Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,458,048 T→C S558P (TCA→CCA)  gspD → Type II secretion system protein GspD

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,458,0480TC98.2% 188.5 / ‑4.3 54S558P (TCA→CCA) gspDType II secretion system protein GspD
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base C (25/28);  total (25/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.72e-01

AGCGTTGACTCTTCCTCTAACTCGACGCTCGGCCCGACGTTTAATACCCGTACTATTCAAAACGCCGTGCTGGTCAAAACCGGTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGTCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGCTATACCTCCACCGAGCGCGCTAAACGCAACCTGATGGTATTTATCCGTCCGACGATTATCCGTGACGATGATGTTTATCGCTCAC  >  NC_000913/3457913‑3458183
                                                                                                                                       |                                                                                                                                       
aGCGTTGACTCTTCCTCTAACTCGACGCTCGGCCCGACGTTTAATACCCGTACTATTCAAAACGCCGTGCTGGTCAAAACCGGTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCaaa                                                                                                                                     <  2:781970/140‑1 (MQ=255)
 gCGTTGACTCTTCCTCTAACTCGACGCTCGGCCCGACGTTTAATACCCGTACTATTCAAAACGCCGTGCTGGTCAAAACCGGTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAg                                                                                                                                    <  1:725167/140‑1 (MQ=255)
  cGTTGACTCTTCCTCTAACTCGACGCTCGGCCCGACGTTTAATACCCGTACTATTCAAAACGCCGTGCTGGTCAAAACCGGTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAgg                                                                                                                                   <  1:955864/140‑1 (MQ=255)
     tGACTCTTCCTCTAACTCGACGCTCGGCCCGACGTTTAATACCCGTACTATTCAAAACGCCGTGCTGGTCAAAACCGGTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTc                                                                                                                                >  2:969915/1‑140 (MQ=255)
     tGACTCTTCCTCTAACTCGACGCTCGGCCCGACGTTTAATACCCGTACTATTCAAAACGCCGTGCTGGTCAAAACCGGTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTc                                                                                                                                >  2:862703/1‑140 (MQ=255)
       aCTCTTCCTCTAACTCGACGCTCGGCCCGACGTTTAATACCCGTACTATTCAAAACGCCGTGCTGGTCAAAACCGGTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCct                                                                                                                              >  1:505424/1‑140 (MQ=255)
                   aCTCGACGCTCGGCCCGACGTTTAATACCCGTACTATTCAAAACGCCGTGCTGGTCAAAACCGGTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGat                                                                                                                  >  1:686459/1‑140 (MQ=255)
                   aCTCGACGCTCGGCCCGACGTTTAATACCCGTACTATTCAAAACGCCGTGCTGGTCAAAACCGGTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGat                                                                                                                  <  1:969915/140‑1 (MQ=255)
                       gACGCTCGGCCCGACGTTTAATACCCGTACTATTCAAAACGCCGTGCTGGTCAAAACCGGTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGATATTc                                                                                                              >  2:524567/1‑140 (MQ=255)
                        aCGCTCGGCCCGACGTTTAATACCCGTACTATTCAAAACGCCGTGCTGGTCAAAACCGGTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGATATTcc                                                                                                             >  2:827507/1‑140 (MQ=255)
                           cTCGGCCCGACGTTTAATACCCGTACTATTCAAAACGCCGTGCTGGTCAAAACCGGTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGat                                                                                                                  >  2:889419/1‑132 (MQ=255)
                           cTCGGCCCGACGTTTAATACCCGTACTATTCAAAACGCCGTGCTGGTCAAAACCGGTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGat                                                                                                                  <  1:889419/132‑1 (MQ=255)
                            tCGGCCCGACGTTTAATACCCGTACTATTCAAAACGCCGTGCTGGTCAAAACCGGTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGATATTCCTTTa                                                                                                         >  1:57359/1‑140 (MQ=255)
                             cGGCCCGACGTTTAATACCCGTACTATTCAAAACGCCGTGCTGGTCAAAACCGGTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGa                                                                                                                   <  2:782551/129‑1 (MQ=255)
                             cGGCCCGACGTTTAATACCCGTACTATTCAAAACGCCGTGCTGGTCAAAACCGGTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGa                                                                                                                   >  1:782551/1‑129 (MQ=255)
                             cGGCCCGACGTTTAATACCCGTACTATTCAAAACGCCGTGCTGGTCAAAACCGGTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAg                                                                                                        >  2:811670/1‑140 (MQ=255)
                             cGGCCCGACGTTTAATACCCGTACTATTCAAAACGCCGTGCTGGTCAAAACCGGTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAg                                                                                                        <  1:811670/140‑1 (MQ=255)
                               gCCCGACGTTTAATACCCGTACTATTCAAAACGCCGTGCTGGTCAAAACCGGTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTg                                                                                                      >  2:344073/1‑140 (MQ=255)
                                 ccGACGTTTAATACCCGTACTATTCAAAACGCCGTGCTGGTAAAAACCGGTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGTCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTggg                                                                                                    <  1:721215/140‑1 (MQ=255)
                                   gACGTTTAATACCCGTACTATTCAAAACGCCGTGCTGGTCAAAACCGGTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGc                                                                                                  >  1:568808/1‑140 (MQ=255)
                                        ttAATACCCGTACTATTCAAAACGCCGTGCTGGTCAAAACCGGTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAActc                                                                                             <  1:71026/140‑1 (MQ=255)
                                         tAATACCCGTACTATTCAAAACGCCGTGCTGGTCAAAACCGGTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAActct                                                                                            <  1:862703/140‑1 (MQ=255)
                                          aaTACCCGTACTATTCAAAACGCCGTGCTGGTCAAAACCGGTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCtt                                                                                           <  2:699989/140‑1 (MQ=255)
                                            tACCCGTACTATTCAAAACGCCGTGCTGGTCAAAACCGGTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTcc                                                                                         <  2:568808/140‑1 (MQ=255)
                                              cccGTACTATTCAAAACGCCGTGCTGGTCAAAACCGGTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGc                                                                                       <  2:57359/140‑1 (MQ=255)
                                               ccGTACTATTCAAAACGCCGTGCTGGTCAAAACCGGTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAActct                                                                                            <  1:755370/134‑1 (MQ=255)
                                               ccGTACTATTCAAAACGCCGTGCTGGTCAAAACCGGTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAActct                                                                                            >  2:755370/1‑134 (MQ=255)
                                                cGTACTATTCAAAACGCCGTGCTGGTCAAAACCGGTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGCta                                                                                     <  2:152945/140‑1 (MQ=255)
                                                       ttCAAAACGCCGTGCTGGTCAAAACCGGTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGCTATACCTcc                                                                              >  2:689498/1‑140 (MQ=255)
                                                         cAAAACGCCGTGCTGGTCAAAACCGGTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGCTATACCTCCAc                                                                            >  1:487800/1‑140 (MQ=255)
                                                           aaaCGCCGTGCTGGTCAAAACCGGTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGCTATACCTCCACCg                                                                          >  1:481841/1‑140 (MQ=255)
                                                              cGCCGTGCTGGTCAAAACCGGTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGCTATACCTCCACCGAgc                                                                       <  2:487800/140‑1 (MQ=255)
                                                                 cGTGCTGGTCAAAACCGGTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGCTATACCTCCACCGAgcgcg                                                                    >  1:777058/1‑140 (MQ=255)
                                                                 cGTGCTGGTCAAAACCGGTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGCTATACCTCCACCGAgcgcg                                                                    >  2:496466/1‑140 (MQ=255)
                                                                        gTCAAAACCGGTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGCTATACCTCCACCGAGCGCGCTAAACg                                                             <  2:686459/140‑1 (MQ=255)
                                                                        gTCAAAACCGGTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGCTATACCTCCACCGAGCGCGCTAAACg                                                             <  1:109496/140‑1 (MQ=255)
                                                                        gTCAAAACCGGTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGCTATACCTCCACCGAGCGCGCTAAACg                                                             <  1:524567/140‑1 (MQ=255)
                                                                                cGGTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGCTATACCTCCACCGAGCGCGCTAAACGCAACCTGa                                                     <  2:481841/140‑1 (MQ=255)
                                                                                cGGTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGCTATACCTCCACCGAGCGCGCTAAACGCAACCTGa                                                     <  1:653696/140‑1 (MQ=255)
                                                                                 ggTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGCTATACCTCCACCGAGCGCGCTAAACGCAACCTGAt                                                    <  1:689498/140‑1 (MQ=255)
                                                                                  gTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGCTATACCTCCACCGAGCGCGCTAAACGCAACCTGATg                                                   >  1:117075/1‑140 (MQ=255)
                                                                                            ggtCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGCTATACCTCCACCGAGCGCGCTAAACGCAAc                                                         >  2:533924/1‑124 (MQ=255)
                                                                                            ggtCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGCTATACCTCCACCGAGCGCGCTAAACGCAAc                                                         <  1:533924/124‑1 (MQ=255)
                                                                                               ccTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGCTATACCTCCACCGAGCGCGCTAAACGCAACCTGATGGTATTTAtccgtc                                      <  1:496466/140‑1 (MQ=255)
                                                                                                 tGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGCTATACCTCCACCGAGCGCGCTAAACGCAACCTGATGGTATTTAtccgtccg                                    <  2:505424/140‑1 (MQ=255)
                                                                                                 tGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGCTATACCTCCACCGAGCGCGCTAAACGCAACCTGATGGTATTTAtccgtccg                                    <  2:651971/140‑1 (MQ=255)
                                                                                                   ggCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGCTATACCTCCACCGAGCGCGCTAAACGCAACCTGATGGTATTTATCCGTCcgac                                  <  1:827507/140‑1 (MQ=255)
                                                                                                        aTTGCTGGATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGCTATACCTCCACCGAGCGCGCTAAACGCAACCTGATGGTATTTATCCGTCCGACGATTa                             >  1:418022/1‑140 (MQ=255)
                                                                                                              ggATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGCTATACCTCCACCGAGCGCGCTAAACGCAACCTGATGGTATTTATCCGTCcgac                                  >  1:411771/1‑129 (MQ=255)
                                                                                                              ggATGATTTTTCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGCTATACCTCCACCGAGCGCGCTAAACGCAACCTGATGGTATTTATCCGTCcgac                                  <  2:411771/129‑1 (MQ=255)
                                                                                                                    tttttCTAAAGAGCAAGTGCCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGCTATACCTCCACCGAGCGCGCTAAACGCAACCTGATGGTATTTATCCGTCCGACGATTATCCGTGACgatg                 >  1:126241/1‑140 (MQ=255)
                                                                                                                                 cAAGTGCCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGCTATACCTCCACCGAGCGCGCTAAACGCAACCTGATGGTATTTATCCGTCCGACGATTATCCGTGACGATGATGTTTATCGCTc    >  1:539528/1‑140 (MQ=255)
                                                                                                                                 cAAGTGCCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGCTATACCTCCACCGAGCGCGCTAAACGCAACCTGATGGTATTTATCCGTCCGACGATTATCCGTGACGATGATGTTTATCGCTc    >  2:306029/1‑140 (MQ=255)
                                                                                                                                   aGTGCCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGCTATACCTCCACCGAGCGCGCTAAACGCAACCTGATGGTATTTATCCGTCCGACGATTATCCGTGACGATGATGTTTATCGCTCAc  <  2:126241/140‑1 (MQ=255)
                                                                                                                                       |                                                                                                                                       
AGCGTTGACTCTTCCTCTAACTCGACGCTCGGCCCGACGTTTAATACCCGTACTATTCAAAACGCCGTGCTGGTCAAAACCGGTGAAACGGTGGTCCTGGGCGGATTGCTGGATGATTTTTCTAAAGAGCAAGTGTCAAAGGTTCCTCTGCTTGGCGATATTCCTTTAGTGGGGCAACTCTTCCGCTATACCTCCACCGAGCGCGCTAAACGCAACCTGATGGTATTTATCCGTCCGACGATTATCCGTGACGATGATGTTTATCGCTCAC  >  NC_000913/3457913‑3458183

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑