Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 3,480,661 G→A 7.1% L201L (CTG→TTG)  PP_3090 ← OmpA domain‑containing protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029473,480,6610GA 7.1% 157.6 / 3.3 56L201L (CTG→TTG) PP_3090OmpA domain‑containing protein
Reads supporting (aligned to +/- strand):  ref base G (30/22);  new base A (2/2);  total (32/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.84e-01

GCAGCGCGCAGCTTTCCTGAATGCGTTCGCGCAGGCGCTTGGCCACGCGCTCCTGGTCTTCGACCGAGCCATGCAGAATATCGGCGATGCTGACGCTGACGATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGCGCCACTTGCCGGCTTCCTCGGGGCTGTTCATGTAACGCCCGGCAGTGTCCAGCAGTACCGCTTCAGAGCTGAAGAACCAGTCGCAGTTGCGCGTGCCGCCCAGGCCCGCGACCCGCACGCCTTCGCGCTCG  >  NC_002947/3480520‑3480809
                                                                                                                                             |                                                                                                                                                    
gcagcGCGCAGCTTTCCTGAATGCGTTCGCGCAGGCGCTTGGCCACGCGCTCCTGGTCTTCGACCGAGCCATGCAGAATATCGGCGATGCTGACGCTGACGATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTg                                                                                                                                                >  2:539213/1‑148 (MQ=255)
gcagcGCGCAGCTTTCCTGAATGCGTTCGCGCAGGCGCTTGGCCACGCGCTCCTGGTCTTCGACCGAGCCATGCAGAATATCGGCGATGCTGACGCTGACGATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTg                                                                                                                                                <  1:539213/148‑1 (MQ=255)
      cgcAGCTTTCCTGAATGCGTTCGCGCAGGCGCTTGGCCACGCGCTCCTGGTCTTCGACCGAGCCATGCAGAATATCGGCGATGCTGACGCTGACGATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGc                                                                                                                                        >  2:171607/1‑150 (MQ=255)
                 tGAATGCGTTCGCGCAGGCGCTTGGCCACGCGCTCCTGGTCTTCGACCGAGCCATGCAGAATATCGGCGATGCTGACGCTGACGATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGCGCCACTTg                                                                                                                             >  2:1533891/1‑150 (MQ=255)
                  gAATGCGTTCGCGCAGGCGCTTGGCCACGCGCTCCTGTTCTTCGACCGAGCCATGCAGAATATCGGCGATGCTGACGATGACGATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGCGCCACTTGc                                                                                                                            >  1:950153/1‑150 (MQ=255)
                         ttCGCGCAGGCGCTTGGCCACGCGCTCCTGGTCTTCGACCGAGCCATGCAGAATATCGGCGATGCTGACGCTGACGATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGCGCCACTTGCCGGCTTc                                                                                                                     >  1:799997/1‑150 (MQ=255)
                              gcAGGCGCTTGGCCACGCGCTCCTGGTCTTCGACCGAGCCATGCAGAATATCGGCGATGCTGACGCTGACGATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGCGCCACTTGCCGGCTTCCTCgg                                                                                                                <  2:799997/150‑1 (MQ=255)
                                aGGCGCTTGGCCACGCGCTCCTGGTCTTCGACCGAGCCATGCAGAATATCGGCGATGCTGACGCTGACGATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGCGCCACTTGCCGGCTTCCTCgggg                                                                                                              <  2:593529/150‑1 (MQ=255)
                                      ttGGCCACGCGCTCCTGGTCTTCGACCGAGCCATGCAGAATATCGGCGATGCTGACGCTGACGATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGCGCCACTTGCCg                                                                                                                          >  1:895359/1‑132 (MQ=255)
                                      ttGGCCACGCGCTCCTGGTCTTCGACCGAGCCATGCAGAATATCGGCGATGCTGACGCTGACGATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGCGCCACTTGCCg                                                                                                                          <  2:895359/132‑1 (MQ=255)
                                         gCCACGCGCTCCTGGTCTTCGCCCGAGCCATGCAGAATATCGGCGATGCTGACGCTGACGATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGtt                                                                                                                                                 <  1:1606124/106‑1 (MQ=255)
                                         gCCACGCGCTCCTGGTCTTCGACCGAGCCATGCAGAATATCGGCGATGCTGACGCTGACGATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGtt                                                                                                                                                 >  2:1606124/1‑106 (MQ=255)
                                         gCCACGCGCTCCTGGTCTTCGACCGAGCCATGCAGAATATCGGCGATGCTGACGCTGACGATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGCGCCACTTGCCGGCTTCCTCGGGGCTGTTCATg                                                                                                     <  1:171607/150‑1 (MQ=255)
                                         gCCACGCGCTCCTGGTCTTCGACCGAGCCATGCAGAATATCGGCGATGCTGACGCTGACGATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGCGCCACTTGCCGGCTTCCTCGGGGCTGTTCATg                                                                                                     >  1:1355849/1‑150 (MQ=255)
                                          ccACGCGCTCCTGGTCTTCGACCGAGCCATGCAGAATATCGGCGATGCTGACGCTGACGATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGCGCCACTTGCCGGCTTCCTCGGGGCTGTTCATGt                                                                                                    <  2:1355849/150‑1 (MQ=255)
                                           cACGCGCTCCTGGTCTTCGACCGAGCCATGCAGAATATCGGCGATGCTGACGCTGACGATCAAGCCGTTAAGGGGACGGTGCTTGCGGTGCTGGCGCAGCAGTTGGAAGAAGCCGCGCCACTTGCCGGCTTCCTCGGGGCTGTTCATGTa                                                                                                   >  2:1419453/1‑150 (MQ=255)
                                           cACGCGCTCCTGGTCTTCGACCGAGCCATGCAGAATATCGGCGATGCTGACGCTGACGATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGCGCCACTTGCCGGCTTCCTCGGGGCTGTTCATGTa                                                                                                   <  1:1590242/150‑1 (MQ=255)
                                            aCGCGCTCCTGGTCTTCGACCGAGCCATGCAGAATATCGGCGATGCTGACGCTGACGATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGCGCCACTTGCCg                                                                                                                          <  2:1164286/126‑1 (MQ=255)
                                            aCGCGCTCCTGGTCTTCGACCGAGCCATGCAGAATATCGGCGATGCTGACGCTGACGATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGCGCCACTTGCCg                                                                                                                          >  1:1164286/1‑126 (MQ=255)
                                                 cTCCTGGTCTTCGACCGAGCCATGCAGAATATCGGCGATGCTGACGCTGACGATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGCGCCACTTGCCGGCTTCCTCGGGGCTGTTCATGTAACGccc                                                                                             >  1:508895/1‑150 (MQ=255)
                                                       gTCTTCGACCGAGCCATGCAGAATATCGGCGATGCTGACGCTGACGATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCAGCGCCACTTGCCGGCTTCCTCGGGGCTGTTCATGTAACGCCCTGCAgt                                                                                       <  2:61910/150‑1 (MQ=255)
                                                          ttCGACCGAGCCATGCAGAATATCGGCGATGCTGACGCTGACGATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGCGCCACTTGCCGGCTTCCTCGGGGCTGTTCATGTaa                                                                                                  <  2:953957/136‑1 (MQ=255)
                                                          ttCGACCGAGCCATGCAGAATATCGGCGATGCTGACGCTGACGATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGCGCCACTTGCCGGCTTCCTCGGGGCTGTTCATGTaa                                                                                                  >  1:953957/1‑136 (MQ=255)
                                                                 gAGCCATGCAGAATATCGGCGATGCTGACGCTGACGATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGCGCCACTTGCCGGCTTCCTCGGGGCTGTTCATGTAACGCCCGGCAGTGTCCAGCAGt                                                                             >  2:628260/1‑150 (MQ=255)
                                                                  aGCCATGCAGAATATCGGCGATGCTGACGCTGACGATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGGGCAGAGGTTGCAAAAAGCCGCGCCACTTGCCGGCTTCCTCGGGGCTGTTCATGTAACGCCCGGCAGTGTCCAGCAGTa                                                                            >  1:608981/1‑150 (MQ=255)
                                                                      aTGCAGAATATCGGCGATGCTGACGCTGACGATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGCGCCACTTGCCGGCTTCCTCGGGGCTGTTCATGTAACGCCCGGCAGTGTCCAGCAGTACCGc                                                                        >  1:289001/1‑150 (MQ=255)
                                                                       tGCAGAATATCGGCGATGCTGACGCTGACGATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGCGCCACTTGCCGGCTTCCTCGGGGCTGTTCATGTAACGCCCGGCAGTGTCCAGCAGTACCGCt                                                                       >  2:1039464/1‑150 (MQ=255)
                                                                             atatCGGCGATGCTGACGCTGACGATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGCGCCACTTGCCGGCTTCCTCGGGGCTGTTCATGTAACGCCCGGCAGTGTCCAGCAGTACCGCTTCagag                                                                 <  2:211832/150‑1 (MQ=255)
                                                                              tatCGGCGATGCTGACGCTGACGATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGCGCCACTTGCCGGCTTCCTCgggg                                                                                                              <  2:181048/104‑1 (MQ=255)
                                                                              tatCGGCGATGCTGACGCTGACGATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGCGCCACTTGCCGGCTTCCTCgggg                                                                                                              >  1:181048/1‑104 (MQ=255)
                                                                                 cGGCGATGCTGACGCTGACGATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGCGCCACTTGCCGGCTTCCTCGGGGCTGTTCATGTAACGCCCGGCAGTGTCCAGCAGTACCGCTTCAGAGCTga                                                             >  1:399843/1‑150 (MQ=255)
                                                                                  ggCGATGCTGACGCTGACGATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGCGCCACTTGCCGGCTTCCTCGGGGCTGTTCATGTAACGCCCGGCAGTGTCCAGCAGTACCGCTTCAGAGCTgaa                                                            >  1:1237035/1‑150 (MQ=255)
                                                                                      aTGCTGACGCTGACGATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGAGCCACTTGCCGGCTTCCTCGGGGCTTTGCGTGTAACGCCCGGCAGTGTCCAGCAGTACCGCTTCAGAGCTGAAGAAc                                                        <  1:860169/150‑1 (MQ=255)
                                                                                          tgacgctgacgATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGCGCCACTTGCCgg                                                                                                                         >  1:1025162/1‑81 (MQ=255)
                                                                                          tgacgctgacgATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGCGCCACTTGCCgg                                                                                                                         <  2:1025162/81‑1 (MQ=255)
                                                                                          tgacgctgacgATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGC‑AAAAGCCGCGCCACTTGCCGGCTTCCCCGGGGCTGGTCATGGAACGCCCGGCAGGGGCCAGCCGTACCGCCTCAGAGCTGAAGAACCAGTc                                                   >  2:1161814/1‑150 (MQ=255)
                                                                                             cgctgacgATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGCGCCACTTGCCGGCTTCCTCGGGGCTGTTCATGTAACGCCCGGCAGTGTCCAGCAGTACCGCTTCAGAGc                                                                >  2:832413/1‑135 (MQ=255)
                                                                                             cgctgacgATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGCGCCACTTGCCGGCTTCCTCGGGGCTGTTCATGTAACGCCCGGCAGTGTCCAGCAGTACCGCTTCAGAGc                                                                <  1:832413/135‑1 (MQ=255)
                                                                                             cgctgacgATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGCGCCACTTGCCGGCTTCCTCGGGGCTGTTCATGTAACGCCCGGCAGTGTCCAGCAGTACCGCTTCAGAGCTGAAGAACCAGTCGc                                                 <  2:508895/150‑1 (MQ=255)
                                                                                              gctgacgATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGCGCCACTTGCCGGCTTCCTCGGGGCTGTTCATGTAACGCCCGGCAGTGTCCAGCAGTACCGCTTCAGAGCTgaagaa                                                         >  1:60372/1‑141 (MQ=255)
                                                                                              gctgacgATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGCGCCACTTGCCGGCTTCCTCGGGGCTGTTCATGTAACGCCCGGCAGTGTCCAGCAGTACCGCTTCAGAGCTgaagaa                                                         <  2:60372/141‑1 (MQ=255)
                                                                                               ctgacgATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGCGCCACTTGCCGGCTTCCTCGGGGCTGTTGATGTAACGCCCGCCCGTGTCCAGCAGTATCGCTTCAGAGCTGAAGAACCAGTCGCAg                                               <  1:451074/150‑1 (MQ=255)
                                                                                                tgacgATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAACAGTTGCAAAAAGCCGCGCCACTTGCCGGCTTCCTCGGGGCTGTTCATGTAACGCCCGGCAGTGTCCAGCAGTACCGCTTCAGAGCTGAAGAACCAGTCGc                                                 >  2:963349/1‑147 (MQ=255)
                                                                                                tgacgATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAACAGTTGCAAAAAGCCGCGCCACTTGCCGGCTTCCTCGGGGCTGTTCATGTAACGCCCGGCAGTGTCCAGCAGTACCGCTTCAGAGCTGAAGAACCAGTCGc                                                 <  1:963597/147‑1 (MQ=255)
                                                                                                tgacgATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAACAGTTGCAAAAAGCCGCGCCACTTGCCGGCTTCCTCGGGGCTGTTCATGTAACGCCCGGCAGTGTCCAGCAGTACCGCTTCAGAGCTGAAGAACCAGTCGc                                                 >  2:963597/1‑147 (MQ=255)
                                                                                                tgacgATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAACAGTTGCAAAAAGCCGCGCCACTTGCCGGCTTCCTCGGGGCTGTTCATGTAACGCCCGGCAGTGTCCAGCAGTACCGCTTCAGAGCTGAAGAACCAGTCGc                                                 <  1:963349/147‑1 (MQ=255)
                                                                                                        aaGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGCGCCACTTGCCGGCTTCCTCGGGGCTGTTCATGTAACGCCCGGCAGTGTCCAGCAGTACCGCTTCAGAGCTGAAGAACCAGTCGCAGTTGcgcggg                                      >  1:900417/1‑148 (MQ=255)
                                                                                                         aGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGCGCCACTTGCCGGCTTCCTCGGGGCTGTTCATGTAACGccc                                                                                             <  2:97200/94‑1 (MQ=255)
                                                                                                         aGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGCGCCACTTGCCGGCTTCCTCGGGGCTGTTCATGTAACGccc                                                                                             >  1:97200/1‑94 (MQ=255)
                                                                                                         aGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGCGCCACTTGCCGGCTTCCTCGGGGCTGTTCATGTAACGCCCGGCAGTGTCCAGCAGTACCGCTTCAGAGCTGAAGAACCAGTCGCAGTTGCGCGTgc                                     >  1:1199823/1‑150 (MQ=255)
                                                                                                             gTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGCGCCACTTGCCGGCTTCCTCGGGGCTGTTCATGTAACGCCCGGCAGTGTCCAGCAGTACCGCTTCAGAGCTGAAGAACCAGTCGCAGTTGCGCGTgccgcc                                 >  2:680987/1‑150 (MQ=255)
                                                                                                              ttAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCcgc                                                                                                                                     >  2:1128024/1‑49 (MQ=255)
                                                                                                              ttAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCcgc                                                                                                                                     <  1:1128024/49‑1 (MQ=255)
                                                                                                                   gggACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGCGCCACTTGCCGGCTTCCTCGGGGCTGTTCATGTAACGCCCGGCAgt                                                                                       <  2:1623916/90‑1 (MQ=255)
                                                                                                                   gggACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGCGCCACTTGCCGGCTTCCTCGGGGCTGTTCATGTAACGCCCGGCAgt                                                                                       >  1:1623916/1‑90 (MQ=255)
                                                                                                                                       ggCGCAGCAGTTGCAAAAAGCCGCGCCACTTGCCGGCTTCCTCGGGGCTGTTCATGTAACGCCCGGCAGTGTCCAGCAGTACCGCTTCAGAGCTGAAGAACCAGTCGCAGTTGCGCGTGCCGCCCAGGCCCGCGACCCGCACGCCTTcgc       >  1:790652/1‑150 (MQ=255)
                                                                                                                                            agcagTTGCAAAAAGCCGCGCCACTTGCCGGCTTCCTCGGGGCTGTTCATGTAACGCCCGGCAGTGTCCAGCAGTACCGCTTCAGAGCTGAAGAACCAGTCGCAGTTGCGCGTGCCGCCCAGGCCCGCGACCCGCACGCCTTCGCGCTCg  <  2:51726/150‑1 (MQ=255)
                                                                                                                                            agcagTTGCAAAAAGCCGCGCCACTTGCCGCCTTATCCCGGTCTGTTCATGTAACGCCCGGCAGTGTCCAGCAGTACCGCTTCAGAGCTGAAGAACCAGTCGCAGTTGCGCCTGCCGCCCAGGCCCGCGACCCGCACGCCTTCGCGCTCg  <  2:950153/150‑1 (MQ=255)
                                                                                                                                             |                                                                                                                                                    
GCAGCGCGCAGCTTTCCTGAATGCGTTCGCGCAGGCGCTTGGCCACGCGCTCCTGGTCTTCGACCGAGCCATGCAGAATATCGGCGATGCTGACGCTGACGATCAAGCCGTTAAGGGGACGGCGCTGGCGGTGCTGGCGCAGCAGTTGCAAAAAGCCGCGCCACTTGCCGGCTTCCTCGGGGCTGTTCATGTAACGCCCGGCAGTGTCCAGCAGTACCGCTTCAGAGCTGAAGAACCAGTCGCAGTTGCGCGTGCCGCCCAGGCCCGCGACCCGCACGCCTTCGCGCTCG  >  NC_002947/3480520‑3480809

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑