Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 2,986,779 G→A 9.1% S540S (AGC→AGT)  PP_2612 ← membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029472,986,7790GA 9.1% 122.0 / 2.6 44S540S (AGC→AGT) PP_2612membrane protein
Reads supporting (aligned to +/- strand):  ref base G (21/19);  new base A (2/2);  total (23/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTCAAATACCGCTGCACCTCCTGGCTAAAGGGATTTTCCGTAATGGCCTGCTCGGTGATTCGATAGCGCGCCGCCAGCAACCCCAGCGCTTTCTCGGCATTCGCCTCCCGCGCTGCCAACTGCACCTGCCGCCGCAGGCCATGGCTGGCATCCCATCGGGTCTGCCCGCGCAGTCGCTTGAGCACCACGGTATTGACCGACTGGGCGGTGAGGTCGGTGATATCCGCCATGGCCGGGAAGCGACCGGCGAGCCCTTCGATCACGTTGTCGCTGGCGCCGAACAAGGTGCCGA  >  NC_002947/2986636‑2986927
                                                                                                                                               |                                                                                                                                                    
ttCAAATACCGCTGCACCTCCTGGCTAAAGGGATTTTCCGTAATGGCCTGCTCGGTGATTCGATAGCGCGCCGCCAGCAACCCCAGCGCTTTCTCGGCATTCGCCTCCCGCGCTGCCAACTGCACCTGCCGCCACAGGCCAtggct                                                                                                                                                    >  6:51649/1‑146 (MQ=255)
ttCAAATACCGCTGCACCTCCTGGCTAAAGGGATTTTCCGTAATGGCCTGCTCGGTGATTCGATAGCGCGCCGCCAGCAACCCCAGCGCTTTCTCGGCATTCGCCTCCCGCGCTGCCAACTGCACCTGCCGCCACAGGCCAtggct                                                                                                                                                    <  5:51649/146‑1 (MQ=255)
 gctcaagcgcctgcgcgggcagacccgatgggatgccagtcATGGCCTGCTCGGTGATTCGATAGCGCGCCGCCAGCAATCCCAGGGCTTTCTCGGCATTAGCCTCACGCGCTGCCAACTGCACCTGTCGCCGCAGGCCATGACTGGCa                                                                                                                                                <  5:262721‑M1/108‑1 (MQ=255)
  ctcaagcgcctgcgcgggcagacccgatgggatgccagtcATGGCCTGCTCGGTGATTCGATAGCGCGCCGCCAGCAATCCCAGGGCTTTCTCGGCATTAGCCTCACGCGCTGCCAACTGCACCTGTCGCCGCAGGCCATGACTGGCAt                                                                                                                                               >  6:262721‑M1/41‑149 (MQ=255)
  cAAATACCGCTGCACCTCCTGGCTAAAGGGATTTTCCGTAATGGCCTGCTCGGTGATTCGATAGCGCGCCGCCAGCAACCCCAGCGCTTTCTCGGCATTCGCCTCCCGCGCTGCCAACTGCACCTGCCGCCGCAGGCCATGGCTGGCa                                                                                                                                                <  3:283385/148‑1 (MQ=255)
     aTACCGCTGCACCTCCTGGCTAAAGGGATTTTCCGTAATGGCCTGCTCGGTGATTCGATAGCGCGCCGCCAGCAACCCCAGCGCTTTCTCGGCATTCGCCTCCCGCGCTGCCAACTGCACCTGCCGCCGCAGGCCATGGCTGGCATcc                                                                                                                                             >  3:88925/1‑148 (MQ=255)
         cGCTGCACCTCCTGGCTAAAGGGATTTTCCGTAATGGCCTGCTCGGTGATTCGATAGCGCGCCGCCAGCAACCCCAGCGCTTTCTCGGCATTCGCCTCCCGCGCTGCCAACTGCACCTGCCGCCGCAGGCCATGGCTGGCATCCCATCg                                                                                                                                        <  4:149861/149‑1 (MQ=255)
           cTGCACCTCCTGGCTAAAGGGATTTTCCGTAATGGCCTGCTCGGTGATTCGATAGCGCGCCGCCAGCAACCCCAGCGCTTTCTCGGCATTCGCCTCCCGCGCTGCCAACTGCACCTGCCGCCGCAGGCCAtggct                                                                                                                                                    <  7:15183/135‑1 (MQ=255)
           cTGCACCTCCTGGCTAAAGGGATTTTCCGTAATGGCCTGCTCGGTGATTCGATAGCGCGCCGCCAGCAACCCCAGCGCTTTCTCGGCATTCGCCTCCCGCGCTGCCAACTGCACCTGCCGCCGCAGGCCAtggct                                                                                                                                                    >  8:15183/1‑135 (MQ=255)
              cACCTCCTGGCTAAAGGGATTTTCCGTAATGGCCTGCTCGGTGATTCGATAGCGCGCCGCCAGCAACCCCAGCGCTTTCTCGGCATTCGCCTCCCGCGCTGCCAACTGCACCTGCCGCCGCAGGCCATGGCTGGCATCCCATCGGGTCt                                                                                                                                   <  7:145890/149‑1 (MQ=255)
                    ctGGCTAAAGGGATTTTCCGTAATGGCCTGCTCGGTGATTCGATAGCGCGCCGCCAGCAACCCCAGCGCTTTCTCGGCATTCGCCTCCCGCGCTGCCAACTGCACCTGCCGCCGCAGGCCATGGCTGGCATCCCATCGGGTCTGCCcgc                                                                                                                             >  5:124226/1‑149 (MQ=255)
                                 atgccagtcatggcctgcggcgacaggtgcagttggcagcgcgtgaggctaatgccgagaaagccctgggattgctggcggcgcgctatcgaatcaccgagcaggccatGACTGGCATCCCATCGGGTCTGCCCGCGCAGGCGCTTGAg                                                                                                                >  6:262721‑M2/110‑149 (MQ=255)
                                  tgccagtcatggcctgcggcgacaggtgcagttggcagcgcgtgaggctaatgccgagaaagccctgggattgctggcggcgcgctatcgaatcaccgagcaggccatGACTGGCATCCCATCGGGTCTGCCCGCGCAGGCGCTTGAGc                                                                                                               <  5:262721‑M2/41‑1 (MQ=255)
                                       gTAATGGCCTGCTCGGTGATTCGATAGCGCGCCGCCAGCAACCCCAGCGCTTTCTCGGCATTCGCCTCCCGCGCTGCCAACTGCACCTGCCGCCGCAGGCCATGGCTGGCATCCCATCGGGTCTGCCCGCGCAGTCGCTTGAGcaccac                                                                                                          >  4:270888/1‑149 (MQ=255)
                                        tAATGGCCTGCTCGGTGATTCGATAGCGCGCCGCCAGCAACCCCAGCGCTTTCTCGGCATTCGCCTCCCGCGCTGCCAACTGCACCTGCCGCCGCAGGCCATGGCTGGCATCCCATCGGGTCTGCCCGCGCAGTCGCTTGAGCACCACg                                                                                                         <  1:158744/149‑1 (MQ=255)
                                        tAATGGCCTGCTCGGTGATTCGATAGCGCGCCGCCAGCAACCCCAGCGCTTTCTCGGCATTCGCCTCCCGCGCTGCCAACTGCACCTGCCGCCGCAGGCCATGGCTGGCATCCCATCGGGTCTGCCCGCGCAGTCGCTTGAGCACCACg                                                                                                         >  1:127192/1‑149 (MQ=255)
                                           tggcctgcggcggcaggtgcagttggcagcgcgggaggcgaatgccgagaaagcgctggggttgctggcggcgcgctatcgaatcaccgagcaggccatGGCTGGCATCCCATCGGGTCTGCCCGCGCAGTCGCTTGCGCACCACGGTa                                                                                                      >  3:185375‑M2/100‑149 (MQ=255)
                                             gcctgcggcggcaggtgcagttggcagcgcgggaggcgaatgccgagaaagcgctggggttgctggcggcgcgctatcgaatcaccgagcaggccatGGCTGGCATCCCATCGGGTCTGCCCGCGCAGTCGCTTGAGCACCACGGTAtt                                                                                                    >  5:329291‑M2/98‑149 (MQ=255)
                                                             gATAGCGCGCCGCCAGCAACCCCAGCGCTTTCTCGGCATTCGCCTCCCGCGCTGCCAACTGCACCTGCCGCCGCAGGCCATGGCTGGCATCCCATCGGGTCTGCCCGCGCAGTCGCTTGAGCACCACGGTATTGACCGACTGGGCGGt                                                                                     <  6:124226/148‑1 (MQ=255)
                                                               tAGCGCGCCGCCAGCAACCCCAGCGCTTTCTCGGCATTCGCCTCCCGCGCTGCCAACTGCACCTGCCGCCGCAGGCCATGGCTGGCATCCCATCGGGTCTGCCCGCGCAGTCGCTTGAGCACCACGGTATTGACCGACTGGGCGGTGAg                                                                                  <  3:270888/149‑1 (MQ=255)
                                                                     gccgccAGCAACCCCAGCGGGTTCTCTGCATTCGCCTCCGGGGCTGCCAACTGCCCATGCCGACGCAGGCCATGGCTGGCATCCCATGGGGTCTGCCCGCGCAGTCTCTGGATCACCACTGTATTGACCGTCTGGGCGGTGAGTTCGGt                                                                            <  2:203697/149‑1 (MQ=255)
                                                                     gccgccAGCAACCCCAGCGCTTTCTCGGCATTCGCCTCCCGCGCTGCCAACTGCACCTGCCGCCGCAGGCCATGGCTGGCATCCCATCGGGTCTGCCCGCGCAGTCGCTTGAGCACCACGGTATTGACCGACTGGGCGGTGAGGTCGGt                                                                            <  3:323914/149‑1 (MQ=255)
                                                                       cgccAGCAACCCCAGCGCTTTCTCGGCATTCGCCTCCCGCGCTGCCAACTGCACCTGCCGCCGCAGGCCATGGCTGGCATCCCATCGGGTCTGCCCGCGCa                                                                                                                          >  8:169892/1‑101 (MQ=255)
                                                                       cgccAGCAACCCCAGCGCTTTCTCGGCATTCGCCTCCCGCGCTGCCAACTGCACCTGCCGCCGCAGGCCATGGCTGGCATCCCATCGGGTCTGCCCGCGCa                                                                                                                          <  7:169892/101‑1 (MQ=255)
                                                                       cgccAGCAACCCCAGCGCTTTCTCGGCATTCGCCTCCCGCGCTGCCAACTGCACCTGCCGCCGCAGGCCATGGCTGGCATCCCATCGGGTCTGCCCGCGCAGTCGCTTGAGCACCACGGTATTGACCGACTGGGCGGTGAGGTCGGTGa                                                                          >  5:112611/1‑149 (MQ=255)
                                                                        cgcgggaggcgaatgccgagaaagcgctggggttgctggcggcgcgctatcgaatcaccgagcaggccatGGCTGGCATCCCATCGGGTCTGCCCGCGCAGTCGCTTGAGCACCACGGTATTGACCGACTGGGCGGTGAGGTCGGTGat                                                                         <  6:329291‑M2/79‑1 (MQ=255)
                                                                            gCAACCCCAGCGCTTTCTCGGCATTCGCCTCCCGCGCTGCCAACTGCACCTGCCGCCGCAGGCCATGGCTGGCATCCCATCGGGTCTGCCCGCGCAGTCGCTTGAGCACCACGGTATTGACCGACTGGGCGGTGAGGTCGGTGATATcc                                                                     >  3:112330/1‑149 (MQ=255)
                                                                                ccccAGCGCTTTCTCGGCATTCGCCTCCCGCGCTGCCAACTGCACCTGCCGCCGCAGGCCATGGCTGGCATCCCATCGGGTCTGCCCGCGCAGTCGCTTGAGCACCACGGTATTGACCGACTGGGCGGTGAGGTCGGTg                                                                           <  8:10983/139‑1 (MQ=255)
                                                                                ccccAGCGCTTTCTCGGCATTCGCCTCCCGCGCTGCCAACTGCACCTGCCGCCGCAGGCCATGGCTGGCATCCCATCGGGTCTGCCCGCGCAGTCGCTTGAGCACCACGGTATTGACCGACTGGGCGGTGAGGTCGGTg                                                                           >  7:10983/1‑139 (MQ=255)
                                                                                 cccAGCGCTTTCTCGGCATTCGCCTCCCGCGCTGCCAACTGCACCTGCCGCCGCAGGCCATGGCTGGCATCCCATCGGGGCTGCCCGCGCAGTCGCTTGAGCACCACGGTATTGACCGACTGGGCGGTGAGGTCGGTGATATCCGCCAt                                                                <  4:88925/149‑1 (MQ=255)
                                                                                   cAGCGCTTTCTCGGCATTCGCCTCCCGCGCTGCCAACTGCACCTGCCGCCGCAGGCCATGGCTGGCATCCCATCGGGTCTGCCCGCGCAGTCGCTTGAGCACCACGGTATTGACCGACTGGGCGGTGAGGTCgg                                                                             >  2:248119/1‑134 (MQ=255)
                                                                                   cAGCGCTTTCTCGGCATTCGCCTCCCGCGCTGCCAACTGCACCTGCCGCCGCAGGCCATGGCTGGCATCCCATCGGGTCTGCCCGCGCAGTCGCTTGAGCACCACGGTATTGACCGACTGGGCGGTGAGGTCgg                                                                             <  1:248119/134‑1 (MQ=255)
                                                                                   cAGCGCTTTCTCGGCATTCGCCTCCCGCGCTGCCAACTGCACCTGCCGCCGCAGGCCATGGCTGGCATCCCATCGGGTCTGCCCGCGCAGTCGCTTGAGCACCACGGTATTGACCGACTGGGCGGTGAGGTCGGTGATATCCGCCATgg                                                              >  3:192233/1‑149 (MQ=255)
                                                                                      cgcTTTCTCGGCATTCGCCTCCCGCGCTGCCAACTGCACCTGCCGCCGCAGGCCATGGCTGGCATCCCATCGGGTCTGCCCGCGCAGTCGCTTGAGCACCACGGTATTGACCGACTGGGCGGTGAGGTCGGTGATATCCGCCATGGCCg                                                           <  1:160168/149‑1 (MQ=255)
                                                                                            ctcGGCATTCGCCTCCCGCGCTGCCAACTGCACCTGCCGCCGCAGGCCATGGCTGGCATCCCATCGGGTCTGCCCGCGCAGTCGCTTGAGCACCACGGTATTGACCGACTGGGCGGTGAGGTCGGTGa                                                                          >  4:175363/1‑128 (MQ=255)
                                                                                            ctcGGCATTCGCCTCCCGCGCTGCCAACTGCACCTGCCGCCGCAGGCCATGGCTGGCATCCCATCGGGTCTGCCCGCGCAGTCGCTTGAGCACCACGGTATTGACCGACTGGGCGGTGAGGTCGGTGa                                                                          <  3:175363/128‑1 (MQ=255)
                                                                                             tcGGCATTCGCCTCCCGCGCTGCCAACTGCACCTGCCGCCGCAGGCCATGGCTGGCATCCCATCGGGTCTGCCCGCGCAGTCGCTTGAGCACCACGGTATTGACCGACTGGGCGGTGAGGTCGGTGATATCCGCCATGGCCGGGAAGc                                                     >  5:137185/1‑148 (MQ=255)
                                                                                             tcGGCATTCGCCTCCCGCGCTGCCAACTGCACCTGCCGCCGCAGGCCATGGCTGGCATCCCATCGGGTCTGCCCGCGCAGTCGCTTGAGCACCACGGTATTGACCGACTGGGCGGTGAGGTCGGTGATATCCGCCATGGCCGGGAAGc                                                     >  6:251160/1‑148 (MQ=255)
                                                                                               ggCATTCGCCTCCCGCGCTGCCAACTGCACCTGCCGCCGCAGGCCATGGCTGGCATCCCATCGGGTCTGCCCGCGCAGTCGCTTGAGCACCACGGTATTGACCGACTGGGCGGTGAGGTCGGTGATATCCGCCATGGCCGGGAAGCGAc                                                  <  2:279670/149‑1 (MQ=255)
                                                                                                      gCCTCCCGCGCTGCCAACTGCACCTGCCGCCGCAGGCCATGGCTGGCATCCCATCGGGTCTGCCCGCGCAGTCGCTTGAGCACCACGGTATTGACCGACTGGGCGGTGAGGTCGGTGATATCCGCCATGGCCGGGAAGCGACCGGCGAg                                           >  5:94886/1‑149 (MQ=255)
                                                                                                       ccTCCCGCGCTGCCAACTGCACCTGCCGCCGCAGGCCATGGCTGGCATCCCATCGGGTCTGCCCGCGCAGTCGCTTGAGCACCACGGTATTGACCGACTGGGCGGTGAGGTCGGTGATATCCGCCATGGCCGGGAAGCGCCCGGCGAGc                                          >  7:290358/1‑149 (MQ=255)
                                                                                                             gcgcTGCCAACTGCACCTGCCGCCGCAGGCCATGGCTGGCATCCCATCGGGTCTGCCCGCGCAGTCGCTTGAGCACCACGGTATTGACCGACTGGGCGGTGAGGTCGGTGATATCCGCCATGGCCGGGAAGCGACCGGCGAGCCCTTc                                     >  5:298711/1‑148 (MQ=255)
                                                                                                                      aCTGCACCTGCCGCCGCAGGCCATGGCTGGCATCCCATCGGGTCTGCCCGCGCAGTCGCTTGAGCACCACGGTATTGACCGACTGGGCGGTGAGGTCGGTGATATCCGCCATGGCCGGGAAGCGACCGGCGAGCCCTTCGATCACGTTg                           <  4:192233/149‑1 (MQ=255)
                                                                                                                           aCCTGCCGCCGCAGGCCATGGCTGGCATCCCATCGGGTCTGCCCGCGCAGTCGCTTGAGCACCACGGTATTGACCGACTGGGCGGTGAGGTCGGTGATATCCGCCATGGCCGGGAAGCGACCGGCGAGCCCTTCGATCACGTTGTCGCt                      <  6:112611/149‑1 (MQ=255)
                                                                                                                           aCCTGCCGCCGCAGGCCATGGCTGGCATCCCATCGGGTCTGCCCGCGCAGTCGCTTGAGCACCACGGTATTGACCGACTGGGCGGTGAGGTCGGTGATATCCGCCATGGCCGGGAAGCGACCGGCGAGCCCTTCGATCACGTTGTCGCt                      >  4:243482/1‑149 (MQ=255)
                                                                                                                             cTGCCGCCGCAGGCCATGGCTGGCATCCCATCGGGTCTGCCCGCGCAGTCGCTTGAGCACCACGGTATTGACCGACTGGGCGGTGAGGTCGGTGATATCCGCCATGGCCGGGAAGCGACCGGCGAGCCCTTCGATCACGTTGTCGCTgg                    >  5:94478/1‑149 (MQ=255)
                                                                                                                                  gccgcAGGCCATGGCTGGCATCCCATCGGGTCTGCCCGCGCAGTCGCTTGAGCACCACGGTATTGACCGACTGGGCGGTGAGGTCGGTGATATCCGCCATGGCCGGGAAGCGACCGGCGAGCCCTTCGATCACGTTGTCGCTGGCGcc                >  4:40167/1‑148 (MQ=255)
                                                                                                                                        ggccatGGCTGGCATCCCATCGGGTCTGCCCGCGCAGTCGCTTGAGCACCACGGTATTGACCGACTGGGCGGTGAGGTCGGTGATATCCGCCATGGCCGGGAAGCGACCGGCGAGCCCTTCGATCACGTTGTCGCTGGCGCCGAACAAg         <  3:243482‑M2/143‑1 (MQ=255)
                                                                                                                                               gctggcATCCCATCGGGTCTGCCCGCGCAGTCGCTTGAGCACCACGGTATTGACCGACTGGGCGGTGAGGTCGGTGATATCCGCCATGGCCGGGAAGCGACCGGCGAGCCCTTCGATCACGTTGTCGCTGGCGCCGAACAAGGTGCCGa  <  6:137185/149‑1 (MQ=40)
                                                                                                                                               gctggcATCCCATCGGGTCTGCCCGCGCAGTCGCTTGAGCACCACGGTATTGACCGACTGGGCGGTGAGGTCGGTGATATCCGCCATGGCCGGGAAGCGACCGGCGAGCCCTTCGATCACGTTGTCGCTGGCGCCGAACAAGGTGCCGa  >  8:259693/1‑149 (MQ=40)
                                                                                                                                               |                                                                                                                                                    
TTCAAATACCGCTGCACCTCCTGGCTAAAGGGATTTTCCGTAATGGCCTGCTCGGTGATTCGATAGCGCGCCGCCAGCAACCCCAGCGCTTTCTCGGCATTCGCCTCCCGCGCTGCCAACTGCACCTGCCGCCGCAGGCCATGGCTGGCATCCCATCGGGTCTGCCCGCGCAGTCGCTTGAGCACCACGGTATTGACCGACTGGGCGGTGAGGTCGGTGATATCCGCCATGGCCGGGAAGCGACCGGCGAGCCCTTCGATCACGTTGTCGCTGGCGCCGAACAAGGTGCCGA  >  NC_002947/2986636‑2986927

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑