Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 1,312,981 A→T 7.3% L561Q (CTG→CAG)  rapA ← RNA polymerase‑associated protein RapA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029471,312,9810AT 7.3% 158.9 / 2.9 55L561Q (CTG→CAG) rapARNA polymerase‑associated protein RapA
Reads supporting (aligned to +/- strand):  ref base A (29/22);  new base T (2/2);  total (31/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.02e-01

CGTGGTACCACTGGAACAGGCGCTCTTGCGGGCTGTCCTGCAGGTACGGGATGTGCAACTGGATAGTGTGCTTCTGGCCGATCCGGTCAAGGCGGCCGATGCGCTGTTCGAGCAGGTCGGGGTGCGCCGGCAGGTCGAACATCACCAGGTGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGATTTCCGAGCAGATCAGCACCTGGGCGCCAAACTCTTCATCGGCAAAGTAGGCAGCGGCACGGTCGCGCTCGAGGATGCTCATGCCTTCATGGAACACCGAGGCCGGG  >  NC_002947/1312835‑1313127
                                                                                                                                                  |                                                                                                                                                  
cGTGGTACCACTGGAACAGGCGCTCTTGCGGGCTGTCCTGCAGGTACGGGATGTGCAACTGGATAGTGTGCTTCTGGCCGATCCGGTCAAGGCGGCCGATGCGCTGTTCGAGCAGGTCGGGCTGTCCCGGCAGGTCGAACATCACCAGGt                                                                                                                                                 <  1:426882/150‑1 (MQ=255)
  tGGTACCACTGGAACAGGCGCTCTTGCGGGCTGTCCTGCAGGTACGGGATGTGCAACTGGATAGTGTGCTTCTGGCCGATCCGGTCAAGGCGGCCGATGCGCTGTTCGAGCAGGTCGGGGTGCGCCGGCAGGTCGAACATCACCAGGtga                                                                                                                                               >  1:907712/1‑150 (MQ=255)
     tACCACTGGAACAGGCGCTCTTGCGGGCTGTCCTGCAGGTACGGGATGTGCAACTGGATAGTGTGCTTCTGGCCGATCCGGTCAAGGCGGCCGATGCGCTGTTCGAGCAGGTCGGGGTGCGCCGGCAGGTCGAACATCACCAGGtgatga                                                                                                                                            <  1:671595/150‑1 (MQ=255)
      aCCACTGGAACAGGCGCTCTTGCGGGCTGTCCTGCAGGTACGGGATGTGCAACTGGATAGTGTGCTTCTGGCCGATCCGGTCAAGGCGGCCGATGCGCTGTTCGAGCTGGTCGGGGTGCGCCGGCAGGTCGAACATCACCAGGTGATGAg                                                                                                                                           >  1:1017802/1‑150 (MQ=255)
       ccACTGGAACAGGCGCTCTTGCGGGCTGTCCTGCAGGTACGGGATGTGCAACTGGATAGTGTGCTTCTGGCCGATCCGGTCAAGGCGGCCGATGCGCTGTTCGAGCAGGTCGGGGTGCGCCGGCAGGTCGAACATCACCTGGtgatgttc                                                                                                                                          <  1:1075073/150‑4 (MQ=255)
       ccACTGGAACAGGCGCTCTTGCGGGCTGTCCTGCAGGTACGGGATGTGCAACTGGATAGTGTGCTTCTGGCCGATCCGGTCAAGGCGGCCGATGCGCTGTTCGAGCAGGTCGGGGTGCGCCGGCAGGTCGAACATCACCAGGTGATGAGc                                                                                                                                          <  2:956599/150‑1 (MQ=255)
               aCAGGCGCTCTTGCGGGCTGTCCTGCAGGTACGGGATGTGCAACTGGATAGTGTGCTTCTGGCCGATCCGGTCAAGGCGGCCGATGCGCTGTTCGAGCAGGTCGGGGTGCGCCGGCAGGTCGAACATCACCAGGTGATGAGCGAACTGGa                                                                                                                                  <  1:790304/150‑1 (MQ=255)
                 aGGCGCTCTTGCGGGCTGTCCTGCAGGTACGGGATGTGCAACTGGATAGTGTGCTTCTGGCCGATCCGGTCAAGGCGGCCGATGCGCTGTTCGAGCAGGTCGGGGTGCGCCGGCAGGTCGAACATCACCAGGTGATGAGCGAACTGGAAg                                                                                                                                >  2:986713/1‑150 (MQ=255)
                 aGGCGCTCTTGCGGGCTGTCCTGCAGGTACGGGATGTGCAACTGGATAGTGTGCTTCTGGCCGATCCGGTCAAGGCGGCCGATGCGCTGTTCGAGCAGGGCGGGGTGCGCCGGCAGGTCGAACATCACCAGGTGATGAGCGCACTGGAAg                                                                                                                                >  1:49417/1‑150 (MQ=255)
                      ctctTGCGGGCTGTCCTGCAGGTACGGGATGTGCAACTGGATAGTGTGCTTCTGGCCGATCCGGTCAAGGCGGCCGATGCGCTGTTCGAGCAGGTCGGGGTGCGCCGGCAGGTCGAACATCACCAGGTGATGAGCGAACTGGAAGTTGCg                                                                                                                           <  1:434824/150‑1 (MQ=255)
                         ttGCGGGCTGTCCTGCAGGTACGGGATGTGCAACTGGATAGTGTGCTTCTGGCCGATCCGGTCAAGGCGGCCGATGCGCTGTTCGAGCAGGTCGGGGTGCGCCCGCAGGTCGAACATCTCCAGTTTATGAGCTAACTGGAAATTGCGGcc                                                                                                                        >  2:607853/1‑150 (MQ=255)
                             gggCTGTCCTGCAGGTACGGGATGTGCAACTGGATCGTGTGCTTCTGGCCGATCCGGTCAATGCGGCCGATGCGCTGTTCGAGCAGGGCGGGGTGCGCCGGCAGGTCGAACATCACCAGGTGATGAGCGAACTGGAAGTTGCGGCCTTCg                                                                                                                    >  2:402703/1‑150 (MQ=255)
                                   tCCTGCAGGTACGGGATGTGCAACTGGATAGTGTGCTTCTGGCCGATCCGGTCAAGGCGGCCGATGCGCTGTTCGAGCAGGTCGGGGTGCGCCGGCAGGTCGAACATCACCAGGTGATGAGCGAACTGGGCGTTGCGGCCTTCGCTGCCg                                                                                                              >  2:22440/1‑150 (MQ=255)
                                    ccTGCAGGTACGGGATGTGCAACTGGATAGTGTGCTTCTGGCCGATCCGGTCAAGGCGGCCGATGCGCTGTTCGAGCAGGTCGGGGTGCGCCGGCAGGTCGAACATCACCAGGTGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGa                                                                                                             >  2:135232/1‑150 (MQ=255)
                                     cTGCAGGTACGGGATGTGCAACTGGATAGTGTGCTTCTGGCCGATCCGGTCAAGGCGGCCGATGCGCTGTTCGAGCAGGTCGGGGTGCGCCGGCAGGTCGAACATCACCAGGTGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGAt                                                                                                            >  1:201144/1‑150 (MQ=255)
                                         aGGTACGGGATGTGCAACTGGATAGTGTGCTTCTGGCCGATCCGGTCAAGGCGGCCGATGCGCTGTTCGAGCAGGTCGGGGTGCGCCGGCAGGTCGAACATCACCAGGTGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGACGATTTcc                                                                                                        <  2:49417/150‑1 (MQ=255)
                                                 gATGTGCAACTGGATAGTGTGCTTCTGGCCGATCCGGTCAAGGCGGCCGATGCGCTGTTCGAGCAGGTCGGGGTGCGCCGGCAGGTCGAACATCACCAGGTGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGATTTCCGAGCAGAt                                                                                                >  2:418169/1‑150 (MQ=255)
                                                  aTGTGCAACTGGATAGTGTGCTTCTGGCCGATCCGGTCAAGGCGGCCGATGCGCTGTTCGAGCAGGTCGGGGTGCGCCGGCAGGTCGAACATCACCAGGTGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGATTTCCGAGCAGATc                                                                                               >  2:269818/1‑150 (MQ=255)
                                                  aTGTGCAACTGGATAGTGTGCTTCTGGCCGATCCGGTCAAGGCGGCCGATGCGCTGTTCGAGCAGGTCGGGGTGCGCCGGCAGGTCGAACATCACCAGGTGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGATTTCCGAGCAGATc                                                                                               <  1:51186/150‑1 (MQ=255)
                                                   tgtgCAACTGGATAGTGTGCTTCTGGCCGATCCGGTCAAGGCGGCCGATGCGCTGTTCGAGCAGGTCGGGGTGCGCCGGCAGGTCGAACATCACCAGGTGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGATTTCCGAGCAGATCa                                                                                              <  2:907712/150‑1 (MQ=255)
                                                        aaCTGGATAGTGTGCTTCTGGCCGATCCGGTCAAGGCGGCCGATGCGCTGTTCGAGCAGGTCGGGGTGCGCCGGCAGGTCGAACATCACCAGGTGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGATTTCCGAGCAGATCAGCAcc                                                                                         >  1:268786/1‑150 (MQ=255)
                                                             gATAGTGTGCTTCTGGCCGATCCGGTCAAGGCGGCCGATGCGCTGTTCGAGCAGGTCGGGGTGCGCCGGCAGGTCGAACGTCACCAGGTGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGATTTCCGAGCAGATCAGCACCTGGgc                                                                                    <  1:215975/150‑1 (MQ=255)
                                                                 gtgtGCTTCTGGCCGATCCGGTCAAGGCGGCCGATGCGCTGTTCGAGCAGGTCGGGGTGCGCCGGCAGGTCGAACATCACCAGGTGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGATTTCCGAGCAGATCAGCACCTGGGCGCCa                                                                                >  1:967749/1‑150 (MQ=255)
                                                                    tgCTTGTGGCCGATCCGGTCAAGGCGGCCGATGCGCTGTTCGAGCAGGTCGGGGTGCGCCGGCAGGTCGAACATCACCAGGTGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGATTTCCGAGCAGATCAGCACCTGGGCGCCAAAc                                                                             >  1:323362/1‑150 (MQ=255)
                                                                    tgCTTCTGGCCGATCCGGTCAAGGCGGCCGATGCGCTGTTCGAGCAGGTCGGGGTGCGCCGGCAGGTCGAACATCACCAGGTGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGATTTCCGCGCAGATCAGCACCTGGGCGCCAAAc                                                                             >  1:9634/1‑150 (MQ=255)
                                                                     gCTTCTGGCCGATCCGGTCAAGGCGGCCGATGCGCTGTTCGAGCAGGTCGGGGTGCGCCGGCAGGTCGAACATCACCAGGTGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGATTTCCGAGCAGATCAGCACCTGGGCGCCAAAct                                                                            <  2:607139/150‑1 (MQ=255)
                                                                          tGGCCGATCCGGTCAAGGCGGCCGATGCGCTGTTCGAGCAGGTCGGGGTGCGCCGGCAGGTCGAACATCACCAGGTGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGATTTCCGAGCAGATCAGCACCTGGGCGCCAAACTCTTCa                                                                       >  2:215931/1‑150 (MQ=255)
                                                                             gcGATCCGGTCAAGGGGGCCGCTGCGCTGTTCGAGCAGGTTGGGGTGCGCCCGCAGGTCGATCATCACCAGGTGATGTTCGAACTGGAAGTGGCTGCCTTCCCTGCCGATTTCCGAGCAGATCAGCACCTGGGCGCCAAACTCTTCACCg                                                                    <  2:520043/149‑1 (MQ=255)
                                                                                 tCCGGTCAAGGCGGCCGAGGCGCTGTTCGAGCAGGTCGGGGGGCAGCGGCAGGTCGAACATCACCAGGTGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGATTTCCGAGCAGATCAGCACCTGGGCGCCAAACTCTTCATCGGCaa                                                                >  1:257349/1‑150 (MQ=255)
                                                                                   cGGTCAAGGCGGCCGATGCGCTGTTCGAGCAGGTCGGGGTGCGCCGGCAGGTCGAACATCACCAGGTGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGATTTCCGAGCAGATCAGCACCTGGGCGCCAAACTCTTCATCGGCAAAg                                                              >  1:634375/1‑150 (MQ=255)
                                                                                      tCAAGGCGGCCGATGCGCTGTTCGAGCAGGTCGGGGTGCGCCGGCAGGTCGAACATCACCAGGTGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGATTTCCGAGCAGATCAGCACCTGGGCGCCAAACTCTTCATCGGCAAAGTAg                                                           >  1:32101/1‑150 (MQ=255)
                                                                                            cggcCGATGCGCTGTTCGAGCAGGTCGGGGTGCGAAGTAGAGTCGAACATCACCAGGTGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGATTTCCGAGCAGATCAGCACCTGGGCGCCAAACTCTTCATCGGCAAAGTAGGCAGCg                                                     <  1:607853/150‑1 (MQ=255)
                                                                                                    gcgcTGTTCGAGCTGGTCGGGGTGCGCCGGCAGGTCGAACATCACCAGGTGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGATTTCCGAGCAGATCAGCACCTGGGCGCCAAACTCTTCATCGGCAAAGTAGGCAGCGGCACGGTc                                             <  2:1017802/150‑1 (MQ=255)
                                                                                                    gcgcTGTTCGAGCAGGTCGGGGTGCGCCGGCAGGTCGAACATCACCAGGTGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGATTTCCGAGCAGATCAGCACCTGGGCGCCAAACTCTTCATCGGCAAAGTAGGCAGCGGCACGGTc                                             >  2:80402/1‑150 (MQ=255)
                                                                                                      gcTGTTCGAGCAGGTCGGGGTGCGCCGGCAGGTCGAACATCACCAGGTGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGATTTCCGAGCAGATCAGCACCTGGGCGCCAAACTCTTCATCGGCAAAGTAGGCAGCGGCACGGTcgc                                           >  2:585775/1‑150 (MQ=255)
                                                                                                                cAGGTCGGGGTGCGCCGGCAGGTCGAACATCACCAGGTTATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGATTTCCGAGCAGATCAGCACCTGGGCGCCAAACTCTTCATCGGCAAAGTAGGCAGCGGCACGGTCGCGCTCGAGGAt                                 <  2:1005590/150‑1 (MQ=255)
                                                                                                                   gTCGGGGTGCGCCGGCAGGTCGAACATCACCAGGTGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGATTTCCGAGCAGATCAGCACCTGGGCGCCAAACTCTTCATCGGCAAAGTAGGCAGCg                                                     >  2:114776/1‑127 (MQ=255)
                                                                                                                   gTCGGGGTGCGCCGGCAGGTCGAACATCACCAGGTGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGATTTCCGAGCAGATCAGCACCTGGGCGCCAAACTCTTCATCGGCAAAGTAGGCAGCg                                                     <  1:114776/127‑1 (MQ=255)
                                                                                                                   gTCGGGGTGCGCCGGCAGGTCGAACATCACCAGGTGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGATTTCCGAGCAGATCAGCACCTGGGCGCCAAACTCTTCATCGGCAAAGTAGGCAGCGGCACGGTCGCGCTCGAGgctgct                              >  2:863587/1‑150 (MQ=255)
                                                                                                                   gTCGGGGTGCGCCGGCAGGTCGAACATCACCAGGTGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGATTTCCGAGCAGATCAGCACCTGGGCGCCAAACTCTTCATCGGCAAAGTAGGCAGCGGCACGGTCGCGCTCGAGGATGCt                              >  2:51833/1‑150 (MQ=255)
                                                                                                                       gggTGCGCCGGCAGGTCGAACATCACCAGGTGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGATTTCCGAGCAGATCAGCACCTGGGCGCCAAACTCTTCATCGGCAAAGTAGGCAGCGGCACGGTCGCGCTCGAGGATGCTCATg                          <  1:585775/150‑1 (MQ=255)
                                                                                                                        ggTGCGCCGGCAGGTCGAACATCACCAGGTGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGATTTCCGAGCAGATCAGCACCTGGGCGCCAAACTCTTCATCGGCAAAGTAGGCAGCGGCACGGTCGCGCTCGAGGATGCTCATGc                         <  1:215931/150‑1 (MQ=255)
                                                                                                                             gcCGGCAGGTCGAACATATGCAGATGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGATTTCCGAGCAGATCAGCACCTGGGCGCCAAACTCTTCATCGGCAAAGTAGGCACCGGCACGGTCGCGCTCGAGGATGGTCATGCCTTCa                    <  2:257349/150‑1 (MQ=255)
                                                                                                                              ccGGCAGGTCGAACATCACCAGGTGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGATTTCCGAGCAGATCAGCACCTGGGCGCCAAACTCTTCATCGGCAAAGTAGGCAGCGGCACGGTCGCGCTCGAGGATGCTCATGCCTTCAt                   <  1:986713/150‑1 (MQ=255)
                                                                                                                                   aGGTCGAACATCACCAGGTGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGATTTCCGAGCAGATCAGCACCTGGGCGCCAAACTCTTCATCGGCAAAGTAGGCAGCGGCACGGTCGCGCCCGAGGAAGCTCATGCCTTCATGGAac              >  2:361602/1‑150 (MQ=255)
                                                                                                                                      tCGAACATCACCAGGTGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGATTTCCGAGCAGATCAGCACCTGGGCGCCAAACTCTTCATCGGCAAAGTAGGCAGCGGCACGGTCGCGCTCGAGGATGCTCATGCCTTCATGGAACAcc           >  2:127102/1‑150 (MQ=255)
                                                                                                                                        gctcATCACCTGGTGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGATTTCCGAGCAGATCAGCACCTGGGCGCCAAACTCTTCATCGGCAAAGTAGGCAGCGGCACGGTCGCGCTCGAGGATGCTCATGCCTTCATGGAACACCGa         >  1:645835/4‑150 (MQ=255)
                                                                                                                                        gAACATCACCAGGTGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGATTTCCGAGCAGATCAGCACCTGGGCGCCAAACTCTTCATc                                                                     >  2:652233/1‑90 (MQ=255)
                                                                                                                                        gAACATCACCAGGTGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGATTTCCGAGCAGATCAGCACCTGGGCGCCAAACTCTTCATc                                                                     <  1:652233/90‑1 (MQ=255)
                                                                                                                                         ctcATCACCTGGTGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGATTTCCGAGCAGATCAGCACCTGGGCGCCAAACTCTTCATCGGCAAAGTACGCATCGGCACGGTCGCGCTCGAGGATGCTCATGCCTTCATGGAACACCGAg        >  1:345851/3‑150 (MQ=255)
                                                                                                                                         aaCATCACCAGGTGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGATTTCCGAGCAGATCAGCACCTGGGCGCCAAACTCTTCATCGGCAAAGTAGGCAGCGGCACGGTCGCGCTCGAGGATGCTCATGCCTTCATGGAACACCGAg        <  2:323362/150‑1 (MQ=255)
                                                                                                                                          tcATCACCTGGTGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGATTTCCGAGCAGATCAGCACCTGGGCGCCAAACTCTTCATCGGCAAAGTAGGCAGCGGCACGGTCGCGCTCGAGGATGCTCATGCCTTCATGGAACACCGAgg       <  2:645835/149‑1 (MQ=255)
                                                                                                                                               aCCAGGTGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGATTTCCGAGCAGATCAGCACCTGGGCGCCAAACTCTTCATCGGCAAAGTAGGCAGCGGCACGGTCGCGCTCGAGGATGCTCATGCCTTCATGGAACACCGAg        <  2:1124546/144‑1 (MQ=255)
                                                                                                                                               aCCAGGTGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGATTTCCGAGCAGATCAGCACCTGGGCGCCAAACTCTTCATCGGCAAAGTAGGCAGCGGCACGGTCGCGCTCGAGGATGCTCATGCCTTCATGGAACACCGAg        >  1:1124546/1‑144 (MQ=255)
                                                                                                                                               aCCAGGTGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGATTTCCGAGCAGATCAGCACCTGGGCGCCAAACTCTTCATCGGCAAAGTAGGCAGCGGCACGGTCGCGCTCGAGGATGCTCATGCCTTCATGGAACACCGAGGCCggg  >  2:525229/1‑150 (MQ=255)
                                                                                                                                                  |                                                                                                                                                  
CGTGGTACCACTGGAACAGGCGCTCTTGCGGGCTGTCCTGCAGGTACGGGATGTGCAACTGGATAGTGTGCTTCTGGCCGATCCGGTCAAGGCGGCCGATGCGCTGTTCGAGCAGGTCGGGGTGCGCCGGCAGGTCGAACATCACCAGGTGATGAGCGAACTGGAAGTTGCGGCCTTCGCTGCCGATTTCCGAGCAGATCAGCACCTGGGCGCCAAACTCTTCATCGGCAAAGTAGGCAGCGGCACGGTCGCGCTCGAGGATGCTCATGCCTTCATGGAACACCGAGGCCGGG  >  NC_002947/1312835‑1313127

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑