Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,659,825 C→T 11.3% M193I (ATG→ATA)  wzxE ← O‑antigen translocase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,659,8250CT11.3% 208.9 / 14.1 71M193I (ATG→ATA) wzxEO‑antigen translocase
Reads supporting (aligned to +/- strand):  ref base C (27/36);  new base T (4/4);  total (31/40)
Fisher's exact test for biased strand distribution p-value = 7.22e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.48e-01

CTGCCCTGCCAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGACCCAGCAACGCCCCTTCATAACC  >  W3110S.gb/3659756‑3659893
                                                                     |                                                                    
ctgccctgccAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACa                                                                     >  1:3763992/1‑71 (MQ=255)
 tgccctgccAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAAc                                                                      >  1:1449679/1‑69 (MQ=255)
 tgccctgccAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACat                                                                    >  1:2282685/1‑71 (MQ=255)
   ccctgccAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACatga                                                                  <  1:3461025/71‑1 (MQ=255)
   ccctgccAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACatg                                                                   <  1:780806/70‑1 (MQ=255)
   ccctgccAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACat                                                                    <  1:3428840/69‑1 (MQ=255)
     ctgccAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAATatgatg                                                                >  1:3100792/1‑71 (MQ=255)
     ctgccAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACat                                                                    <  1:514712/67‑1 (MQ=255)
      tgtcAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATgg                                                               >  1:478103/4‑71 (MQ=255)
      tgccAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATgg                                                               >  1:4148938/1‑71 (MQ=255)
            aCCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAg                                                         >  1:538421/1‑71 (MQ=255)
             ccGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAgg                                                        <  1:1367268/71‑1 (MQ=255)
             ccGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAgg                                                        <  1:4361151/71‑1 (MQ=255)
             ccGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAg                                                         >  1:3975779/1‑70 (MQ=255)
             ccGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATCATGGCGGCAgg                                                        <  1:55552/71‑1 (MQ=255)
                ttATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAAt                                                     <  1:402325/71‑1 (MQ=255)
                  aTCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAAc                                                                      >  1:859798/1‑52 (MQ=255)
                     ccAGCTGGGTTTCAGATAGCTTAAAGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTacca                                                <  1:1616171/71‑1 (MQ=255)
                      cAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTaccac                                               <  1:1237547/71‑1 (MQ=255)
                       aGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTaccac                                               >  1:2085712/1‑70 (MQ=255)
                       aGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTacca                                                >  1:160767/1‑69 (MQ=255)
                       aGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTa                                                   >  1:2909941/1‑66 (MQ=255)
                       aGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTa                                                   >  1:2915140/1‑66 (MQ=255)
                         cTGGGTTTCAGATAGCTTAACGGGACGACACCACGTTTGATCAAc                                                                      <  1:1352693/45‑1 (MQ=255)
                          tGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAAtt                                                    <  1:4403947/62‑1 (MQ=255)
                          tGGGGTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAAtt                                                    <  1:4224736/62‑1 (MQ=255)
                            ggTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAAc                                                                      >  1:532018/1‑42 (MQ=255)
                            ggTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACat                                                                    <  1:1691684/44‑1 (MQ=255)
                            ggTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACat                                                                    <  1:313745/44‑1 (MQ=255)
                            ggTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAgcgc                                         >  1:3343865/1‑71 (MQ=255)
                            ggTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAgcgc                                         <  1:976262/71‑1 (MQ=255)
                            ggTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAgcgc                                         >  1:3094004/1‑71 (MQ=255)
                            ggTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAgcgc                                         <  1:1225733/71‑1 (MQ=255)
                            ggTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAgcgc                                         <  1:155451/71‑1 (MQ=255)
                            ggTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAgcg                                          <  1:2848483/70‑1 (MQ=255)
                              tttCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCTgcg                                          <  1:2762990/68‑1 (MQ=255)
                                tCAGATAGCTTAACGGGATGACACCACGTTTGATCAATatga                                                                  >  1:1193365/1‑42 (MQ=255)
                                tCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCggg                                      <  1:1749249/70‑1 (MQ=255)
                                 cAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGa                                     <  1:3402230/70‑1 (MQ=255)
                                  aGATAGCTTAACGGGATGACACCACGTTTGATCAATATGATGGCGGCAGGAATTACCACCAGCGCGGGaa                                    <  1:2012363/70‑1 (MQ=255)
                                    aTAGCTTAACGGGATGACACCACGTTTGATCAATATGATGGCGGCAGGAATTACCACCAGCGCGGGAAt                                   >  1:2407272/1‑69 (MQ=255)
                                    aTAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTaccac                                               >  1:3951702/1‑57 (MQ=255)
                                     tAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAgt                                                        <  1:3683504/47‑2 (MQ=255)
                                      aGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAgc                               >  1:1037756/1‑71 (MQ=255)
                                       gCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAgc                               <  1:2016163/70‑1 (MQ=255)
                                         ttAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAg                                                         <  1:4483951/42‑1 (MQ=255)
                                         ttAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAg                                                         <  1:4478682/42‑1 (MQ=255)
                                         ttAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAgcg                              <  1:66852/69‑1 (MQ=255)
                                          tAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAAt                                                     >  1:1456424/1‑45 (MQ=255)
                                          tAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAgcgc                             >  1:3483590/1‑69 (MQ=255)
                                           aaCGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCa                                 >  1:1917721/1‑64 (MQ=255)
                                           aaCGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCTCCa                           <  1:1584959/70‑1 (MQ=255)
                                            aCGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAAt                                   <  1:4153643/61‑1 (MQ=255)
                                             cGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTAccacca                                             <  1:106959/50‑1 (MQ=255)
                                              gggATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGAcc                       >  1:4258975/1‑71 (MQ=255)
                                                gATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAg                                            >  1:3075216/1‑48 (MQ=255)
                                                 aTGACACCACGTTTGATCAATATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGACCCAg                    <  1:3242351/71‑1 (MQ=255)
                                                 aTGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGACCCAg                    <  1:3435578/71‑1 (MQ=255)
                                                   gACACCACGTTTGATCAATATGATGGCGGCAGGAATTaccac                                               <  1:2441522/42‑1 (MQ=255)
                                                     caccacGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGa                                     <  1:3514373/50‑1 (MQ=255)
                                                      accacGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCggg                                      <  1:3752572/48‑1 (MQ=255)
                                                      accacGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCa                           >  1:3224287/1‑59 (MQ=255)
                                                       ccacGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAAt                                   >  1:4072058/1‑50 (MQ=255)
                                                        cacGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGACCCAGCAACGcc             >  1:4524795/1‑71 (MQ=255)
                                                          cGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGaa                                    >  1:1527505/1‑46 (MQ=255)
                                                          cGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGACCCAGCAACGcccc           <  1:4493628/71‑1 (MQ=255)
                                                            tttGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGACCCAGCAACGCCCCt          >  1:3127393/1‑70 (MQ=255)
                                                              tGATCAACATGATGGCGGCAGGAATTACCACCAGCGCggg                                      >  1:4502530/1‑40 (MQ=255)
                                                                atgaaCATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGACCCAGCAACGCCCCTTCATa     <  1:1464346/68‑1 (MQ=255)
                                                                aTCAATATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGACCCAGCAACGCCCCTTCAt      <  1:1850890/70‑1 (MQ=255)
                                                                aTCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGACCCAGCAACGCCCCTTCAt      >  1:2147701/1‑70 (MQ=255)
                                                                 tCAATATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCa                           >  1:3937717/1‑48 (MQ=255)
                                                                  cAACATGATGGCGGCAGGAATTACCACCAGCGCGGGTATc                                  <  1:3046934/40‑1 (MQ=255)
                                                                  cAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGACCCAGCAACGCCCCTTCATAAc   >  1:2824385/1‑71 (MQ=255)
                                                                   aaCATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGACCCAGCAACGCCCCTTCATAAcc  <  1:1829541/71‑1 (MQ=255)
                                                                     |                                                                    
CTGCCCTGCCAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGACCCAGCAACGCCCCTTCATAACC  >  W3110S.gb/3659756‑3659893

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑