=255)
                                                                                                               tcctccATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTCCCTTCg  <  3:1045035/126‑1 (MQ=255)
                                                                                                               tcctccATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTCCCTTCg  >  4:1045035/1‑126 (MQ=255)
                                                                                                                       cAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTcacac               <  2:9489/105‑1 (MQ=255)
                                                                                                                       cAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTcacac               >  1:9489/1‑105 (MQ=255)
                                                                                                                              atGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATa                                               <  2:960040/66‑1 (MQ=255)
                                                                                                                              atGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATa                                               >  1:960040/1‑66 (MQ=255)
                                                                                                                                  aCATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACg                           <  1:61496/82‑1 (MQ=255)
                                                                                                                                  aCATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACg                           >  2:61496/1‑82 (MQ=255)
                                                                                                                                       ggCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTCGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACg                           <  1:383687/77‑1 (MQ=255)
                                                                                                                                       ggCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTCGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACg                           >  2:383687/1‑77 (MQ=255)
                                                                                                                                        tcTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTCCCTTCg  <  4:763345/100‑1 (MQ=255)
                                                                                                                                        gCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTCCCTTCg  >  3:763345/1‑101 (MQ=255)
                                                                                                                                         cTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTc                                         >  1:242891/1‑61 (MQ=255)
                                                                                                                                         cTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTc                                         <  2:242891/61‑1 (MQ=255)
                                                                                                                                         cTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTCCCt     >  2:827560/1‑97 (MQ=255)
                                                                                                                                         cTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTCCCt     <  1:827560/97‑1 (MQ=255)
                                                                                                                                           ttCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGt                                          >  1:187246/1‑58 (MQ=255)
                                                                                                                                           ttCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGt                                          <  2:187246/58‑1 (MQ=255)
                                                                                                                                           ttCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTccc      <  4:32465/94‑1 (MQ=255)
                                                                                                                                           ttCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTccc      >  3:32465/1‑94 (MQ=255)
                                                                                                                                               cAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTccc      <  4:475377/90‑1 (MQ=255)
                                                                                                                                               cAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTccc      >  3:475377/1‑90 (MQ=255)
                                                                                                                                               |                                                                                             
TCCGGTTTATCGCAAGTTATGAGGCGGATCGCATTTTTGTACTGATATTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTCCCTTCG  >  NC_000913/4142369‑4142605

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: