Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 3,440,147 G→A 83.8% L295F (CTT→TTT)  rpoA ← RNA polymerase subunit alpha

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,440,1470GA83.8% 104.1 / 13.8 50L295F (CTT→TTT) rpoARNA polymerase subunit alpha
Reads supporting (aligned to +/- strand):  ref base G (5/3);  new base A (21/20);  total (27/23)
Fisher's exact test for biased strand distribution p-value = 7.06e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.96e-01

CCTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAA  >  NC_000913/3440008‑3440285
                                                                                                                                           |                                                                                                                                          
ccTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAAGtt                                                                                                                                         >  1:931849/1‑143 (MQ=255)
      cAGTAAACCCTTATCCTGTGATCCTGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCGCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAAGTTAGGCGt                                                                                                                                   <  2:234152/143‑1 (MQ=255)
       aGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAAGTTAGGCGtt                                                                                                                                  <  2:950198/143‑1 (MQ=255)
           aacccTTGACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAAGTTAGGCGTTTTaa                                                                                                                              <  1:1008313/140‑1 (MQ=255)
            aggcTTGACCTGTGAGCCGGTTACGCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGGCCACGGGAAGCCAGCACGTCGTTAATCTCAGTAAGAGATTTTTTACCAAAGTTAGGCGTTTTAAg                                                                                                                             <  2:107576/140‑1 (MQ=255)
             aCCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAAGTTAGGCGTGTTAAgg                                                                                                                            <  1:309322/143‑1 (MQ=255)
                  gaCCGGTGATCTGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAAGTTAGGCGTTTTAAGGAGCTc                                                                                                                       <  2:946474/142‑1 (MQ=255)
                         gATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAAGTTAGGCGTTTTAAGGAGCTCAACCTCg                                                                                                                <  1:263483/143‑1 (MQ=255)
                         gATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCACAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCGCAGTAAGAGATTTTTTACCAACGATAGGCGTTTTAAGGAGCTAAACCACg                                                                                                                >  2:392747/1‑143 (MQ=255)
                          acccGGTGACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCTCGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCgg                                                                                                               <  2:579626/141‑1 (MQ=255)
                           tCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAAGTTAGGCGTTTTAAGGAGCTCAACCTCGGt                                                                                                              >  2:597928/1‑143 (MQ=255)
                            ccGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCGTGCCCGGACACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAAGTTAGGCGTTTTAAGGAGCTCAACCTCGGTa                                                                                                             <  1:38972/143‑1 (MQ=255)
                               gTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAAGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGc                                                                                                          <  1:812612/143‑1 (MQ=255)
                                   cTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAAGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTa                                                                                                      <  1:579079/143‑1 (MQ=255)
                                   cTCGTCACCTATAGTGGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAAGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTa                                                                                                      <  2:252623/143‑1 (MQ=255)
                                       tCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGAACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGATTGAAGGAGCTCAACCTCGGTAAGCTGTACCAg                                                                                                  >  2:869211/1‑143 (MQ=255)
                                         aGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATGTTTTACCAAAGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGAt                                                                                                >  1:897482/1‑143 (MQ=255)
                                                   gCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAAGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGAtata                                                                                      <  1:669587/143‑1 (MQ=255)
                                                          gCCAGTTTTCCCGGCGCATGCCCAGCGACCGCCCACGTGCAGCCACCACGTCTTTAATCTCGGGGAGTGAGGCTCTACGACAGCTCGCCGCTGTAAGGAGTTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATa                                                                               <  1:1069774/143‑1 (MQ=255)
                                                             aGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAAGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCAGCGATATAGGGGCTCGCt                                                                            >  2:736321/1‑143 (MQ=255)
                                                             aGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAAGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGcg                                                                            >  2:149451/1‑142 (MQ=255)
                                                               ttttCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAAGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTc                                                                          >  2:122792/1‑143 (MQ=255)
                                                                  gccAGGCGCATGCCCAGCGACAGGCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAAGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGc                                                                       <  1:133437/142‑1 (MQ=255)
                                                                    cAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAAGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCtt                                                                     >  1:235755/1‑143 (MQ=255)
                                                                     aGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAAGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCttt                                                                    >  1:178833/1‑143 (MQ=255)
                                                                       gcgcATGCCCAGAGACAGTACACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAATTTAGGCGCTATAAGGAGCTCAACCTCGGTACGCTGTACTATATGACCGACGTAGTGGAGAGCATATGCTATaa                                                                  >  2:531214/1‑143 (MQ=255)
                                                                               ccAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAAGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGCTATAGTGGATAGCTGCTGCTTTAAGGCAGTTa                                                          >  2:539195/1‑143 (MQ=255)
                                                                                  gagaCAGTCTTTGGGAAGTCAGCACGTCTTTAATCTCAGAAAGAGATTTTTTACCAAAGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCa                                                       <  1:225322/143‑1 (MQ=255)
                                                                                    gaCAGTCGACGGGAAGCCAGCACGTCTTGAATCGCAGTAAGAGATTTTTTACCAAAGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCaga                                                     <  1:620422/143‑1 (MQ=255)
                                                                                         tCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAAGTTAGGCGTTAAAAGGAGCTGAACCTCGGTACGCTGTACCAGACTACCTGCGTAGTGGCACGGTCCTGCGTGAAGGCAGTTAGCAGAGCGGa                                                >  1:775847/1‑143 (MQ=255)
                                                                                             cGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAAGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGt                                            >  1:659125/1‑143 (MQ=255)
                                                                                                gcaGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCaa                                         <  1:166538/141‑1 (MQ=255)
                                                                                                   gCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTATAAGGCAGTTAGCAGAGCGGACAGTCAATTc                                      >  1:645559/1‑143 (MQ=255)
                                                                                                     cAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAAGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCa                                    <  2:235755/143‑1 (MQ=255)
                                                                                                           gTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATCGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGCCAGTCCCTTCCAGATCGt                              >  1:292270/1‑143 (MQ=255)
                                                                                                           gTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGt                              >  1:264985/1‑143 (MQ=255)
                                                                                                           gTCTTTAATCTCAGTAAGAGATTTTTTACCAAAGTTAGGCGTTTTAAGAAGCTCAACCTCGGTACACTGTACCAGATCACCGATATAGTGGATAGCTTACGCTTTAAGGCAGTTAGCATACCGGACAGTCAATTCCAGATCgg                              >  2:380193/1‑142 (MQ=255)
                                                                                                             cTTTAATCTCAGTAAGAGATTTTTTACCAAAGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCa                            >  1:1053768/1‑143 (MQ=255)
                                                                                                              tttAATCTCAGTAAGAGATTTTTTACCAAAGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCaa                           <  1:597928/143‑1 (MQ=255)
                                                                                                                  aTCTCAGTAAGAGATTTTTTACCAAAGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACGGTCAGTTCCAGGTCGTCACCAgg                       >  1:405493/1‑143 (MQ=255)
                                                                                                                     tcAGTAAGAGATTTTTTACCAAAGTTAGGCGTTTTAAGGAGCTCAACCTCTGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTACGGCAGTTCGCAGAGCGGACAGTCCATTCCAGATCATCAGCAGGgcg                    >  2:79450/1‑143 (MQ=255)
                                                                                                                       aGTAAGAGATTTTTTACCAAAGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGTCAGTCAATTCCAGATCGTCAACAGGGCgca                  >  1:464867/1‑143 (MQ=255)
                                                                                                                        gTAAGAGATTTTTTACCAAAGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCgcag                 <  1:559682/143‑1 (MQ=255)
                                                                                                                         taggagaTTTGTTACCAAGGTTAGGCGGTTTAAGGCGCTCAACCTCGGTACGCTGTACCAGATCACGGATAGAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCgcagc                <  1:166198/140‑1 (MQ=255)
                                                                                                                         tAAGAGATTTTTTACCAAAGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCgcagc                >  1:675787/1‑143 (MQ=255)
                                                                                                                           agagATTTTTTACCAAAGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCGcagcag              >  1:23874/1‑143 (MQ=255)
                                                                                                                               aTTTTTTACCAAAGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCGCAGCAggatc          >  1:386065/1‑143 (MQ=255)
                                                                                                                                   tttACCAAAGGTAGGCGTATTAAGGAGCGCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCGCAGCAggatcggat      <  1:277925/143‑1 (MQ=255)
                                                                                                                                     tACCAAAGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACAGATAGAGTGGACAGCTTCTCCTTTCACGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCGCAGCAGgatcggatcg    >  2:1047030/1‑143 (MQ=255)
                                                                                                                                       ccAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCGCAGCAGGAGAGGACCGaa  >  2:969059/1‑143 (MQ=255)
                                                                                                                                           |                                                                                                                                          
CCTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAA  >  NC_000913/3440008‑3440285

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑