Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 1,623,234 A→G E209G (GAA→GGA)  ydfH → DNA‑binding transcriptional regulator rspR

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,623,2340AG98.0% 176.8 / ‑3.6 51E209G (GAA→GGA) ydfHDNA‑binding transcriptional regulator rspR
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base G (28/21);  total (28/23)
Fisher's exact test for biased strand distribution p-value = 4.40e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.89e-01

GCGCTATATGAGTTTCGACCACGTTTCTCCACCAGAAATGCTGTTACGCCAGCATCTTGATATTTTCTCTGCCCTGCAAAAACGTGATGGCGATGCGGTAGAACGTGCAATGACGCAACATTTGCAGGAAATCAGCGAATCCGTGCGCCAGATCCGCCAGGAAAACAGCGACTGGTTTAGCGAAGAGTAATTCATTTCCTCTCATCCCATCCGGGGTGAGAGTCTTTTCCCCCGCCTTATGGCTCATGCATGCATCAAAAA  >  NZ_CP009273/1623106‑1623366
                                                                                                                                |                                                                                                                                    
gcgcTATATGAGTTTCGACCACGTTTCTCCACCAGAAATGCTGTTACGCCAGCATCTTGATATTTTCTCTGCCCTGCAAAAACGTGATGGCGATGCGGTAGAACGTGCAATGACGCAACATTTGCAGGGAATCAGCGaa                                                                                                                            >  1:511069/1‑139 (MQ=255)
   cTATATGAGTTTCGACCACGTTTCTCCACCAGAAATGCTGTTACGCCAGCATCTTGATATTTTCTCTGCCCTGCAAAAACGTGATGGCGATGCGGTAGAACGTGCAATGACGCAACATTTGCAGGGAATCAGCGAATcc                                                                                                                         >  1:57157/1‑139 (MQ=255)
             ttCGACCACGTTTCTCCACCAGAAATGCTGTTACGCCAGCATCTTGATATTTTCTCTGCCCTGCAAAAACGTGATGGCGATGCGGTAGAACGTGCAATGACGCAACATTTGCAGGGAATCAGCGAATCCGTgcgc                                                                                                                   >  1:643770/1‑135 (MQ=255)
              tCGACCACGTTTCTCCACCAGAAATGCTGTTACGCCAGCATCTTGATATTTTCTCTGCCCTGCAAAAACGTGATGGCGATGCGGTAGAACGTGCAATGACGCAACATTTGCAGGGAATCAGCGAATCCGTgcgc                                                                                                                   >  1:240419/1‑134 (MQ=255)
              tCGACCACGTTTCTCCACCAGAAATGCTGTTACGCCAGCATCTTGATATTTTCTCTGCCCTGCAAAAACGTGATGGCGATGCGGTAGAACGTGCAATGACGCAACATTTGCAGGGAATCAGCGAATCCGTgcgc                                                                                                                   >  2:530916/1‑134 (MQ=255)
              tCGACCACGTTTCTCCACCAGAAATGCTGTTACGCCAGCATCTTGATATTTTCTCTGCCCTGCAAAAACGTGATGGCGATGCGGTAGAACGTGCAATGACGCAACATTTGCAGGGAATCAGCGAATCCGTgcgc                                                                                                                   >  1:336334/1‑134 (MQ=255)
              tCGACCACGTTTCTCCACCAGAAATGCTGTTACGCCAGCATCTTGATATTTTCTCTGCCCTGCAAAAACGTGATGGCGATGCGGTAGAACGTGCAATGACGCAACATTTGCAGGGAATCAGCGAATCCGTGCGCCAGa                                                                                                               <  1:768774/138‑1 (MQ=255)
                gACCACGTTTCTCCACCAGAAATGCTGTTACGCCAGCATCTTGATATTTTCTCTGCCCTGCAAAAACGTGATGGCGATGCGGTAGAACGTGCAATGACGCAACATTTGCAGGGAATCAGCGAATCCGTGCGCCAGATcc                                                                                                            >  1:80930/1‑139 (MQ=255)
                gACCACGTTTCTCCACCAGAAATGCTGTTACGCCAGCATCTTGATATTTTCTCTGCCCTGCAAAAACGTGATGGCGATGCGGTAGAACGTGCAATGACGCAACATTTGCAGGGAATCAGCGAATCCGTGCGCCAGATcc                                                                                                            >  2:207717/1‑139 (MQ=255)
                gACCACGTTTCTCCACCAGAAATGCTGTTACGCCAGCATCTTGATATTTTCTCTGCCCTGCAAAAACGTGATGGCGATGCGGTAGAACGTGCAATGACGCAACATTTGCAGGGAATCAGCGAATCCGTGCGCCAGATcc                                                                                                            >  1:406501/1‑139 (MQ=255)
                gACCACGTTTCTCCACCAGAAATGCTGTTACGCCAGCATCTTGATATTTTCTCTGCCCTGCAAAAACGTGATGGCGATGCGGTAGAACGTGCAATGACGCAACATTTGCAGGGAATCAGCGAATCCGTGCGCCAGATcc                                                                                                            >  2:549402/1‑139 (MQ=255)
                  ccACGTTTCTCCACCAGAAATGCTGTTACGCCAGCATCTTGATATTTTCTCTGCCCTGCAAAAACGTGATGGCGATGCGGTAGAACGTGCAATGACGCAACATTTGCAGGGAATCAGCGAATCCGTGCGCCAGATCCGc                                                                                                          <  2:606655/139‑1 (MQ=255)
                  ccACGTTTCTCCACCAGAAATGCTGTTACGCCAGCATCTTGATATTTTCTCTGCCCTGCAAAAACGTGATGGCGATGCGGTAGAACGTGCAATGACGCAACATTTGCAGGGAATCAGCGAATCCGTGCGCCAGATCCGc                                                                                                          <  1:610469/139‑1 (MQ=255)
                         tctcCACCAGAAATGCTGTTACGCCAGCATCTTGATATTTTCTCTGCCCTGCAAAAACGTGATGGCGATGCGGTAGAACGTGCAATGACGCAACATTTGCAGGGAATCAGCGAATCCGTGCGCCAGATCCGCCAGGaa                                                                                                    <  1:207717/138‑1 (MQ=255)
                                           ttACGCCAGCATCTTGATATTTTCTCTGCCCTGCAAAAACGTGATGGCGATGCGGTAGAACGTGCAATGACGCAACATTTGCAGGGAATCAGCGAATCCGTGCGCCAGATCCGCCAGGAAAACAGCGACTGGTTTAg                                                                                   <  1:530916/137‑1 (MQ=255)
                                           ttACGCCAGCATCTTGATATTTTCTCTGCCCTGCAAAAACGTGATGGCGATGCGGTAGAACGTGCAATGACGCAACATTTGCAGGGAATCAGCGAATCCGTGCGCCAGATCCGCCAGGAAAACAGCGACTGGTTTAGCg                                                                                 <  2:177340/139‑1 (MQ=255)
                                             aCGCCAGCATCTTGATATTTTCTCTGCCCTGCAAAAACGTGATGGCGATGCGGTAGAACGTGCAATGACGCAACATTTGCAGGGAATCAGCGAATCCGTGCGCCAGATCCGCCAGGAAAACAGCGACTGGTTTAGCg                                                                                 >  2:134924/1‑137 (MQ=255)
                                                   gCATCTTGATATTTTCTCTGCCCTGCAAAAACGTGATGGCGATGCGGTAGAACGTGCAATGACGCAACATTTGCAGGGAATCAGCGAATCCGTGCGCCAGATCCGCCAGGAAAACAGCGACTGGTTTAGCGAAGAGTaa                                                                         >  1:334522/1‑139 (MQ=255)
                                                   gCATCTTGATATTTTCTCTGCCCTGCAAAAACGTGATGGCGATGCGGTAGAACGTGCAATGACGCAACATTTGCAGGGAATCAGCGAATCCGTGCGCCAGATCCGCCAGGAAAACAGCGACTGGTTTAGCGAAGAGTaa                                                                         >  2:152941/1‑139 (MQ=255)
                                                    cATCTTGATATTTTCTCTGCCCTGCAAAAACGTGATGGCGATGCGGTAGAACGTGCAATGACGCAACATTTGCAGGGAATCAGCGAATCCGTGCGCCAGATCCGCCAGGAAAACAGCGAc                                                                                           <  1:340841/120‑1 (MQ=255)
                                                    cATCTTGATATTTTCTCTGCCCTGCAAAAACGTGATGGCGATGCGGTAGAACGTGCAATGACGCAACATTTGCAGGGAATCAGCGAATCCGTGCGCCAGATCCGCCAGGAAAACAGCGAc                                                                                           >  2:340841/1‑120 (MQ=255)
                                                     aTCTTGATATTTTCTCTGCCCTGCAAAAACGTGATGGCGATGCGGTAGAACGTGCAATGACGCAACATTTGCAGGGAATCAGCGAATCCGTGCGCCAGATCCGCCAGGAAAACAGCGACTGGTTTAGCGaa                                                                               <  1:304717/131‑1 (MQ=255)
                                                     aTCTTGATATTTTCTCTGCCCTGCAAAAACGTGATGGCGATGCGGTAGAACGTGCAATGACGCAACATTTGCAGGGAATCAGCGAATCCGTGCGCCAGATCCGCCAGGAAAACAGCGACTGGTTTAGCGaa                                                                               >  2:304717/1‑131 (MQ=255)
                                                              ttttCTCTGCCCTGCAAAAACGTGATGGCGATGCGGTAGAACGTGCAATGACGCAACATTTGCAGGGAATCAGCGAATCCGTGCGCCAGATCCGCCAGGAAAACAGCGACTGGTTTAGCGAAGAGTAATTCATTTCctc                                                              <  1:442451/139‑1 (MQ=255)
                                                                  ctctGCCCTGCAAAAACGTGATGGCGATGCGGTAGAACGTGCAATGACGCAACATTTGCAGGGAATCAGCGAATCCGTGCGCCAGATCCGCCAGGAAAACAGCGACTGGTTTAGCGAAGAGTAATTCATTTCCTCTcat                                                          >  2:131396/1‑139 (MQ=255)
                                                                     tGCCCTGCAAAAACGTGATGGCGATGCGGTAGAACGTGCAATGACGCAACATTTGCAGGGAATCAGCGAATCCGTGCGCCAGATCCGCCAGGAAAACAGCGACTGGTTTAGCGAAGAGTAATTCATTTCCTCTcat                                                          <  2:80930/136‑1 (MQ=255)
                                                                          tGCAAAAACGTGATGGCGATGCGGTAGAACGTGCAATGACGCAACATTTGCAGGGAATCAGCGAATCCg                                                                                                                        >  1:699447/1‑69 (MQ=255)
                                                                          tGCAAAAACGTGATGGCGATGCGGTAGAACGTGCAATGACGCAACATTTGCAGGGAATCAGCGAATCCg                                                                                                                        <  2:699447/69‑1 (MQ=255)
                                                                          tGCAAAAACGTGATGGCGATGCGGTAGAACGTGCAATGACGCAACATTTGCAGGGAATCAGCGAATCCGTGCGCCAGATCCGCCAGGAAAACAGCGACTGGTTTAGCGAAGAGTAATTCATTTCCTCTCATCCCATCCg                                                  >  2:753076/1‑139 (MQ=255)
                                                                                aaCGTGATGGCGATGCGGTAGAACGTGCAATGACGCAACATTTGCAGGGAATCAGCGAATCCGTGCGCCAGATCCGCCAGGAAAACAGCGACTGGTTTAGCGAAGAGTAATTCATTTCCTCTCATCCCATCCGGGGTga                                            <  1:753076/139‑1 (MQ=255)
                                                                                  cGTGATGGCGATGCGGTAGAACGTGCAATGACGCAACATTTGCAGGGAATCAGCGAATCCGTGCGCCAGATCCGCCAGGAAAACAGCGACTGGTTTAGCGAAGAGTAATTCATTTCCTCTCATCCCATCCGGGGTgaga                                          <  2:334522/139‑1 (MQ=255)
                                                                                      aTGGCGATGCGGTAGAACGTGCAATGACGCAACATTTGCAGGGAATCAGCGAATCCGTGCGCCAGATCCGCCAGGAAAACAGCGACTGGTTTAGCGAAGAGTAATTCATTTCCTCTCATCCCATCCGGGGTGAGAGTCt                                      <  2:662240/139‑1 (MQ=255)
                                                                                       tGGCGATGCGGTAGAACGTGCAATGACGCAACATTTGCAGGGAATCAGCGAATCCGTGCGCCAGATCCGCCAGGAAAACAGCGACTGGTTTAGCGAAGAGTAATTCATTTCCTCTCATCCCATCCGGGGTGAGAGTCtt                                     >  2:1085/1‑139 (MQ=255)
                                                                                             tGCGGTAGAACGTGCAATGACGCAACATTTGCAGGGAATCAGCGAATCCGTGCGCCAGATCCGCCAGGAAAACAGCGACTGGTTTAGCGAAGAGTAATTCATTTCCTCTCATCCCATCCGGGGTGAGAGTCTTTTcccc                               >  1:562872/1‑139 (MQ=255)
                                                                                                    gAACGTGCAATGACGCAACATTTGCAGGGAATCAGCGAATCCGTGCGCCAGATCCGCCAGGAAAACAGCGACTGGTTTAGCGGAGAGTAATTCATTTCCTCTCATCCCATCCGGGGTGAGAGTCTTTTCCCCCGCCTTa                        <  2:643770/139‑1 (MQ=255)
                                                                                                    gAACGTGCAATGACGCAACATTTGCAGGAAATCAGCGAATCCGTGCGCCAGATCCGCCAGGAAAACAGCGACTGGTTTAGCGAAGAGTAATTCATTTCCTCTCATCCCATCCGGGGTGAGAGTCTTTTCCCCCGCCTTa                        <  1:310242/139‑1 (MQ=255)
                                                                                                     aaCGTGCAATGACGCAACATTTGCAGGGAATCAGCGAATCCGTGCGCCAGATCCGCCAGGAAAACAGCGACTGGTTTAGCGAAGAGTAATTCATTTCCTCTCATCCCATCCGGGGTGAGAGTCTTTTCCCCCGCCTTAt                       <  1:631509/139‑1 (MQ=255)
                                                                                                       cGTGCAATGACGCAACATTTGCAGGGAATCAGCGAATCCGTGCGCCAGATCCGCCAGGAAAACAGCGAc                                                                                           <  1:121366/69‑1 (MQ=255)
                                                                                                       cGTGCAATGACGCAACATTTGCAGGGAATCAGCGAATCCGTGCGCCAGATCCGCCAGGAAAACAGCGAc                                                                                           >  2:121366/1‑69 (MQ=255)
                                                                                                         tGCAATGACGCAACATTTGCAGGGAATCAGCGAATCCGTGCGCCAGATCCGCCAGGAAAACAGCGACTGGTTTAGCGAAGAGTAATTCATTTCCTCTCATCCCATCCGGGGTGAGAGTCTTTTCCCCCGCCTTa                        >  2:688765/1‑134 (MQ=255)
                                                                                                         tGCAACGACGCAACATTTGCAGGCAATCAGCGAATCCGTGCGCCAGATCCGCCAGGAAAACAGCGACTGGTTTAGCGAAGAGTAATTCATTTCCTCTCATCCCATCCGGGGTGAGAGTCTTTTCCCCCGCCTTa                        <  1:688765/134‑1 (MQ=255)
                                                                                                          gCAATGACGCAACATTTGCAGGGAATCAGCGAATCCGTGCGCCAGATCCGCCAGGAAAACAGCGACTGGTTTAGCGAAGAGTAATTCATTTCCTCTCATCCCATCCGGGGTGAGAGTCTTTTcccc                               >  2:754241/1‑126 (MQ=255)
                                                                                                          gCAATGACGCAACATTTGCAGGGAATCAGCGAATCCGTGCGCCAGATCCGCCAGGAAAACAGCGACTGGTTTAGCGAAGAGTAATTCATTTCCTCTCATCCCATCCGGGGTGAGAGTCTTTTcccc                               <  1:754241/126‑1 (MQ=255)
                                                                                                          gCAATGACGCAACATTTGCAGGGAATCAGCGAATCCGTGCGCCAGATCCGCCAGGAAAACAGCGACTGGTTTAGCGAAGAGTAATTCATTTCCTCTCATCCCATCCGGGGTGAGAGTCTTTTCCCCCGCCTTATGGCt                   >  1:542136/1‑138 (MQ=255)
                                                                                                          gCAATGACGCAACATTTGCAGGGAATCAGCGAATCCGTGCGCCAGATCCGCCAGGAAAACAGCGACTGGTTTAGCGAAGAGTAATTCATTTCCTCTCATCCCATCCGGGGTGAGAGTCTTTTCCCCCGCCTTATGGCt                   >  1:324057/1‑138 (MQ=255)
                                                                                                            aaTGACGCAACATTTGCAGGGAATCAGCGAATCCGTGCGCCAGATCCGCCAGGAAAACAGCGACTGGTTTAGCGAAGAGTAATTCATTTCCTCTCATCCCATCCGGGGTGAGAGTCTTTTCCCCCGCCTTATGGCTcat                >  1:29610/1‑139 (MQ=255)
                                                                                                                          tGCAGGGAATCAGCGAATCCGTGCGCCAGATCCGCCAGGAAAACAGCGACTGGTTTAGCGAAGAGTAATTCATTTCCTCTCATCCCATCCGGGGTga                                            >  2:208143/1‑97 (MQ=255)
                                                                                                                          tGCAGGGAATCAGCGAATCCGTGCGCCAGATCCGCCAGGAAAACAGCGACTGGTTTAGCGAAGAGTAATTCATTTCCTCTCATCCCATCCGGGGTga                                            <  1:208143/97‑1 (MQ=255)
                                                                                                                           gCAGGGAATCAGCGAATCCGTGCGCCAGATCCGCCAGGAAAACAGCGACTGGTTTAGCGAAGAGTAATTCATTTCCTCTCATCCCATCCGGGGTGAGAGTCTTTTCCCCCGCCTTa                        <  2:341275/116‑1 (MQ=255)
                                                                                                                           gCAGGGAATCAGCGAATCCGTGCGCCAGATCCGCCAGGAAAACAGCGACTGGTTTAGCGAAGAGTAATTCATTTCCTCTCATCCCATCCGGGGTGAGAGTCTTTTCCCCCGCCTTa                        >  1:341275/1‑116 (MQ=255)
                                                                                                                           gCAGGGAATCAGCGAATCCGTGCGCCAGATCCGCCAGGAAAACAGCGACTGGTTTAGCGAAGAGTAATTCATTTCCTCTCATCCCATCCGGGGTGAGAGTCTTTTCCCCCGCCTTATGGCTCATGCATGCATCaaaaa  <  1:1085/138‑1 (MQ=255)
                                                                                                                                |                                                                                                                                    
GCGCTATATGAGTTTCGACCACGTTTCTCCACCAGAAATGCTGTTACGCCAGCATCTTGATATTTTCTCTGCCCTGCAAAAACGTGATGGCGATGCGGTAGAACGTGCAATGACGCAACATTTGCAGGAAATCAGCGAATCCGTGCGCCAGATCCGCCAGGAAAACAGCGACTGGTTTAGCGAAGAGTAATTCATTTCCTCTCATCCCATCCGGGGTGAGAGTCTTTTCCCCCGCCTTATGGCTCATGCATGCATCAAAAA  >  NZ_CP009273/1623106‑1623366

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑