Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 60,701 T→C 7.1% Q855R (CAG→CGG)  rapA ← RNA polymerase remodeling/recycling factor ATPase; RNA polymerase‑associated, ATP‑dependent RNA translocase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_00091360,7010TC 7.1% 164.0 / 3.2 56Q855R (CAG→CGG) rapARNA polymerase remodeling/recycling factor ATPase; RNA polymerase‑associated, ATP‑dependent RNA translocase
Reads supporting (aligned to +/- strand):  ref base T (24/28);  new base C (2/2);  total (26/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.34e-01

CACGGGCAGATTTCTCGATCTGCGCTTCACCCAGTTGAAGGATAGCGTGAACATCCTGCTGCACGGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCTGGGCTTCAACCACATAAATCAGTTCCACCAACAGCGTACCTACCGGCAAC  >  NC_000913/60564‑60841
                                                                                                                                         |                                                                                                                                            
cACGGGCAGATTTCTCGATCTGCGCTTCACCCAGTTGAAGGATAGCGTGAACATCCTGCTGCACGGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAgg                                                                                                                                   >  1:153492/1‑149 (MQ=255)
   gggCAGATTTCTCGATCTGCGCTTCACCCAGTTGAAGGATAGCGTGAACATCCTGCTGCACGGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGgttg                                                                                                                                >  7:85102/1‑149 (MQ=255)
     gCAGATTTCTCGCTCTGCGCTTCACCCAGTTGAAGGATAGCGTGAACATCCTGCTGCACGGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGgttgtt                                                                                                                              <  5:75505/149‑1 (MQ=255)
      cAGATTTCTCGATCTGCGCTTCACCCAGTTGAAGGATAGCGTGAACATCCTGCTGCACGGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGttgttg                                                                                                                             <  1:69170/149‑1 (MQ=255)
       aGATTTCTCGATCTGCGCTTCACCCAGTTGAAGGATAGCGTGAACATCCTGCTGCACGGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGc                                                                                                                            <  8:99644/149‑1 (MQ=255)
         aTTTCTCGATCTGCGCTTCACCCAGTTGAAGGATAGCGTGAACATCCTGCTGCACGGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCg                                                                                                                          >  7:58973/1‑149 (MQ=255)
           ttCTTGATCTGCGCTTCACCCAGTTGAAGGATAGCGTGAACATCCTGCTGCACGGCGTTAACCAGTTTGCTGACGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGtt                                                                                                                        >  8:113155/1‑149 (MQ=255)
             ctcGATCTGCGCTTCACCCAGTTGAAGGATAGCGTGAACATCCTGCTGCACGGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGttt                                                                                                                       <  2:153492/148‑1 (MQ=255)
              tcGATCTGCGCTTCACCCAGTTGAAGGATAGCGTGAACATCCTGCTGCACGGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGtttt                                                                                                                      >  1:128980/1‑148 (MQ=255)
                  cttGCGCTTCACCCAGTTGAATGATAGCTTGAACATCCTGCTGCACTGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTGACCTCGTTAAGCTGTCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGGCGTTTTTATc                                                                                                                  <  3:190049/146‑1 (MQ=255)
                     gcgcTTCACCCAGTTGAAGGATAGCGTGAACATCCTGCTGCACGGCGTTAACCAGTTTGCTGCAGGTGTGACGGTTGACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACATGCGCCGCCAGGTTGTTGCAGTTTTTATc                                                                                                                  >  4:190049/1‑145 (MQ=255)
                      cgcTTCACCCAGTTGAAGGATAGCGTGAACATCCTGCTGCACGGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATc                                                                                                                  <  7:132171/144‑1 (MQ=255)
                      cgcTTCACCCAGTTGAAGGATAGCGTGAACATCCTGCTGCACGGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATCcag                                                                                                               >  8:29048/1‑147 (MQ=255)
                      cgcTTCACCCAGTTGAAGGATAGCGTGAACATCCTGCTGCACGGCGTTAACCAGTTTGCTGCCGGTGGGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATc                                                                                                                  <  7:68094/144‑1 (MQ=255)
                         ttCACCCAGTTGAAGGATAGCGTGAACATCCTGCTGCACGGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATCCAgcagca                                                                                                          >  1:62592/1‑149 (MQ=255)
                          tCACCCAGTTGAAGGATAGCGTGAACATCCTGCTGCACGGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATCCAgcagca                                                                                                          >  1:85707/1‑148 (MQ=255)
                            aCCCAGTTGAAGGATAGCGTGAACATCCTGCTGCACGGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATc                                                                                                                  >  1:68522/1‑138 (MQ=255)
                            aCCCAGTTGAAGGATAGCGTGAACATCCTGCTGCACGGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATc                                                                                                                  <  2:68522/138‑1 (MQ=255)
                                       ggATAGCGTGAACATCCTGCTGCACGGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGttt                                                                                                                       >  1:28166/1‑122 (MQ=255)
                                       ggATAGCGTGAACATCCTGCTGCACGGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGttt                                                                                                                       <  2:28166/122‑1 (MQ=255)
                                         aTAGCGTGAACATCCTGCTGCACGGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATCCAGCAGCATACGTACCGGCGTCgg                                                                                          >  1:68307/1‑149 (MQ=255)
                                            gCGTGAACATCCTGCTGCACGGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTgg                                                                                       <  4:205911/149‑1 (MQ=255)
                                              gTGAACATCCTGCTGCACGGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTgg                                                                                       >  8:204205/1‑147 (MQ=255)
                                                       ctgctgCACGGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCgg                                                                             <  8:58973/148‑1 (MQ=255)
                                                       ctgctgCACGGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCgg                                                                             <  7:15240/148‑1 (MQ=255)
                                                          ctgcACGGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGtt                                                                           <  2:128980/147‑1 (MQ=255)
                                                          ctgcACGGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGtt                                                                           <  5:209356/147‑1 (MQ=255)
                                                                        ccAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTc                                                           <  8:85102/149‑1 (MQ=255)
                                                                        ccAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTc                                                           >  7:175533/1‑149 (MQ=255)
                                                                          aGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCg                                                          >  8:94792/1‑148 (MQ=255)
                                                                               gctgcCGGTGTGACGGGTAACCGCGTTAAGCTGGCGGGTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGGTGTTGCCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCt                                                    <  5:157667/149‑1 (MQ=255)
                                                                                ctgcCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCt                                                    <  7:94792/148‑1 (MQ=255)
                                                                                ctgcCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCTg                                                   <  7:113155/149‑1 (MQ=255)
                                                                                ctgcCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCTg                                                   <  8:175533/149‑1 (MQ=255)
                                                                                ctgcCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCTg                                                   <  5:107830/149‑1 (MQ=255)
                                                                                 tgcCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTg                                                                     >  3:201048/1‑130 (MQ=255)
                                                                                 tgcCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTg                                                                     <  4:201048/130‑1 (MQ=255)
                                                                                 tgcCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCTgg                                                  >  4:8969/1‑149 (MQ=255)
                                                                                   ccGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCTGGGc                                                <  7:204205/149‑1 (MQ=255)
                                                                                         tgACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCTGGGCTTCAAc                                          >  1:214128/1‑149 (MQ=255)
                                                                                           aCGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCTGGGCTTCAACca                                        >  2:7039/1‑149 (MQ=255)
                                                                                           aCGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCCGCGCCGCCAGGTTGTTGCCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCtt                                                            <  5:179208/129‑1 (MQ=255)
                                                                                           aCGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCCGCGCCGCCAGGTTGTTGCCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCtt                                                            >  6:179208/1‑129 (MQ=255)
                                                                                           aCGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCCGCGCCGCCAGGTTGTTGCCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCtt                                                            >  4:44104/1‑129 (MQ=255)
                                                                                           aCGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCCGCGCCGCCAGGTTGTTGCCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCtt                                                            <  3:44104/129‑1 (MQ=255)
                                                                                               ttAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCTGGGCTTCAACCACAt                                     >  7:109295/1‑148 (MQ=255)
                                                                                                  acctctttAAGCTGGCGGTTAAAGGTTTCAAAATCTACCTTCGCCGCCAGGTTGTTGCCGTTTTTCTACAGCTGCATACGTACCGTCGTCTGTGGCATGAAGCGTTTGAGCTGCAACTGCTTCTGAGCCTGTGCTTCAACCACATAAAt                                 <  8:84337/143‑1 (MQ=255)
                                                                                                  aCCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCTGGGCTTCAACCACATaaa                                  <  2:186593/148‑1 (MQ=255)
                                                                                                    cgcgTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCTGGGCTTCAACCACATAAATCa                               <  6:97286/149‑1 (MQ=255)
                                                                                                       gTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCTGGGCTTCAACCACATAAATCAGtt                            <  2:214128/149‑1 (MQ=255)
                                                                                                           aGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCTGGGCTTCAACCACATAAATCAGTTccac                        <  7:29048/149‑1 (MQ=255)
                                                                                                           aGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCTGGGCTTCAACCACATAAATCAGTTcca                         <  2:68307/148‑1 (MQ=255)
                                                                                                                     tAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCTGGGCTTCAACCACATAAATCAGTTCCACCAACAGCGta              >  7:216935/1‑149 (MQ=255)
                                                                                                                        aGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCTGGGCTTCAACCACATAAATCAGTTCCACCAACAGCGtacc            >  6:30778/1‑148 (MQ=255)
                                                                                                                          gTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCTGGGCTTCAACCACATAAATCAGTTCCACCAACAGCGtacctac         >  3:184274/1‑149 (MQ=255)
                                                                                                                                 aCTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCTGGGCTTCAACCACATAAATCAGTTCCACCAACAGCGTACCTACCGGCAAc  >  3:229697/1‑149 (MQ=255)
                                                                                                                                         |                                                                                                                                            
CACGGGCAGATTTCTCGATCTGCGCTTCACCCAGTTGAAGGATAGCGTGAACATCCTGCTGCACGGCGTTAACCAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCCGCCAGGTTGTTGCCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCAACTGCTTCGGAGCCTGGGCTTCAACCACATAAATCAGTTCCACCAACAGCGTACCTACCGGCAAC  >  NC_000913/60564‑60841

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: ‑