Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 3,593,877 T→C A89A (GCA→GCG)  rpoH ← RNA polymerase sigma factor RpoH

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092733,593,8770TC100.0% 135.6 / NA 40A89A (GCA→GCG) rpoHRNA polymerase sigma factor RpoH
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (20/20);  total (20/20)

TTTGCGCTGCGCTTTGGTGGTCGCAACTTTGACGATACGCCAGTTACGCAGAACGTATTCGTGGATCTCTGCTTTGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACTGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTACGAGCAATATGAACAACAAACCGCAGGTGAGACAGGATCAGCGTTTTAGCTGCTTCCAGATCGCCA  >  NZ_CP009273/3593742‑3594012
                                                                                                                                       |                                                                                                                                       
tttGCGCTGCGCTTTGGTGGTCGCAACTTTGACGATACGCCAGTTACGCAGAACGTATTCGTGGATCTCTGCTTTGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCt                                                                                                                                      >  1:483597/1‑139 (MQ=255)
tttGCGCTGCGCTTTGGTGGTCGCAACTTTGACGATACGCCAGTTACGCAGAACGTATTCGTGGATCTCTGCTTTGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCt                                                                                                                                      <  1:468866/139‑1 (MQ=255)
         cgctTTGGTGGTCGCAACTTTGACGATACGCCAGTTACGCAGAACGTATTCGTGGATCTCTGCTTTGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAgg                                                                                                                             <  1:547514/139‑1 (MQ=255)
          gctTTGGTGGTCGCAACTTTGACGATACGCCAGTTACGCAGAACGTATTCGTGGATCTCTGCTTTGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTtcat                                                                                                                                 >  2:355864/1‑134 (MQ=255)
          gctTTGGTGGTCGCAACTTTGACGATACGCCAGTTACGCAGAACGTATTCGTGGATCTCTGCTTTGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTtcat                                                                                                                                 <  1:355864/134‑1 (MQ=255)
          gctTTGGTGGTCGCAACTTTGACGATACGCCAGTTACGCAGAACGTATTCGTGGATCTCTGCTTTGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGc                                                                                                                            <  2:428069/139‑1 (MQ=255)
                      gCAACTTTGACGATACGCCAGTTACGCAGAACGTATTCGTGGATCTCTGCTTTGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCtt                                                                                                                >  2:279541/1‑139 (MQ=255)
                                    aCGCCAGTTACGCAGAACGTATTCGTGGATCTCTGCTTTGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGCTGTTACCTTCCTGAATCAAATcc                                                                                                  >  2:40868/1‑139 (MQ=255)
                                              cGCAGAACGTATTCGTGGATCTCTGCTTTGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCCCTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGc                                                                                         <  2:162741/138‑1 (MQ=255)
                                                    aCGTATTCGTGGATCTCTGCTTTGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCa                                                                                   <  2:484345/138‑1 (MQ=255)
                                                    aCGTATTCGTGGATCTCTGCTTTGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCa                                                                                   >  1:484345/1‑138 (MQ=255)
                                                            gTGGATCTCTGCTTTGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCa                                                                          <  2:22152/139‑1 (MQ=255)
                                                                    ctGCTTTGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTAc                                                                   >  2:92323/1‑138 (MQ=255)
                                                                       cTTTGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTACGa                                                                 <  1:92323/137‑1 (MQ=255)
                                                                          tGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTACGAGCa                                                              <  1:279541/137‑1 (MQ=255)
                                                                          tGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTACGAGCa                                                              <  2:512432/137‑1 (MQ=255)
                                                                          tGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTACGAGCa                                                              <  1:197573/137‑1 (MQ=255)
                                                                            aTCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGc                                                                                                <  2:560291/101‑1 (MQ=255)
                                                                            aTCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGc                                                                                                >  1:560291/1‑101 (MQ=255)
                                                                            aTCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCa                                                                          >  2:87111/1‑123 (MQ=255)
                                                                            aTCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCa                                                                          <  1:87111/123‑1 (MQ=255)
                                                                            aTCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTACGa                                                                 >  1:236121/1‑132 (MQ=255)
                                                                            aTCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTACGa                                                                 <  2:236121/132‑1 (MQ=255)
                                                                                 gTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGcc                                                                                               <  2:11412/97‑1 (MQ=255)
                                                                                 gTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGcc                                                                                               >  1:11412/1‑97 (MQ=255)
                                                                                 gTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTACGAGCAATATGaac                                                      >  1:520380/1‑138 (MQ=255)
                                                                                 gTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTACGAGCAATATGaac                                                      >  1:385402/1‑138 (MQ=255)
                                                                                    aaCGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGc                                                                                         >  2:275574/1‑100 (MQ=255)
                                                                                    aaCGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGc                                                                                         <  1:275574/100‑1 (MQ=255)
                                                                                    aaCGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTACGAGCAATATGaacaac                                                   >  2:137305/1‑138 (MQ=255)
                                                                                    aaCGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTACGAGCAATATGaacaac                                                   >  2:348940/1‑138 (MQ=255)
                                                                                      cGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTACGAGCAATATGAACAACaaa                                                >  1:469492/1‑139 (MQ=255)
                                                                                                   cAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTACGAGCAATATGAACAACAAACCGCAGGTgaga                                    >  1:247457/1‑138 (MQ=255)
                                                                                                        gcACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTACGAGCAATATGAACAACAAACCGCAGGTGAGACAGGAt                              <  1:29332/139‑1 (MQ=255)
                                                                                                           cacCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTACGAGCAATATGAACAACAAACCGCAGGTGAGACAGGATCAg                           >  2:142501/1‑139 (MQ=255)
                                                                                                                            aaaCGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGc                                                                                         <  2:274918/60‑1 (MQ=255)
                                                                                                                            aaaCGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTACGAGCAATATGAACAACAAACCGCAGGTGAGACAGGATCAGCGTTTTAGCTGCTTc            >  2:119911/1‑137 (MQ=255)
                                                                                                                            aaaCGGCGCACCGCTTTCATAAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGc                                                                                         >  1:274918/1‑60 (MQ=255)
                                                                                                                               cGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTACGAGCAATATGAACAACAAACCGCAGGTGAGACAGGATCAGCGTTTTAGCTGCTTCCAGAt       <  2:247457/139‑1 (MQ=255)
                                                                                                                                    cACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTACGAGCAATATGAACAACAAACCGCAGGTGAGACAGGATCAGCGTTTTAGCTGCTTCCAGATCGCCa  <  1:119911/139‑1 (MQ=255)
                                                                                                                                       |                                                                                                                                       
TTTGCGCTGCGCTTTGGTGGTCGCAACTTTGACGATACGCCAGTTACGCAGAACGTATTCGTGGATCTCTGCTTTGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACTGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTACGAGCAATATGAACAACAAACCGCAGGTGAGACAGGATCAGCGTTTTAGCTGCTTCCAGATCGCCA  >  NZ_CP009273/3593742‑3594012

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑