Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 36,161 T→C 10.8% I131V (ATT→GTT)  USA300HOU_0026 ← IS431mec transposase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP00073036,1610TC10.8% 71.4 / 2.9 37I131V (ATT→GTT) USA300HOU_0026IS431mec transposase
Reads supporting (aligned to +/- strand):  ref base T (16/17);  new base C (2/2);  total (18/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01

TATGACGGTGATCTTGCTCAATGAGGTTATTCAGATATTTCGATGTACAATGACAGTCAGGTTTAAGTTTAAAAGCTTTAATTACTTTAGCCATTGCTACCTTCGTTGAAGGTGCCTGATCTGTAATTACCTTTTGAGGTTTACCAAATTGTTTAATGAGACGTTTGATAAACGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTC  >  CP000730/36035‑36301
                                                                                                                              |                                                                                                                                            
tatGACGGTGATCTTGCTCAATGAGGTTATTCAGATATTTCGATGTACAATGACAGTCAGGTTTAAGTTTAAAAGCTTTAATTACTTTAGCCATTGCTACCTCTGTTGAAGGTGCCTGATCGGTAATTACCTTTTGAGGtt                                                                                                                                >  2:83435/1‑141 (MQ=255)
   gACGGTGATCTTGCTCAATGAGGTTATTCAGATATTTCGATGTACAATGACAGTCAGGTTTAAGTTTAAAAGCTTTAATTACTTTAGCCATTGCTACCTTCGTTGAAGGTGCCTGATCTGTAATTACCTTTTGAGGTTTAc                                                                                                                             <  1:393541/141‑1 (MQ=35)
      ggTGATCTTGCTCAATGAGGTTATTCAGATCTTTCGATGTACAATGACAGTCAGGTTTAAGTTTAAAAGCTTTAATTACTTTAGCCATTGCTACCTTCGTTGAAGGTGCCTGATCTGTAATTACCTTTTGAGGTTTACCaa                                                                                                                          >  1:66623/1‑141 (MQ=17)
       gTGATCTTGCTCAATGAGGTTATTCAGATATTTCGATGTACAATGACAGTCAGGTTTAAGTTTAAAAGCTTTAATTACTTTAGCCATTGCTACCTTCGTTGAAGGTGCCTGATCTGTAATTACCTTTTGAGGTTTACCaaa                                                                                                                         <  1:169690/141‑1 (MQ=32)
         tatctgtcTCGATGAGGTTATTCAGATAATTCGATGTACAATGGCAGTCAGGTTTAAGTTTAAAAGCTTTAATTACTTTAACCATTGCTACCTTCGTTGAAGGTGCCTGATCTGTAATTACCTTTTGAGGTTTACCAAAtt                                                                                                                       <  2:415335/134‑1 (MQ=11)
           tCTTGCTCAATGAGGTTATTCAGATATTTCGATGTACAATGACAGTCAGGTTTAAGTTTAAAAGCTTTAATTACTTTAGCCATTGCTACCTTCGTTGAAGGTGCCTGATCTGTAATTACCTTTTGAGGTTTACCAAATTGt                                                                                                                     >  1:304469/1‑141 (MQ=32)
             ttGCTCAATGAGGTTATTCAGATATTTCGATGTACAATGACAGTCAGGTTTAAGTTTAAAAGCTTTAATTATTTTAGCCATTGCTGCCTTCGTTGAAGGTGCCTGATCTGTAACTACCTTTTGAGGCTTACCAAATTGttt                                                                                                                   >  1:231761/1‑141 (MQ=255)
               gCTCAATGAGGTTATTCAGATATTTCGATGTACAATGGCAGTCAGGTTTAAGTTTAAAAGCTTTAATTACTTTAACCATTGCTACCTTCGTTGAAGGTGCCTGATCTGTAATTACCTTTTGAGGTTTACCAAATTGTTTat                                                                                                                 >  1:438116/1‑140 (MQ=12)
               gCTCAATGAGGTTATTCAGATATTTCGATGTACAATGGCAGTCAGGTTTAAGTTTAAAAGCTTTAATTACTTTAACCATTGCTACCTTCGTTGAAGGTGCCTGATCTGTAATTACCTTTTGAGGTTTACCAAATTGTTTaa                                                                                                                 >  1:438068/1‑141 (MQ=12)
                 tCAATGAGGTTATTCAGATATTTCGATGTACAATGACAGTCAGGTTTAAGTTTAAAAGCTTTAATTATTTTAGCCATTGCTGCCTTCGTTGAAGGTGCCTGATCTGTAACTACCTTTTGAGGCTTACCAAATTGTTTAATg                                                                                                               <  1:220065/141‑1 (MQ=11)
                  cAATGAGGTTATTCAGATATTTCGATGTACAATGACAGTCAGGTTTAAGTTTAAAAGCTTTAATTACTTTAGCCATTGCTACCTTCGTTGAAGGTGCCTGATCTGTAATTACCTTTTGAGGTTTACCAAATTGTTTAATga                                                                                                              <  2:426989/141‑1 (MQ=32)
                       aGGTTATTCAGATATTTCGATGTACAATGACAGTCAGGTTTAAGTTTAAAAGCTTTAATTACTTTAGCCATTGCTACCTTCGTTGAAGGTGCCTGATCTGTAATTACCTTTTGAGGTTTACCAAATTGTTTAATGAGACGt                                                                                                         <  2:431134/141‑1 (MQ=32)
                       aGGTTATTCAGATATTTCGATGTACAATGACAGTCAGGTTTAAGTTTAAAAGCTTTAATTACTTTAGCCATTGCTACCTTCGTTGAAGGTGCCTGATCTGTAATTACCTTTTGAGGTTTACCAAATTGTTTAATGAGACGt                                                                                                         <  2:176123/141‑1 (MQ=32)
                         gTTATTCAGATATTTCGATGTACAATGACAGTCAGGTTTAAGTTTAAAAGCTTTAATTATTTTAGCCATTGCTGCCTTCGTTGAAGGTGCCTGATCTGTAACTACCTTTTGAGGCTTACCAAATTGTTTAATGAGACGttt                                                                                                       >  1:268284/1‑141 (MQ=255)
                          ttATTCAGATATTTCGATGTACAATGACAGTCAGGTTTAAGTTTAAAAGCTTTAATTACTTTAGCCATTGCTACCTTCGTTGAAGGTGCCTGATCTGTAATTACCTTTTGAGGTTTACCAAATTGTTTAATGAGACGTTTg                                                                                                      <  2:377697/141‑1 (MQ=32)
                           tATTTAGATAGTTCGATGTACAATGGCAGTCAGGTTTAAGTTTAAAAGCTTTAATTACTTTAACCATTGCTACCTTCGTTGAAGGTGCCTGATCTGTAATTACCTTTTGAGGTTTACCAAATTGTTTAATGAGACGTTTGa                                                                                                     <  1:244460/141‑1 (MQ=255)
                           tATTCAGATATTTCGATGTACAATGACAGTCAGGTTTAAGTTTAAAAGCTTTAATTACTTTAGCCATTGCTACCTTCGTTGAAGGTGCCTGATCTGTAATTACCTTTTGAGGTTTACCAAATTGTTTAATGAGACGTTTGa                                                                                                     <  2:171419/141‑1 (MQ=32)
                               cAGATATTTCGATTTACAAGGACAGTCAGGTTTAAGTTTAAAAGCTTTATTTATTTTAGCCACTGCTGCCTTCGTTGAAGGTGCCTGACCTGTAACTACCTTTTGAGGCTTACCAAATTGTTTAATGAGACGTTTGATaaa                                                                                                 <  1:285979/141‑1 (MQ=11)
                                 gATATTTCGATGTACAATGGCAGTCAGGTTTAAGTTTAAAAGCTTTAATTACTTTCACAATTGCTACATTAGTTAAAGGTGCCTGATTTGTAATATCCTATTGAGGTTTACCAAATTGTCTAATGAGACGTTTGTTAAACg                                                                                               >  2:12044/1‑141 (MQ=11)
                                   tatTTCGATGTACAATGACAGTCAGGTTTAAGTTTAAAAGCTTTAATTACTTTAGCCATTGCTACCTTCGTTGAAGGTGCCTGATCTGTAATTACCTTTTGAGGTTTACCACATTGTTTAATGAGACGTTTGATAAACGCa                                                                                             >  2:214765/1‑141 (MQ=17)
                                    agttCGATGTACAATGACAGTCAGGTTTAAGTTTAAAAGCTTTAATTACTTTAGCCATTGCTACCTTCGTTGAAGGTGCCTGATCTGTAATTACCTTTTGAGGTTTACCAAATTGTTTAATGAGACGTTTGATAAACGCat                                                                                            <  2:374127/139‑1 (MQ=17)
                                        cGATGTACAATGGCAGTCAGGTTTAAGTTTAAAAGCTTTAATTAAGTTAACCATTGCTACCTTCGTTGAAGGTGCCTGATCTGTAATTACCTTTTGAGGTTTACCAAATTGTTTAATGAGACGTTTGATAACAGCATATGc                                                                                        >  2:52349/1‑141 (MQ=11)
                                         gATGTACAATGACAGTCAGGTTTAAGTTTAAAAGCTTTAATTACTTTAGCCATTGCTACCTTCGTTGAAGGTGCCTGATCTGTAATTACCTTTTGAGGTTTACCAAATTGTTTAATGAGACGTTTGATAAACGCCTATGCt                                                                                       >  1:348516/1‑141 (MQ=17)
                                         gATGTACAATGACAGTCAGGTTTAAGTTTAAAAGCTTTAATTACTTTAGCCATTGCTACCTTCGTTGAAGGTGCCTGATCTGTAATTACCTTTTGAGGTTTACCAAATTGTTTAATGAGACGTTTGATAAACGCATATGCt                                                                                       >  1:413688/1‑141 (MQ=32)
                                         gATGTACAATGACAGTCAGGTTTAAGTTTAAAAGCTTTAATTACTTTAGCCATTGCTACCTTCGTTGAAGGTGCCTGATCTGTAATTACCTTTTGAGGTTTACCAAATTGTTTAATGAGACGTTTGATAAACGCATATGCt                                                                                       >  1:348159/1‑141 (MQ=32)
                                                                                     tttAGCCATTGCTTCCTTCGTTGAAGGTGCCTGATCTGTAATTGCCTTTTGAGGTTTACCAAATTGTTTAATGAGACGTTTGATAAACTCATATGCTGAATTATTATCTCGTTGCTTACGCAACCAAATAACTAatgtatg                                           >  1:11958/1‑141 (MQ=11)
                                                                                     ttcaGCCATTGTTCCCTTCGTTGAAGGTGCCTGATCTGTAATTAGCTTTTGAGGTTTACCAAATTGTTTAATGAGACGTTTGATAAACGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAatgtatg                                           <  1:350907/138‑1 (MQ=2)
                                                                                        aGCCATTGCTACCTTCGTTGAAGGTGCCTGATCTGTAATTACCTTTTGAGGTTCTTACCTTTAGTTAATGAGACGTTTGATAAACGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAATGTATGTcc                                        <  1:454004/141‑1 (MQ=11)
                                                                                               gCTACCTTCGTTGAAGGTGCCTGATCTGTAATTACCTTTTGAGGTTTACCAAATTTTTTAATGAGACGTTTGATAAACGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCa                                 >  1:51367/1‑141 (MQ=17)
                                                                                                 ttccTTCGTTGAAGGTGCCTGATCTGTAATTACCTTTTGAGGTTTACCAAATTGTTTAATGAGACGTTTGATAAACGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATc                               <  2:152715/139‑1 (MQ=17)
                                                                                                 tACCTTCGTTGAAGGTGCCTGATCTGTAATTACCTTTTGAGGTTTACCAAATTGTTTAATGAGACGTTTGATAAACGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTTCATc                               >  1:112489/1‑141 (MQ=17)
                                                                                                     ttCGTTGAAGGTGCCTGATCTGTAATTACCTTTTGAGGTTTACCAAATTGTTTAATGAGACGTTTGATAAACGCATAAGCTGAATAATTATCTCGTTGCATACGCAACCAAATATCTAATGTATGTACCTCTGCATCAATg                           >  2:439835/1‑141 (MQ=255)
                                                                                                         ttGAAGGTGCCTGATCTGTAATTACCTTTTGAGGTTTACCAAATTGTTTAATGAGACGTTTGATAAACGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTCCATCAATGGccc                       >  2:2304/1‑139 (MQ=17)
                                                                                                          tGAAGGTGCCTTATCTGTAATTACCTTTTGAGGTTTACCAAATTGTTTAATGAGACGTTTGATAAACGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTCATGTATGTCCCTCTGCATCAATGGCACg                      <  1:293167/141‑1 (MQ=17)
                                                                                                                      atgtGTAATTACCTTTTGAGGTTTACCAAATTGTTTAATGAGACGTTTGACAAACGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGAGATAAATAGCt          <  2:169548/138‑1 (MQ=12)
                                                                                                                      aTCTGGAATTACCCTTTGAGGTTTACCAAATTGTTTAATGAGACGTTTGATAAACGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCt          <  2:84554/141‑1 (MQ=17)
                                                                                                                             aTTACCTTTTGAGGTTTACCAAATTGTTTAATGAGACGTTTGATAAACGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCAtttt   <  1:393107/141‑1 (MQ=32)
                                                                                                                              ttACCTTTTGAGGTTTACCAAATTGTTTAATGAGACGTTGGATAAACGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTc  <  1:61339/141‑1 (MQ=17)
                                                                                                                              |                                                                                                                                            
TATGACGGTGATCTTGCTCAATGAGGTTATTCAGATATTTCGATGTACAATGACAGTCAGGTTTAAGTTTAAAAGCTTTAATTACTTTAGCCATTGCTACCTTCGTTGAAGGTGCCTGATCTGTAATTACCTTTTGAGGTTTACCAAATTGTTTAATGAGACGTTTGATAAACGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTC  >  CP000730/36035‑36301

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑