Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP009273 4,176,299 A→G 100% N341S (AAC→AGC)  rpoC → RNA polymerase, beta prime subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0092734,176,2990AG99.4% 3027.7 / ‑0.3 805N341S (AAC→AGC) rpoCRNA polymerase, beta prime subunit
Reads supporting (aligned to +/- strand):  ref base A (2/3);  new base G (341/459);  total (343/462)
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
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.

Only 100 of 806 total aligned reads displayed.

TAACAAGCGTCCTCTGAAATCTTTGGCCGACATGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAACCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTAATCACCGTAGGTCCATACCTGCGT  >  CP009273/4176234‑4176363
                                                                 |                                                                
tAACAAGCGTCCTCTGAAATCTTTGGCCGACATGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGcc                                                                <  1:2837552/68‑1 (MQ=255)
 aaCAAGCGTCCTCTGAAATCTTTGGCCGTCATGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCt                                                               <  1:9159580/68‑1 (MQ=255)
  aCAAGCGTCCTCTGAAATCTTTGGCCGACATGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCt                                                               >  1:260021/1‑67 (MQ=255)
   cAAGCGTCCTCTGAAATCTTTGGCCGACATGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCt                                                               >  1:4123850/1‑66 (MQ=255)
   cAAGCGTCCTCTGAAATCTTTGGCCGACATGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCt                                                               >  1:15751073/1‑66 (MQ=255)
   cAAGCGTCCTCTGAAATCTTTGGCCGACATGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCt                                                               >  1:30576237/1‑66 (MQ=255)
   cAAGCGTCCTCTGAAATCTTTGGCCGACATGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCt                                                               >  1:7995436/1‑66 (MQ=255)
   cAAGCGTCCTCTGAAATCTTTGGCCGACATGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCt                                                               >  1:29728123/1‑66 (MQ=255)
   cAAGCGTCCTCTGAAATCTTTGGCCGACATGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCt                                                               >  1:6679062/1‑66 (MQ=255)
   cAAGCGTCCTCTGAAATCTTTGGCCGACATGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCTGc                                                             <  1:7651542/68‑1 (MQ=255)
   cAAGCGTCCTCTGAAATCTTTGGCCGACATGATCAAAGGTAAACAGGGTCGTTTCCGTAAGAGCCt                                                               >  1:16368229/1‑66 (MQ=255)
     aGCGTCCTCTGAAATCTTTGGCCGACATGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCTGCTc                                                           >  1:11760573/1‑68 (MQ=255)
     aGCGTCCTCTGAAATCTTTGGCCGACATGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCTGCTc                                                           >  1:16695438/1‑68 (MQ=255)
     aGCGTCCTCTGAAATCTTTGGCCGACATGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCTGCTc                                                           >  1:12731048/1‑68 (MQ=255)
     aGCGTCCTCTGAAATCTTTGGCCGACATGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCTGCTc                                                           <  1:27631936/68‑1 (MQ=255)
      gCGTCCTCTGAAATCTTTGGCCGACATGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCg                                                          >  1:6902159/1‑68 (MQ=255)
       cGTCCTCTGAAATCTTTGGCCGACATGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCgg                                                         >  1:29088107/1‑68 (MQ=255)
        ggccTCTGAAATCTTTGGCCGACATGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCg                                                          <  1:22083207/64‑1 (MQ=255)
        gTCCTCTGAAATCTTTGGCCGACATGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCg                                                          <  1:30085105/66‑1 (MQ=255)
        gTCCTCTGAAATCTTTGGCCGACATGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCGGt                                                        >  1:3675868/1‑68 (MQ=255)
          ccTCTGAAATCTTTGGCCGACATGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCGGTa                                                       <  1:14950694/67‑1 (MQ=255)
          ccTCTGAAATCTTTGGCCGACATGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCGGTa                                                       <  1:15317805/67‑1 (MQ=255)
          ccTCTGAAATCTTTGGCCGACATGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCGGTa                                                       <  1:18213476/67‑1 (MQ=255)
           ctctGAAATCTTTGGCCGACATGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAg                                                     <  1:27243831/68‑1 (MQ=255)
             ctGAAATCTTTGGCCGACATGATCAAAGGTAAACAGGGGCGTTTCCGTCAGAGCCTGCTCGGTAAGCg                                                   <  1:11387094/68‑1 (MQ=255)
              tGAAATCTTTGGCCGACATGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCgt                                                  <  1:17102808/68‑1 (MQ=255)
              tGAAATCTTTGGCCGACATGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCgt                                                  <  1:12372317/68‑1 (MQ=255)
                  aTCTTTGGCCTACATGATCTAAGGTATACAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTg                                              <  1:19022726/68‑1 (MQ=255)
                  aTCTTTGGCCGACATGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTg                                              <  1:2330135/68‑1 (MQ=255)
                  aTCTTTGGCCGACATGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTg                                              <  1:16928597/68‑1 (MQ=255)
                  aTCTTTGGCCGACATGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTg                                              <  1:19526483/68‑1 (MQ=255)
                  aTCTTTGGCCGACATGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTg                                              <  1:5481027/68‑1 (MQ=255)
                  aTCTTTGGCCGACATGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTg                                              <  1:22814766/68‑1 (MQ=255)
                  aTCTTTGGCCGACATGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTg                                              <  1:24402541/68‑1 (MQ=255)
                  aTCTTTGGCCGACATGATCAAACGTAAACAGGGTCGTTTCAGTCAGAGCCTGCTCGGTAAGCGTGTTg                                              <  1:5603157/68‑1 (MQ=255)
                   tCTTTGGCCGACATGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTg                                              >  1:30345554/1‑67 (MQ=255)
                   tCTTTGGCCGACATGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTg                                              >  1:1730176/1‑67 (MQ=255)
                   tCTTTGGCCGACATGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGa                                             <  1:28592915/68‑1 (MQ=255)
                    cTTTGGCCGACATGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTg                                              >  1:12038080/1‑66 (MQ=255)
                    cTTTGGCCGACATGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTg                                              >  1:20584815/1‑66 (MQ=255)
                    cTTTGGCCGACATGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTg                                              >  1:24764779/1‑66 (MQ=255)
                     tttGGCCGACATGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGact                                           <  1:10184823/68‑1 (MQ=255)
                         gCCGACATGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGactact                                        >  1:27920241/1‑67 (MQ=255)
                                tGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGt                                <  1:3394424/68‑1 (MQ=255)
                                tGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGt                                <  1:20857379/68‑1 (MQ=255)
                                tGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGt                                <  1:31027341/68‑1 (MQ=255)
                                   tCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGt                                >  1:2378230/1‑65 (MQ=255)
                                   tCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTc                              <  1:23507823/67‑1 (MQ=255)
                                   tCAAAGGTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTc                              <  1:14470266/67‑1 (MQ=255)
                                     aaaGGTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGt                           >  1:29489723/1‑68 (MQ=255)
                                     aaaGGTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGt                           >  1:9407016/1‑68 (MQ=255)
                                     aaaGGTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGt                           >  1:13311581/1‑68 (MQ=255)
                                     aaaGGTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGt                           >  1:17480750/1‑68 (MQ=255)
                                      aaGGTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTa                          <  1:31573781/68‑1 (MQ=255)
                                       aGGTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTaa                         <  1:11286072/68‑1 (MQ=255)
                                        ggTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTaa                         >  1:15960523/1‑67 (MQ=255)
                                        ggTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTaa                         >  1:7124568/1‑67 (MQ=255)
                                        ggTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTaa                         >  1:26746168/1‑67 (MQ=255)
                                        ggTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTaa                         >  1:12932248/1‑67 (MQ=255)
                                        ggTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTaa                         >  1:11125609/1‑67 (MQ=255)
                                         gTAAACAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGGCGTTCTGTAAt                        >  1:13994783/1‑67 (MQ=255)
                                           aaaCAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTAATCa                      <  1:28795661/67‑1 (MQ=255)
                                            aaCAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTAATCAcc                    <  1:25134338/68‑1 (MQ=255)
                                            aaCAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTAATCAcc                    <  1:14197630/68‑1 (MQ=255)
                                             aCAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTAATCACCg                   >  1:6541887/1‑68 (MQ=255)
                                             aCAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTAATCACCg                   >  1:5194766/1‑68 (MQ=255)
                                             aCAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTAATCACCg                   >  1:9625775/1‑68 (MQ=255)
                                             aCAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTAATCACCg                   >  1:31963688/1‑68 (MQ=255)
                                             aCAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTAATCACCg                   >  1:13598213/1‑68 (MQ=255)
                                             aCAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTAATCACCg                   >  1:26385059/1‑68 (MQ=255)
                                             aCAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTAATCACCg                   >  1:20389708/1‑68 (MQ=255)
                                             aCAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTAATCACCg                   >  1:21927236/1‑68 (MQ=255)
                                              cAGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTACTGTAATCACCGt                  >  1:11531741/1‑68 (MQ=255)
                                               aGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTAATCACCGTa                 >  1:27788484/1‑68 (MQ=255)
                                               aGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTAATCACCGTa                 >  1:19692037/1‑68 (MQ=255)
                                               aGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTAATCACCGTa                 >  1:21480909/1‑68 (MQ=255)
                                               aGGGTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTAATCACCGTa                 >  1:25465774/1‑68 (MQ=255)
                                                  gTCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTAATCACCGTa                 <  1:1084767/65‑1 (MQ=255)
                                                   tCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTAATCACCGTAGGt              <  1:31278065/67‑1 (MQ=255)
                                                   tCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTAATCACCGTAGGt              <  1:8238701/67‑1 (MQ=255)
                                                   tCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTAATCACCGTAGGt              <  1:8796397/67‑1 (MQ=255)
                                                   tCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTAATCACCGTAGGt              <  1:3813580/67‑1 (MQ=255)
                                                   tCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTAATCACCGTAGGt              <  1:21237230/67‑1 (MQ=255)
                                                   tCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTAATCACCGTAGGt              <  1:4522762/67‑1 (MQ=255)
                                                   tCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTAATCACCGTAGGt              <  1:22453512/67‑1 (MQ=255)
                                                   tCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTAATCACCGTAGGt              <  1:10438651/67‑1 (MQ=255)
                                                   tCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTAATCACCGTAGGt              <  1:19960267/67‑1 (MQ=255)
                                                   tCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTAATCACCGTAGGt              <  1:18680683/67‑1 (MQ=255)
                                                   tCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTAATCACCGTAGGt              <  1:18475317/67‑1 (MQ=255)
                                                   tCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTAATCACCGTAGGt              <  1:17752833/67‑1 (MQ=255)
                                                   tCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTAATCACCGTAGGt              <  1:14774331/67‑1 (MQ=255)
                                                   tCGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGGCGTTCTGTAATCACCGTAGGt              <  1:29340690/67‑1 (MQ=255)
                                                    cGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTAATCACCGTAGGTcc            >  1:4717821/1‑68 (MQ=255)
                                                    cGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTAATCACCGTAGGTcc            <  1:23899635/68‑1 (MQ=255)
                                                    cGTTTCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTAATCACCGTAGGTcc            >  1:3085983/1‑68 (MQ=255)
                                                       ttCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTAATCACCGTAGGTCCATa         <  1:10059610/68‑1 (MQ=255)
                                                        tCCGTCAGAGCCTGCTCGGTACGCGTGTTGACTACTCCGGTCGTTCTGTAATCACCGTAGGTCCATAc        <  1:21627529/68‑1 (MQ=255)
                                                        tCCGTCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTAATCACCGTAGGTCCATa         >  1:24218902/1‑67 (MQ=255)
                                                            tCAGAGCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTAATCACCGTAGGTCCATACCTGc    >  1:3917018/1‑68 (MQ=255)
                                                              agagCCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTAATCACCGTAGGTCCATACCTGCg   >  1:8581354/1‑67 (MQ=255)
                                                                 |                                                                
TAACAAGCGTCCTCTGAAATCTTTGGCCGACATGATCAAAGGTAAACAGGGTCGTTTCCGTCAGAACCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTAATCACCGTAGGTCCATACCTGCGT  >  CP009273/4176234‑4176363

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