Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 3,674,531 C→T 7.4% V9I (GTT→ATT)  PP_3238 ← transcriptional regulator PyrR

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029473,674,5310CT 7.4% 150.8 / 2.3 54V9I (GTT→ATT) PP_3238transcriptional regulator PyrR
Reads supporting (aligned to +/- strand):  ref base C (25/24);  new base T (2/2);  total (28/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.21e-01

TGCAGTTGCAGGCGCTGCGCCAGCGGCTCACCACGCCGCTGAATGCCTACCAGCGCGACTTCAGACGTAGGCAAGCAGGCCATGGCCTGGCGGGCCATCGAGCGCAGCACACTGTCCAGATCGTCTTCGTCATACAGGCGAACCCTCGATGGAGCGGGGCGATTCATGGTGTTTTTCCTTTATTGGATATCACTCTGTTCGGGAGCCTACCCGGGCACCTTGAGGTGGGCTTGATAAAAGCCAAGTGATCGAATCGAAAACAAGCCCGTTTTGTGCATTACATGC  >  NC_002947/3674389‑3674673
                                                                                                                                              |                                                                                                                                              
tGCAGTTGCAGGCGCTGCGCCAGCGGCTCACCACGCCGCTGAATGCCTACCAGCGCGACTTCAGACGTAGGCAAGCAGGCCATGGCCTGGCGGGCCATCGAGCGCAGCACACTGTCCAGATCGTCTTCGTCATACAGGCGAACCCTCGa                                                                                                                                          <  2:317863/149‑1 (MQ=255)
        cAGGCGCTGCGCCAGCGGCTCACCACGCCGCTGAATGCCTACCAGCGCGACTTCAGACGTAGGCAAGCAGGCCATGGCCTGGCGGGCCATCGAGCGCCGCACACTGTCCAGATCGGCTTCGTCATACAGGCGAACCCTCGATGGCGCgg                                                                                                                                  >  8:237272/1‑149 (MQ=255)
        cAGGCGCTGCGCCAGCGGCTCACCACGCCGCTGAATGCCTACCAGCGCGACTTCAGACGTAGGCAAGCAGGCCATGGCCTGGCGGGCCATCGAGCGCAGCACACTGTCCAGATCGTCTTCGTCATACAGGCGAACCCTCGATGGAGCgg                                                                                                                                  >  3:111512/1‑149 (MQ=255)
           gcgcTGCGCCAGCGGCTCACCACGCCGCTGAATGCCTACCAGCGCGACTTCAGACGTAGGCAAGCAGGCCATGGCCTGGCGGGCCATCGAGCGCAGCACACTGTCCAGATCGTCTTCGTCATACAGGCGAACCCTCGATGGAGCGGGGc                                                                                                                               >  8:211234/1‑149 (MQ=255)
              cTGCGCCAGCGGCTCACCACGCCGCTGAATGCCTACCAGCGCGACTTCAGACGTAGGCAAGCAGGCCATGGCCTGGCGGGCCATCGAGCGCAGCACACTGTCCAGATCGTCTTCGTCATACAGGCGAACGCTCGATGGAGCGGGGCGAt                                                                                                                            <  2:228403/149‑1 (MQ=255)
               tGCGCCAGCGGCTCACCACGCCGCTGAATGCCTACCAGCGCGACTTCAGACGTAGGCAAGCAGGCCATGGCCTGGCGGGCCATCGAGCGCAGCACCCGGTCCAGATCGTCTTCGTCATACAGGCGCACCCTCGATGGAGCGGGGCGAtt                                                                                                                           >  5:14845/1‑149 (MQ=255)
                     aGCGGCTCACCACGCCGCTGAATGCCTACCAGCGCGACTTCAGACGTAGGCAAGCAGGCCATGGCCTGGCGGGCCATCGAGCGCAGCACACTGTCCAGATCGTCTTCGTCATACAGGCGAACCCTCGATGGAGCGGGGCGATTCATGgt                                                                                                                     >  5:341955/1‑149 (MQ=255)
                            caccacGCCGCTGAATGCCTACCAGCGCGACTTCAGATGTAGGCAAGCAGGCCATGGCCTGGCGGGCCATCGAGCGCAGCACACTGTCCAGATCGTCTTCGTCATACAGGCGAACCCTCGATGGAGCGGGGCGATTCATg                                                                                                                       >  3:185769/1‑140 (MQ=255)
                            caccacGCCGCTGAATGCCTACCAGCGCGACTTCAGATGTAGGCAAGCAGGCCATGGCCTGGCGGGCCATCGAGCGCAGCACACTGTCCAGATCGTCTTCGTCATACAGGCGAACCCTCGATGGAGCGGGGCGATTCATg                                                                                                                       <  4:185769/140‑1 (MQ=255)
                             accacGCCGCTGAATGCCTACCAGCGCGACTTCAGACGTAGGCAAGCAGGCCATGGCCTGGCGGGCCATCGAGCGCAGCACACTGTCCAGATCGTCTTCGTCATACAGGCGAACCCTCGATGGAGCGGGGCGATTCATGGTGTTTTTc                                                                                                              <  4:111512/148‑1 (MQ=255)
                              ccacGCCGCTGAATGCCTACCAGCGCGACTTCAGACGTAGGCAAGCAGGCCATGGCCTGGCGGGCCATCGAGCGCAGCACACTGTCCAGATCGTCTTCGTCATACAGGCGAACCCTCGa                                                                                                                                          <  2:65520/119‑1 (MQ=255)
                              ccacGCCGCTGAATGCCTACCAGCGCGACTTCAGACGTAGGCAAGCAGGCCATGGCCTGGCGGGCCATCGAGCGCAGCACACTGTCCAGATCGTCTTCGTCATACAGGCGAACCCTCGa                                                                                                                                          >  1:65520/1‑119 (MQ=255)
                              ccacGCCGCTGAATGCCTACCAGCGCGACTTCAGACGTAGGCAAGCAGGCCATGGCCTGGCGGGCCATCGAGCGCAGCACACTCTCCAGATCGTCTTCGTCATACAGGCGAACCCTCGATGGAGCGGGGCGCTTCATGTTGTTTTTCCt                                                                                                            >  7:300102/1‑149 (MQ=255)
                                  gccgcTGAATGCCTACCAGCGAGACTTCAGACGTAGGCAAGCAGGCCATGGCCTCGCGGGCCAACGACCGCAGCACACTCTCCAGATCGTCTTCGTCATACAGGCGAAACCTCCATGGACCCGGGCGATTCATACTGTTTTTCCTTTaa                                                                                                        >  5:258228/1‑148 (MQ=255)
                                   ccgcTGAATGCCTACCAGCGCGACTTCAGACGTAGGCAAGCAGGCCATGGCCTGGCGGGCCATCGAGCGCAGCACACTGTCCAGATCGTCTTCGTCATACAGGCGAACCCTCGATGGAGCGGGGCGATTCATGGTGTTTTTCCTTTAtt                                                                                                       <  4:217916/149‑1 (MQ=255)
                                    cgcTGAATGCCTACCAGCGCGACTTCAGACGTAGGCAAGCAGGCCATGGCCTGGCGTGCCATCGAGCGCAGCACACTGTCCAGATCGTCTTCGTCATACAGGCGAACCCTCGATGGAGCGGGGCGATTCATGGTGTTTTTCCTTTATTg                                                                                                      <  6:127649/149‑1 (MQ=255)
                                         aaTGCCTACCAGCGCGACTTCAGACGTAGGCAAGCAGGCCATGGCCTGGCGGGCCATCGAGCGCAGCACACTGTCCAGATCGTCTTCGTCATACAGGCGAACCCTCGATGGAGCGGGGCGATTCATGGTGTTTTTCCTTTATTGGat                                                                                                   <  4:271473/147‑1 (MQ=255)
                                              cTACCAGCGCGACTTCAGACGTAGGCAAGCAGGCCATGGCCTGGCGGGCCATCGAGCGCAGCACACTGTCCAGATCGTCTTCGTCATACAGGCGAACCCTCGATGGAGCGGGGCGATTCATGGTGTTTTTCCTTTATTGGATATCAatc                                                                                            >  1:229617/1‑149 (MQ=255)
                                                          cTTCAGACGTAGGCAAGCAGGCCATGGCCTGGCGGGCCATCGAGCGCAGCACACTGTCCAGATCGTCTTCGTCATACAGGCGAACCCTCGATGGAGCGGGGCGATTCATGGTGTTTTTCCTTTATTGGATATCACTCTGTTCGGGAGcc                                                                                <  7:173874/149‑1 (MQ=255)
                                                            tCAGACGTAGGCAAGCAGGCCATGGCCTGGCGGGCCATCGAGCGCAGCACACTGTCCAGATCGTCTTCGTCATACAGGCGAACCCTCGATGGAGCGGGGCGATTCATGGTGTTTTTCCTTTATTGGATATCACTCTGTTCGGGAGCCTa                                                                              >  5:64131/1‑149 (MQ=255)
                                                            tCAGACGTAGGCAAGCAGGCCATGGCCTGGCGGGCCATCGAGCGCAGCACACTGTCCAGATCGTCTTCGTCATACAGGCGAACCCTCGATGGAGCGGGGCGATTCATGGTGTTTTTCCTTTATTGGATATCACTCTGTTCGGGAGCCTa                                                                              >  6:303846/1‑149 (MQ=255)
                                                                     ggCAAGCAGGCCATGGCCTGGCGGGCCATCGAGCGCAGCACACTGTCCAGATCGTCTTCGTCATACAGGCGAACCCTCGATGGAGCGGGGCGATTCATGGTGTTTTTCCTTTATTGGATATCACTCTGTTCGGGAGCCTACCCGGGCAc                                                                     <  4:310328/149‑1 (MQ=255)
                                                                      gCAAGCAGGCCATGGCCTGGCGGGCCATCGAGCGCAGCACACTGTCCAGATCGTCTTCGTCATACAGGCGAACCCTCGATGGAGCGGGGCGATTCATGGTGTTTTTCCTTTATTGGATATCCCTCTGTTCGGGAGCCTCCCCGGGcccc                                                                    >  8:301090/1‑149 (MQ=255)
                                                                        aaGCAGGCCATGGCCTGGCGGGCCATCGAGCGCAGCACACTGTCCAGATCGTCTTCGTCATACAGGCGAACCCTCGATGGAGCgggg                                                                                                                                >  8:177485/1‑87 (MQ=255)
                                                                        aaGCAGGCCATGGCCTGGCGGGCCATCGAGCGCAGCACACTGTCCAGATCGTCTTCGTCATACAGGCGAACCCTCGATGGAGCgggg                                                                                                                                <  7:177485/87‑1 (MQ=255)
                                                                        aaGCAGGCCATGGCCTGGCGGGCCATCGAGCGCAGCACACTGTCCAGATCGTCTTCGTCATACAGGCGAACCCTCGATGGAGCGGGGCGATTCATGGTGTTTTTCCTTTATTGGATATCACTCTGTTCGGGAGCCTACCCGGGCACCtt                                                                  >  4:242581/1‑149 (MQ=255)
                                                                          gaacgCCATGGCCTGGCGGCCCATCGAGCGCAGCACACTGTCCAGATATTATTCGTCATACAGGCCAACACTCGAAGGAGCAGGGCGATTAATGGTGTTTTTCCTTTATTGAATATCACACACATCCGTAGACAACCAGGGCACCtt                                                                  >  4:301692/5‑147 (MQ=255)
                                                                           cAGGCCATGGCCTGGCGGGCCATCGAGCGCAGCACACTGTCCAGATCGTCTTCGTCATACAGGCGAACCCTCGATGGAGCGGGGCGATTCATGGTGTTTTTCCTTTATTGGATATCAATCTGTTCGGGAGCCTACCCGGGCACCTTGAg                                                               <  2:229617/149‑1 (MQ=255)
                                                                              gCCATGGCCTGGCGGGCCATCGAGCGCAGCACACTGTCCAGATCGTCTTCGTCATACAGGCGAACCCTCGATGGAGCGGGGCGATTCATGGTGTTTTTCCTTTATTGGATATCACTCTGTTCGGGAGCCTACCCGGGCACCTTGAGGTg                                                            <  6:64131/149‑1 (MQ=255)
                                                                              gCCATGGCCTGGCGGGCCATCGAGCGCAGCACACTGTCCAGATCGTCTTCGTCATACAGGCGAACCCTCGATGGAGCGGGGCGATTCATGGTGTTTTTCCTTTATTGGATATCACTCTGTTCGGGAGCCTACCCGGGCACCTTGAGGTg                                                            >  3:49830/1‑149 (MQ=255)
                                                                                cATGGCCTGGCGGGCCATCGAGCGCAGCACACTGTCCAGATCGTCTTCGTCATACAGGCGAACCCTCGATGGAGCGGGGCGATTCATGGTGTTTTTCCTTTATTGGATATCACTCTGTTCGGGAGCCTACCCGGGCACCTTGAGGTggg                                                          >  5:306915/1‑149 (MQ=255)
                                                                                 aTGGCCTGGCGGGCCATCGAGCGCAGCACACTGTCCAGATCGTCTTCGTCATACAGGCGAACCCTCGATGGAGCGGGGCGATTCATGGTGTTTTTCCTTTATTGGATATCACTCTGTTCGGGAGCCTACCCGGGCACCTTGAGGTGGGc                                                         >  8:203355/1‑149 (MQ=255)
                                                                                 aTGGCCTGGCGGGCCATCGAGCGCAGCACACTGTCCAGATCGGCTTCGTCATACAGGCGAACCCTCGATGGAGCGGGGCGATTCATGGTGTTTTTCCTTTATTGGATATCACTCTGTTCGGGAGCCTACCCGGGCACCTTGAGGTGGGc                                                         <  6:341955/149‑1 (MQ=255)
                                                                                    gCCTGGCGGGCCATCGAGCGCAGCACTCTGTCGAGAGCGTCTGCGTCATACAGGGGATCGCTCGATGGAGCGGGGCGAGTCATGGTGTTTTTCCTTTATTGGTTATCACTCTGTTCGGGTGCCTACCCGGGCACCTTGAGGTGGGCTTg                                                      <  4:2618/149‑1 (MQ=255)
                                                                                    gCCTGGCGGGCCATCGAGCGCAGCACACTGTCCAGATCGTCTTCGTCATACAGGCGAACCCTCGATGGAGCGGGGCGATTCATGGTGTTTTTCCTTTATTGGATATCACTCTGTTCGGGAGCCTACCCGGGCACCTTGAGGTGGGCTTg                                                      <  4:49830/149‑1 (MQ=255)
                                                                                          cGGGCCATCGAGCGCAGCACACTGTCCAGATCGTCTTCGTCATACAGGCGAACCCTCGATGGAGCGGGGCGATTCATGGTGTTTTTCCTTTATTGGATATCACTCTGTTCGGGAGCCTACCCGGGCACCTTGAGGTGGGCTTGATaaaa                                                <  3:242581/149‑1 (MQ=255)
                                                                                          cGGGCCATCGAGCGCAGCACACTGTCCAGATCGTCTTCGTCATACAGGCGAACCCTCGATGGAGCGGGGCGATTCATGGTGTTTTTCCTTTATTGGATATCACTCTGTTCGGGAGCCTACCCGGGCACCTTGAGGTGGGCTTGATaaaa                                                <  7:211234/149‑1 (MQ=255)
                                                                                           gggCCATAGAGCGCAGCACACTGTGCAGATCGTCTTCTTCATACTGGCGAACGCTCGATGGAGTGGGGCGATTCATGGTGTTTTTGATTTATTGGATATGACTGTGTTCGGGTGCCTACCGGTGCACCTTGAGGTGGGGTTGATaaaa                                                <  6:258228/148‑1 (MQ=255)
                                                                                               cATCGAGCGCAGCACACTGTCCAGATCGTCTTCGTCATACAGGCGAACCCTCGATGGAGCGGGGCGATTCATGGTGTTTTTCCTTTATTGGATATCACTCTGTTCGGGAGCCTACCCGGGCACCTTGAGGTGGGCTTGATAAAAGCCaa                                           <  5:303846/149‑1 (MQ=255)
                                                                                                        cagcaCACTGTCCAGATACTCTTCGTCATACAGGCGAACCCTCGATCGAGCGGGGCGATTCATGGTGTTTTTCCTTTATTGGATATCACTCTGTTCGGCAGCCTACCCGGGCACCGTGAGGTGGGCTTGATAAAAGCGAAGTGatcgaa                                  >  4:13860/1‑149 (MQ=255)
                                                                                                           cacaCTGTCCAGATCGTCTTCGTCATACAGGCGAACCCTCGATGGAGCGGGGCGATTCATGGTGTTTTTCCTTTATTGGATATCACTCTGTTCGGGAGCCTACCCGGGCACCTTGAGGTGGGCTTGATAAAAGCCAAGTGatcgaatc                                >  2:199520/1‑148 (MQ=255)
                                                                                                              acTGTCCAGATCGTCTTCGTCATACAGGCGAACCCTCGATGGAGCGGGGCGATTCATGGTGTTTTTCCTTTATTGGATATCACTCTGTTCGGGAGCCTACCCGGGCACCTTGAGGTGGGCTTGATAAAAGCCAAGTGAtcgaatcgaa                             >  5:205916/1‑148 (MQ=255)
                                                                                                                  tCCAGATCGTCTTCGTCATACAGGCGAACCCTCGATGGAGCGGGGCGATTCATGGTGTTTTTCCTTTATTGGATATCACTCTGTTCGGGAGCCTACCCGGGCACCTTGAGGTGGGCTTGATAAAAGCCAAGTGATCGAATCGAAAAc                          <  1:290226/147‑1 (MQ=255)
                                                                                                                      gATCGTCTTCGTCATACAGGCGAACCCTCGATGGAGCGGGGCGATTCATGGTGTTTTTCCTTTATTGGATATCACTCTGTTCGGGAGCCTACCCGGGCACCTTGAGGTGGGCTTGATAAAAGCCAAGTGATCGAATCGAAAACAAGccc                    <  6:205916/149‑1 (MQ=255)
                                                                                                                             ttCGTCATACAGGCGAACCCTCGATGGAGCGGGGCGATTCATGGTGTTTTTCCTTTATTGGATATCACTCTGTTCGGGAGCCTACCCGGGCACCTTGAGGTGGGCTTGATAAAAGCCAAGTGATCGAATCGAAAACAAGCCCGTTTtgt             >  1:127103/1‑149 (MQ=255)
                                                                                                                                gTCATACAGGCGAACCCTCGATGGAGCGGGTCGATTCATGGTGTTTTTCCTTTATTGGATATCACTCTGTTCGGGAGCCTACCCGGGCACCTTGAGGTGGGCTTGATAAAAGCCAAGTGATCGAATCGAAAACAAGCCCGTTTTGTGc           <  3:301692/148‑1 (MQ=255)
                                                                                                                                 tCATACAGGCGAACCCTCGATGGAGCGGGGCGATTCATGGTGTTTTTCATTTATTGGATATCACTCTGTTCGGGAGCCTACCCGGGCACCTTGAGGTGGGCTTGATAAAAGCCAAGTGATCGAATCTAATACAAGCCCGTTTTGTGCAt         >  4:199330/1‑149 (MQ=255)
                                                                                                                                 tCATACAGGCGAACCCTCGATGGAGCGGGGCGAATCATGGTGTTTTTCCTTTATTGGATATCACTCTGTTCGGGAGCCTACCCGGGCACCTTGAGGTGGGCTTGATAAAAGCCAAGTGATCGAATCGAAAACAAGCCCGTTTTGTGCAt         <  8:300102/149‑1 (MQ=255)
                                                                                                                                       aGGCGAATCCTCGATGGAGCGGGGCGATTCATGGTGTTTTTCCTTTATTGGATATCACTCTGTTCGGGAGCCTACCCGGGCACCTTGAGGTGGGCTTGATAAAAGCCAAGTGATCGAATCGAAACCAAGCCCGTTTTGTGCATTa       >  8:174937/1‑145 (MQ=255)
                                                                                                                                       aGGCGAATCCTCGATGGAGCGGGGCGATTCATGGTGTTTTTCCTTTATTGGATATCACTCTGTTCGGGAGCCTACCCGGGCACCTTGAGGTGGGCTTGATAAAAGCCAAGTGATCGAATCGAAACCAAGCCCGTTTTGTGCATTa       >  8:179802/1‑145 (MQ=255)
                                                                                                                                       aGGCGAATCCTCGATGGAGCGGGGCGATTCATGGTGTTTTTCCTTTATTGGATATCACTCTGTTCGGGAGCCTACCCGGGCACCTTGAGGTGGGCTTGATAAAAGCCAAGTGATCGAATCGAAACCAAGCCCGTTTTGTGCATTa       <  7:179802/145‑1 (MQ=255)
                                                                                                                                       aGGCGAATCCTCGATGGAGCGGGGCGATTCATGGTGTTTTTCCTTTATTGGATATCACTCTGTTCGGGAGCCTACCCGGGCACCTTGAGGTGGGCTTGATAAAAGCCAAGTGATCGAATCGAAACCAAGCCCGTTTTGTGCATTa       <  7:174937/145‑1 (MQ=255)
                                                                                                                                         gCGAACCCTCGATGGAGCGGGGCGATTCATGGTGTTTTTCCTTTATTGGATATCACTCTGTTCGGGAGCCTACCCGGGCACCTTGAGGTGGGCTTGATAAAAGCCAAGTGATCGAATCGAAAACAAGCCCGTTTTGTGCATTACATGc  >  8:179155/1‑148 (MQ=255)
                                                                                                                                         gCGAACCCTCGATGGAGCGGGGCGATTCATGGTGTTTTTCCTTTATTGGATATCACTCTGTTCGGGAGCCTACCCGGGCACCTTGAGGTGGGCTTGATAAAAGCCAAGTGATCGAATCGAAAACAAGCCCGTTTTGTGCATTACATGc  >  4:186491/1‑148 (MQ=255)
                                                                                                                                              |                                                                                                                                              
TGCAGTTGCAGGCGCTGCGCCAGCGGCTCACCACGCCGCTGAATGCCTACCAGCGCGACTTCAGACGTAGGCAAGCAGGCCATGGCCTGGCGGGCCATCGAGCGCAGCACACTGTCCAGATCGTCTTCGTCATACAGGCGAACCCTCGATGGAGCGGGGCGATTCATGGTGTTTTTCCTTTATTGGATATCACTCTGTTCGGGAGCCTACCCGGGCACCTTGAGGTGGGCTTGATAAAAGCCAAGTGATCGAATCGAAAACAAGCCCGTTTTGTGCATTACATGC  >  NC_002947/3674389‑3674673

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑