Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 1,196,042 A→G I74T (ATC→ACC)  intE ← site‑specific integrase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,196,0420AG97.8% 158.7 / ‑4.2 46I74T (ATC→ACC) intEsite‑specific integrase
Reads supporting (aligned to +/- strand):  ref base A (1/0);  new base G (27/18);  total (28/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

AGCAAGGATACTGGTTTAGCTTTTTGTTTATAGGTGTTGAGTCTTATATCACCACTTTTAAGCCTGTCATCCTGGATCGCTTGATAGCGATCTAACCAGGTTGACGTTGTGATAGCCTTTCCTTTGCTGGTTGCGATCCTGTCACTGATAGCCAGAATCTGCCGGGTTCTTTGTTCAGCCAGGCGAGTGTTGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGAATTTTCCTGTCACTGGATGC  >  NZ_CP009273/1195907‑1196170
                                                                                                                                       |                                                                                                                                
aGCAAGGATACTGGTTTAGCTTTTTGTTTATAGGTGTTGAGTCTTATATCACCACTTTTAAGCCTGTCATCCTGGATCGCTTGATAGCGATCTAACCAGGTTGACGTTGTGATAGCCTTTCCTTTGCTGGTTGCGGTc                                                                                                                                <  2:73816/138‑1 (MQ=255)
    aGGATACTGGTTTAGCTTTTTGTTTATAGGTGTTGAGTCTTATATCACCACTTTTAAGCCTGTCATCCTGGATCGCTTGATAGCGATCTAACCAGGTTGACGTTGTGATAGCCTTTCCTTTGCTGGTTGCGGTCCTGt                                                                                                                            >  2:471918/1‑138 (MQ=255)
     ggATACTGGTTTAGCTTTTTGTTTATAGGTGTTGAGTCTTATATCACCACTTTTAAGCCTGTCATCCTGGATCGCTTGATAGCGATCTAACCAGGTTGACGTTGTGATAGCCTTTCCTTTGCTGGTTGCGGTCCTGTCa                                                                                                                          >  2:819004/1‑139 (MQ=255)
          cTGGTTTAGCTTTTTGTTTATAGGTGTTGAGTCTTATATCACCACTTTTAAGCCTGTCATCCTGGATCGCTTGATAGCGATCTAACCAGGTTGACGTTGTGATAGCCTTTCCTTTGCTGGTTGCGGTCCTGTCACTGa                                                                                                                      <  1:1086010/138‑1 (MQ=255)
          cTGGTTTAGCTTTTTGTTTATAGGTGTTGAGTCTTATATCACCACTTTTAAGCCTGTCATCCTGGATCGCTTGATAGCGATCTAACCAGGTTGACGTTGTGATAGCCTTTCCTTTGCTGGTTGCGGTCCTGTCACTGa                                                                                                                      <  1:906290/138‑1 (MQ=255)
          cTGGTTTAGCTTTTTGTTTATAGGTGTTGAGTCTTATATCACCACTTTTAAGCCTGTCATCCTGGATCGCTTGATAGCGATCTAACCAGGTTGACGTTGTGATAGCCTTTCCTTTGCTGGTTGCGGTCCTGTCACTGa                                                                                                                      <  1:1177855/138‑1 (MQ=255)
          cTGGTTTAGCTTTTTGTTTATAGGTGTTGAGTCTTATATCACCACTTTTAAGCCTGTCATCCTGGATCGCTTGATAGCGATCTAACCAGGTTGACGTTGTGATAGCCTTTCCTTTGCTGGTTGCGGTCCTGTCACTGa                                                                                                                      >  1:426862/1‑138 (MQ=255)
                       ttGTTTATAGGTGTTGAGTCTTATATCACCACTTTTAAGCCTGTCATCCTGGATCGCTTGATAGCGATCTAACCAGGTTGACGTTGTGATAGCCTTTCCTTTGCTGGTTGCGGTCCTGTCACTGATAGCCAGAATCTGc                                                                                                        >  1:849774/1‑139 (MQ=255)
                       ttGTTTATAGGTGTTGAGTCTTATATCACCACTTTTAAGCCTGTCATCCTGGATCGCTTGATAGCGATCTAACCAGGTTGACGTTGTGATAGCCTTTCCTTTGCTGGTTGCGGTCCTGTCACTGATAGCCAGAATCTGc                                                                                                        >  2:675934/1‑139 (MQ=255)
                                    ttGAGTCTTATATCACCACTTTTAAGCCTGTCATCCTGGATCGCTTGATAGCGATCTAACCAGGTTGACGTTGTGATAGCCTTTCCTTTGCTGGTTGCGGTCCTGTCACTGATAGCCAGAATCTGc                                                                                                        >  1:1184757/1‑126 (MQ=255)
                                    ttGAGTCTTATATCACCACTTTTAAGCCTGTCATCCTGGATCGCTTGATAGCGATCTAACCAGGTTGACGTTGTGATAGCCTTTCCTTTGCTGGTTGCGGTCCTGTCACTGATAGCCAGAATCTGc                                                                                                        <  2:1184757/126‑1 (MQ=255)
                                    ttGAGTCTTATATCACCACTTTTAAGCCTGTCATCCTGGATCGCTTGATAGCGATCTAACCAGGTTGACGTTGTGATAGCCTTTCCTTTGCTGGTTGCGGTCCTGTCACTGATAGCCAGAATCTGCCGGGTTCTTTGtt                                                                                           >  1:898464/1‑139 (MQ=255)
                                    ttGAGTCTTATATCACCACTTTTAAGCCTGTCATCCTGGATCGCTTGATAGCGATCTAACCAGGTTGACGTTGTGATAGCCTTTCCTTTGCTGGTTGCGGTCCTGTCACTGATAGCCAGAATCTGCCGGGTTCTTTGtt                                                                                           >  2:773160/1‑139 (MQ=255)
                                            tataTCACCACTTTTAAGCCTGTCATCCTGGATCGCTTGATAGCGATCTAACCAGGTTGACGTTGTGATAGCCTTTCCTTTGCTGGTTGCGGTCCTGTCACTGATAGCCAGAATCTGCCGGGTTCTTTGTTCAGCCAgg                                                                                   >  2:62990/1‑139 (MQ=255)
                                              tatCACCACTTTTAAGCCTGTCATCCTGGATCGCTTGATAGCGATCTAACCAGGTTGACGTTGTGATAGCCTTTCCTTTGCTGGTTGCGGTCCTGTCACTGATAGCCAGAATCTGCCGGGTTCTTTGTTCAGCCAGGc                                                                                  <  2:377015/138‑1 (MQ=255)
                                              tatCACCACTTTTAAGCCTGTCATCCTGGATCGCTTGATAGCGATCTAACCAGGTTGACGTTGTGATAGCCTTTCCTTTGCTGGTTGCGGTCCTGTCACTGATAGCCAGAATCTGCCGGGTTCTTTGTTCAGCCAGGc                                                                                  <  2:1238005/138‑1 (MQ=255)
                                                tCACCACTTTTAAGCCTGTCATCCTGGATCGCTTGATAGCGATCTAACCAGGTTGACGTTGTGATAGCCTTTCCTTTGCTGGTTGCGGTCCTGTCACTGATAGCCAGAATCTGCCGGGTTCTTTGTTCAGCCAGGCGa                                                                                <  1:639400/138‑1 (MQ=255)
                                                  accacTTTTAAGCCTGTCATCCTGGATCGCTTGATAGCGATCTAACCAGGTTGACGTTGTGATAGCCTTTCCTTTGCTGGTTGCGGTCCTGTCACTGATAGCCAGAATCTGCCGGGTTCTTTGTTCAGCCAGGCGAgtg                                                                             <  2:849774/139‑1 (MQ=255)
                                                          tAAGCCTGTCATCCTGGATCGCTTGATAGCGATCTAACCAGGTTGACGTTGTGATAGCCTTTCCTTTGCTGGTTGCGGTCCTGTCACTGATAGCCAGAATCTGCCGGGTTCTTTGTTCAGCCAGGCGAGTGTTGGCCt                                                                      >  2:223528/1‑138 (MQ=255)
                                                                 gTCATCCTGGATCGCTTGATAGCGATCTAACCAGGTTGACGTTGTGATAGCCTTTCCTTTGCTGGTTGCGGTCCTGTCACTGATAGCCAGAATCTGCCGGGTTCTTTGTTCAGCCAGGCGAGTGTTGGCCTCAGTGGc                                                               >  2:669096/1‑138 (MQ=255)
                                                                       cTGGATCGCTTGATAGCGATCTAACCAGGTTGACGTTGTGATAGCCTTTCCTTTGCTGGTTGCGGTCCTGTCACTGATAGCCAGAATCTGCCGGGTTCTTTGTTCAGCCAGGCGAGTGTTGGCCTCAGTGGCAATAGCg                                                        <  1:819004/139‑1 (MQ=255)
                                                                               cTTGATAGCGATCTAACCAGGTTGACGTTGTGATAGCCTTTCCTTTGCTGGTTGCGGTCCTGTCACTGATAGCCAGAATCTGCCGGGTTCTTTGTTCAGCCAGGCGAGTGTTGGCCTCAGTGGCAATAGCGATagctt                                                 >  2:931090/1‑138 (MQ=255)
                                                                               cTTGATAGCGATCTAACCAGGTTGACGTTGTGATAGCCTTTCCTTTGCTGGTTGCGGTCCTGTCACTGATAGCCAGAATCTGCCGGGTTCTTTGTTCAGCCAGGCGAGTGTTGGCCTCAGTGGCAATAGCGATagctt                                                 >  1:654527/1‑138 (MQ=255)
                                                                               cTTGATAGCGATCTAACCAGGTTGACGTTGTGATAGCCTTTCCTTTGCTGGTTGCGGTCCTGTCACTGATAGCCAGAATCTGCCGGGTTCTTTGTTCAGCCAGGCGAGTGTTGGCCTCAGTGGCAATAGCGATagctt                                                 >  1:681211/1‑138 (MQ=255)
                                                                               cTTGATAGCGATCTAACCAGGCTGACGTTGTGATAGCCTTTCCTTTGCTGGTTGCGGTCCTGTCACTGATAGCCAGAATCTGCCGGGTTCTTTGTTCAGCCAGGCGAGTGTTGGCCTCAg                                                                   >  2:1050770/1‑120 (MQ=255)
                                                                               cTTGATAGCGATCTAACCAGGCTGACGTTGTGATAGCCTTTCCTTTGCTGGTTGCGGTCCTGTCACTGATAGCCAGAATCTGCCGGGTTCTTTGTTCAGCCAGGCGAGTGTTGGCCTCAg                                                                   <  1:1050770/120‑1 (MQ=255)
                                                                                       cGATCTAACCAGGTTGACGTTGTGATAGCCTTTCCTTTGCTGGTTGCGGTCCTGTCACTGATAGCCAGAATCTGCCgg                                                                                                     >  2:366697/1‑78 (MQ=255)
                                                                                       cGATCTAACCAGGTTGACGTTGTGATAGCCTTTCCTTTGCTGGTTGCGGTCCTGTCACTGATAGCCAGAATCTGCCgg                                                                                                     <  1:366697/78‑1 (MQ=255)
                                                                                         aTCTAACCAGGTTGACGTTGTGATAGCCTTTCCTTTGCTGGTTGCGGTCCTGTCACTGATAGCCAGAATCTGCCGGGTTCTTTGTTCAGCCAGGCGCGTGTTGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGttt                                      >  1:1260734/1‑139 (MQ=255)
                                                                                              aCCAGGTTGACGTTGTGATAGCCTTTCCTTTGCTGGTTGCGGTCCTGTCACTGATAGCCAGAATCTGCCGGGTTCTTTGTTCAGCCAGGCGAGTGTTGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGttt                                      <  1:773160/134‑1 (MQ=255)
                                                                                                cAGGTTGACGTTGTGATAGCCTTTCCTTTGCTGGTTGCGGTCCTGTCACTGATAGCCAGAATCTGCCGGGTTCTTTGTTCAGCCAGGCGAGTGTTGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCa                               <  1:62990/139‑1 (MQ=255)
                                                                                                   gTTGACGTTGTGATAGCCTTTCCTTTGCTGGTTGCGGTCCTGTCACTGATAGCCAGAATCTGCCGGGTTCTTTGTTCAGCCAGGCGAGTGTTGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAg                            >  2:668615/1‑139 (MQ=255)
                                                                                                    ttGACGTTGTGATAGCCTTTCCTTTGCTGGTTGCGGTCCTGTCACTGATAGCCAGAATCTGCCGGGTTCTTTGTTCAGCCAGGCGAGTGTTGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAg                            >  2:844083/1‑138 (MQ=255)
                                                                                                        cGTTGTGATAGCCTTTCCTTTGCTGGTTGCGGTCCTGTCACTGATAGCCAGAATCTGCCGGGTTCTTTGTTCAGCCAGGCGAGTGTTGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATg                        >  1:1147707/1‑138 (MQ=255)
                                                                                                             tgATAGCCTTTCCTTTGCTGGTTGCGGTCCTGTCACTGATAGCCAGAATCTGCCGGGTTCTTTGTTCAGCCAGGCGAGTGTTGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGAAttt                  >  1:762858/1‑139 (MQ=255)
                                                                                                             tgATAGCCTTTCCTTTGCTGGTTGCGGTCCTGTCACTGATAGCCAGAATCTGCCGGGTTCTTTGTTCAGCCAGGCGAGTGTTGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGAAttt                  >  2:438024/1‑139 (MQ=255)
                                                                                                             tgATAGCCTTTCCTTTGCTGGTTGCGGTCCTGTCACTGATAGCCAGAATCTGCCGGGTTCTTTGTTCAGCCAGGCGAGTGTTGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGAAttt                  >  2:434145/1‑139 (MQ=255)
                                                                                                                  gCCTTTCCTTTGCTGGTTGCGGTCCTGTCACTGATAGCCAGAATCTGCCGGGTTCTTTGTTCAGCCAGGCGAGTGTTGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGAATTTTCCTg             >  1:216417/1‑139 (MQ=255)
                                                                                                                     tttcctttGCTGGTTGCGGTCCTGTCACTGATAGCCAGAATCTGCCGGGTTCTTTGTTCAGCCAGGCGAGTGTTGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGttt                                      >  1:170040/1‑111 (MQ=255)
                                                                                                                     tttcctttGCTGGTTGCGGTCCTGTCACTGATAGCCAGAATCTGCCGGGTTCTTTGTTCAGCCAGGCGAGTGTTGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGttt                                      <  2:170040/111‑1 (MQ=255)
                                                                                                                       tcctttGCTGGTTGCGATCCTGTCACTGATAGCCAGAATCTGCCGGGTTCTTTGTTCAGCCAGGCGAGTGTTGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGAATTTTCCTGTCACt        >  1:877383/1‑139 (MQ=255)
                                                                                                                         ctttGCTGGTTGCGGTCCTGTCACTGATAGCCAGAATCTGCCGGGTTCTTTGTTCAGCCAGGCGAGTGTTGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGAATTTTCCTGTCACTgg      <  2:787018/139‑1 (MQ=255)
                                                                                                                            tGCTGGTTGCGGTCCTGTCACTGATAGCCAGAATCTGCCGGGTTCTTTGTTCAGCCAGGCGAGTGTTGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGAATTTTc                <  1:462632/126‑1 (MQ=255)
                                                                                                                            tGCTGGTTGCGGTCCTGTCACTGATAGCCAGAATCTGCCGGGTTCTTTGTTCAGCCAGGCGAGTGTTGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGAATTTTc                >  2:462632/1‑126 (MQ=255)
                                                                                                                            tGCTGGTTGCGGTCCTGTCACTGATAGCCAGAATCTGCCGGGTTCTTTGTTCAGCCAGGCGAGTGTTGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGAATTTTCCTGTCACTGGa     <  2:898464/137‑1 (MQ=255)
                                                                                                                             gCTGGTTGCGGTCCTGTCACTGATAGCCAGAATCTGCCGGGTTCTTTGTTCAGCCAGGCGAGTGTTGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGAATTTTCCTGTCACTGGATGc  >  1:248464/1‑139 (MQ=255)
                                                                                                                                       |                                                                                                                                
AGCAAGGATACTGGTTTAGCTTTTTGTTTATAGGTGTTGAGTCTTATATCACCACTTTTAAGCCTGTCATCCTGGATCGCTTGATAGCGATCTAACCAGGTTGACGTTGTGATAGCCTTTCCTTTGCTGGTTGCGATCCTGTCACTGATAGCCAGAATCTGCCGGGTTCTTTGTTCAGCCAGGCGAGTGTTGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGAATTTTCCTGTCACTGGATGC  >  NZ_CP009273/1195907‑1196170

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑