Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,213,803 T→C S253P (TCT→CCT)  rpoD → RNA polymerase, sigma 70 (sigma D) factor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,213,8030TC100.0% 666.9 / NA 165S253P (TCT→CCT) rpoDRNA polymerase, sigma 70 (sigma D) factor
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (76/89);  total (76/89)

Only 100 of 165 total aligned reads displayed.

CGAAAGGTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGTCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGTTTGACTA  >  NC_000913/3213756‑3213849
                                               |                                              
cGAAAGGTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCt                                              <  2:1509627/50‑1 (MQ=255)
cGAAAGGTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCt                                              >  1:3349560/1‑50 (MQ=255)
cGAAAGGTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCt                                              <  2:2960040/50‑1 (MQ=255)
 gAAAGGTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCt                                              >  1:1227631/1‑49 (MQ=255)
 gAAAGGTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTg                                             <  1:673655/50‑1 (MQ=255)
 gAAAGGTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTg                                             <  2:4241191/50‑1 (MQ=255)
  aaaGGTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTg                                             >  2:3063590/1‑49 (MQ=255)
  aaaGGTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTg                                             >  1:5093519/1‑49 (MQ=255)
  aaaGGTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTg                                             >  2:4567731/1‑49 (MQ=255)
   aaGGTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTg                                             >  2:4431546/1‑48 (MQ=255)
   aaGGTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTg                                             >  1:2676753/1‑48 (MQ=255)
   aaGGTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGaa                                           <  2:1095725/50‑1 (MQ=255)
    aGGTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAg                                          >  1:5589805/1‑50 (MQ=255)
    aGGTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAg                                          <  1:5527910/50‑1 (MQ=255)
     ggTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAg                                          >  2:4089731/1‑49 (MQ=255)
     ggTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGt                                         <  2:4391073/50‑1 (MQ=255)
     ggTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGt                                         <  1:4908279/50‑1 (MQ=255)
     ggTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGt                                         <  1:231681/50‑1 (MQ=255)
      gTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTa                                        >  2:3431310/1‑50 (MQ=255)
      gTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTa                                        >  1:5040474/1‑50 (MQ=255)
       tCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTAt                                       <  2:4632353/50‑1 (MQ=255)
       tCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTAt                                       <  1:11560/50‑1 (MQ=255)
         gCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTAtt                                      >  2:4656841/1‑49 (MQ=255)
         gCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTc                                     <  2:1948158/50‑1 (MQ=255)
          cAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTc                                     >  2:3726214/1‑49 (MQ=255)
          cAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTc                                     >  2:2609914/1‑49 (MQ=255)
          cAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCa                                    <  2:4005166/50‑1 (MQ=255)
          cAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCa                                    <  1:1440582/50‑1 (MQ=255)
           aGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCaa                                   <  1:3904030/50‑1 (MQ=255)
           aGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCa                                    >  1:1864772/1‑49 (MQ=255)
            gTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCaaa                                  <  1:224474/50‑1 (MQ=255)
             tCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCaaa                                  >  1:5633630/1‑49 (MQ=255)
             tCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAAc                                 <  1:3994885/50‑1 (MQ=255)
             tCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAAc                                 <  2:2029476/50‑1 (MQ=255)
             tCACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAAc                                 <  2:5270362/50‑1 (MQ=255)
              cACGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCaaa                                  >  1:2709340/1‑48 (MQ=255)
               aCGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAg                               >  2:5570339/1‑50 (MQ=255)
                cGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGt                              >  2:2833585/1‑50 (MQ=255)
                cGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGt                              <  1:3011538/50‑1 (MQ=255)
                cGCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGt                              >  2:4873822/1‑50 (MQ=255)
                 gCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGtt                             <  1:5342457/50‑1 (MQ=255)
                 gCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGtt                             <  1:1682815/50‑1 (MQ=255)
                 gCTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGtt                             <  2:3764087/50‑1 (MQ=255)
                  cTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTc                            <  1:4568563/50‑1 (MQ=255)
                  cTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTc                            >  2:2564320/1‑50 (MQ=255)
                  cTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTc                            <  2:5599343/50‑1 (MQ=255)
                  cTACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTc                            <  1:4472371/50‑1 (MQ=255)
                   tACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTcc                           >  1:3043314/1‑50 (MQ=255)
                   tACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTcc                           >  1:884556/1‑50 (MQ=255)
                   tACCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTcc                           >  2:277957/1‑50 (MQ=255)
                    aCCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCg                          >  1:2068679/1‑50 (MQ=255)
                    aCCGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCg                          >  2:3859697/1‑50 (MQ=255)
                     ccGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTcc                           <  1:1055422/48‑1 (MQ=255)
                     ccGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCg                          <  2:1680472/49‑1 (MQ=255)
                     ccGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCg                          <  1:3379964/49‑1 (MQ=255)
                     ccGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCg                          <  2:2225986/49‑1 (MQ=255)
                     ccGCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGc                         >  1:724666/1‑50 (MQ=255)
                       gCTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCt                       <  2:821042/50‑1 (MQ=255)
                        cTCAGGAAGAGATCCTGAAACTGCCTGCAGTATTCAAACAGTTCCGCCTg                      <  2:4300672/50‑1 (MQ=255)
                        cTCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTg                      >  2:57791/1‑50 (MQ=255)
                         tCAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTgg                     >  2:4828158/1‑50 (MQ=255)
                          cAGGAAGAGATCCTGCAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGt                    >  2:1874426/1‑50 (MQ=38)
                          cAGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGt                    >  1:2573353/1‑50 (MQ=255)
                           aGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGt                    <  2:5646312/49‑1 (MQ=255)
                           aGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGt                    <  2:3338322/49‑1 (MQ=255)
                           aGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTg                   >  2:60586/1‑50 (MQ=255)
                           aGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTg                   <  1:1449003/50‑1 (MQ=255)
                           aGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTg                   <  1:5425551/50‑1 (MQ=255)
                           aGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTg                   >  2:3178563/1‑50 (MQ=255)
                           aGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTg                   <  1:3158114/50‑1 (MQ=255)
                           aGGAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTg                   >  1:3170349/1‑50 (MQ=255)
                            ggAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGc                  <  2:4921022/50‑1 (MQ=255)
                             gAAGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGcc                 <  1:3246283/50‑1 (MQ=255)
                              aaGAGATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGcc                 >  2:2474414/1‑49 (MQ=255)
                               agagATCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCg                >  1:3571363/1‑49 (MQ=255)
                                gagaTCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGaa              <  2:3867556/50‑1 (MQ=255)
                                 agaTCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAg             >  2:4182027/1‑50 (MQ=255)
                                  gaTCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAg             >  2:4288523/1‑49 (MQ=255)
                                  gaTCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGc            <  1:1099792/50‑1 (MQ=255)
                                   aTCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCa           <  2:3966114/50‑1 (MQ=255)
                                   aTCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCa           <  2:1560006/50‑1 (MQ=255)
                                   aTCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCa           <  1:1880762/50‑1 (MQ=255)
                                    tCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAg          >  1:4826315/1‑50 (MQ=255)
                                    tCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAg          <  2:1048637/50‑1 (MQ=255)
                                    tCCTGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAg          >  1:1877411/1‑50 (MQ=255)
                                      cTGAAACTGCCTGAAGTATTCAAACAGTGCCGCCTGGTGCCGAAGCAgg         <  2:1802149/49‑2 (MQ=38)
                                       tGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGttt       >  1:5022282/1‑50 (MQ=255)
                                       tGAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGttt       >  1:4968726/1‑50 (MQ=255)
                                        gAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGttt       >  1:595679/1‑49 (MQ=255)
                                        gAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGttt       >  1:2085701/1‑49 (MQ=255)
                                        gAAACTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGttt       >  2:726507/1‑49 (MQ=255)
                                         aaaCTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGttt       <  1:4566035/48‑1 (MQ=255)
                                         aaaCTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGTTTGa     >  1:2299377/1‑50 (MQ=255)
                                         aaaCTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGTTTGa     >  2:3560558/1‑50 (MQ=255)
                                          aaCTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGTTTGAc    <  2:5156732/50‑1 (MQ=255)
                                           aCTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGTTTGACt   <  1:1347062/50‑1 (MQ=255)
                                           aCTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGTTTGACt   <  2:2301100/50‑1 (MQ=255)
                                            cTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGTTTGACTa  >  2:3378465/1‑50 (MQ=255)
                                            cTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGTTTGACTa  <  1:1982830/50‑1 (MQ=255)
                                            cTGCCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGTTTGACTa  <  2:725820/50‑1 (MQ=255)
                                               |                                              
CGAAAGGTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGTCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGTTTGACTA  >  NC_000913/3213756‑3213849

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑