Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 36,479 T→C 15.2% T25A (ACA→GCA)  USA300HOU_0026 ← IS431mec transposase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP00073036,4790TC15.2% 86.5 / 9.8 45T25A (ACA→GCA) USA300HOU_0026IS431mec transposase
Reads supporting (aligned to +/- strand):  ref base T (20/18);  new base C (4/3);  total (24/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01

TAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAA  >  CP000730/36340‑36618
                                                                                                                                           |                                                                                                                                           
taataaGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGta                                                                                                                                            <  2:18623/141‑1 (MQ=40)
 aataaGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGtat                                                                                                                                           >  1:198179/1‑141 (MQ=255)
       cTTTTGTGTTCTTTTTCTTACAAATTTGATACAAAATTGGGGTATATTCTTGAACCCAACGGTAGAACGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTa                                                                                                                                     <  2:157256/141‑1 (MQ=11)
          ttgtATGCTTGTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGAt                                                                                                                                  <  1:165218/138‑1 (MQ=25)
             tATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATCTTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGAtagt                                                                                                                               >  1:161027/1‑141 (MQ=25)
             tATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGAtagt                                                                                                                               >  1:238464/1‑141 (MQ=35)
               tGCTTTTTCTTCCAAATTTGATACAAAATTGGGGTATATTCTTGAACCCAACGGTAGACCGTTAAATGATGAACGTTTACACCACGTTCCCTTAATATTTAAGATATCTCACGATAACTCCATGTATTTCTTACAtagtag                                                                                                                             >  2:63843/1‑141 (MQ=11)
                gCTTTTTCTTCCAAATTTTATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGc                                                                                                                            <  1:13687/141‑1 (MQ=21)
                       cttcCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGc                                                                                                                     <  2:63515/141‑1 (MQ=35)
                         tcCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTa                                                                                                                   <  1:102523/141‑1 (MQ=35)
                         aacAAAGTTTATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTCTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTa                                                                                                                   <  2:266484/139‑1 (MQ=255)
                                ttGTTACAAAATTTGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGCTGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGAt                                                                                                            <  1:160250/141‑1 (MQ=255)
                                ttGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGAt                                                                                                            <  2:7160/141‑1 (MQ=35)
                                 tGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCAAACGGCTACAGTGATa                                                                                                           >  2:267110/1‑141 (MQ=25)
                                            tGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGtt                                                                                                <  2:105824/141‑1 (MQ=32)
                                            tGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGtt                                                                                                >  2:285829/1‑141 (MQ=32)
                                            tGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGtt                                                                                                <  2:65203/141‑1 (MQ=32)
                                             ggggCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTa                                                                                               >  1:320257/1‑141 (MQ=32)
                                             ggggCATATTCTTGAACCCAACGGTAGACCGGTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAAAATCCTTGTTa                                                                                               >  1:183682/1‑141 (MQ=17)
                                                      tCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTta                                                                                      <  1:359210/141‑1 (MQ=32)
                                                      tCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTta                                                                                      <  1:256047/141‑1 (MQ=32)
                                                           aaCCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCt                                                                                 <  2:156032/141‑1 (MQ=32)
                                                                      aGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCa                                                                      >  1:205800/1‑141 (MQ=32)
                                                                          cGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACa                                                                  <  1:208113/141‑1 (MQ=32)
                                                                                 tgatgaACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGAcc                                                           >  1:341572/1‑140 (MQ=17)
                                                                                         gTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGACACAACAGTTTACAGCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTg                                                   >  1:170544/1‑141 (MQ=11)
                                                                                           ttACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACCTCCTTGTTAAATTGTTTCTATCTGAAATAGTTCATACAGAAGACTCCTTTTAGtt                                                 >  2:207319/1‑141 (MQ=12)
                                                                                                   cGTTTCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATtat                                         <  2:302329/141‑1 (MQ=17)
                                                                                                   cGTTCCCTGAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATtat                                         <  2:302431/141‑1 (MQ=17)
                                                                                                         cTTAATATTCCAGATATATCACGATAACTCAATGTATATCTTAGATAGCAGCCAACGGCTACAGTGATAACATCCTTGTCAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACtata                                   <  1:261740/141‑1 (MQ=12)
                                                                                                              tttgtCAGATATATCACGATAGCTCAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTc                              <  2:256962/137‑1 (MQ=255)
                                                                                                                  tCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCaaat                          >  1:311228/1‑139 (MQ=21)
                                                                                                                  tCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACt                          >  1:143815/1‑141 (MQ=35)
                                                                                                                  tCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTCCATACAGAAGACTCCTTTTTGTTAAAATTATACTCTAAATTCAACt                          >  1:164453/1‑141 (MQ=21)
                                                                                                                      atatatCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAATGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTGAAAATTATACTATAAATTCAACTTTGc                      >  1:49910/1‑141 (MQ=25)
                                                                                                                         tatCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGCATACAGTGATAACATCCTTGTTAAATTGCTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTCCaaa                   >  2:172205/1‑140 (MQ=255)
                                                                                                                            cACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGa                >  1:92812/1‑141 (MQ=35)
                                                                                                                                aTAACTCAATGTATTTCTTAGATAGTAGCCAACGGCGACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCg            <  2:98122/141‑1 (MQ=25)
                                                                                                                                  agcTCAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGCTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGta          <  2:1101/139‑1 (MQ=255)
                                                                                                                                    cTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGtatt        >  1:324118/1‑141 (MQ=40)
                                                                                                                                     tCAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattt       >  1:83529/1‑140 (MQ=16)
                                                                                                                                     tCAATGCATATCTTAGATAGTAGCCAAAGGCTAAAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGAATCCTTTTTGTTAAAATTATATTATAAATTCAACTTTTCAGCGGCACCGtattt       >  1:85105/1‑140 (MQ=11)
                                                                                                                                      cAATGCATATTTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtatttt      <  2:85732/141‑3 (MQ=255)
                                                                                                                                      cAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtatttt      >  1:348638/1‑139 (MQ=16)
                                                                                                                                      cAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtatttt      >  1:348519/1‑139 (MQ=255)
                                                                                                                                       aaTGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGCTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATg     >  1:318484/1‑141 (MQ=255)
                                                                                                                                          gTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGaa  >  1:236359/1‑141 (MQ=255)
                                                                                                                                           |                                                                                                                                           
TAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAA  >  CP000730/36340‑36618

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑