Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 35,858 T→A 47.9% intergenic (+89/+19) USA300HOU_0025 → / ← USA300HOU_0026 hypothetical protein/IS431mec transposase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP00073035,8580TA47.9% 26.8 / 77.1 57intergenic (+89/+19)USA300HOU_0025/USA300HOU_0026hypothetical protein/IS431mec transposase
Reads supporting (aligned to +/- strand):  ref base T (18/11);  new base A (15/12);  total (33/24)
Fisher's exact test for biased strand distribution p-value = 7.86e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.90e-01

AGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCTTTTTATATAGAGCGTA  >  CP000730/35721‑35963
                                                                                                                                         |                                                                                                          
aGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTAt                                                                                                         >  2:309625/1‑141 (MQ=255)
       aaTGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACAACTAATTTATCATGTCa                                                                                                  >  1:123909/1‑141 (MQ=255)
              aaGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCg                                                                                           <  1:142358/141‑1 (MQ=255)
              aaGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCg                                                                                           >  2:29741/1‑141 (MQ=255)
               aGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGc                                                                                         >  2:175547/1‑141 (MQ=255)
                gCTATTCAGTATAAAGTTTTTGGCGAGAAATGATTACTTGAACAAGAGCTAAAATAAATATGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTTGCt                                                                                        >  2:177437/1‑141 (MQ=255)
                gCTATTCAGTATAAAGTTTTTGGAGAAAAATGATTACTTGAACTAGAGCTAAAATTAAATTGTGATTTAATAAAACTAGAAGGTTATGTTGCATAGTAATAGAATATAGCTAAGCACTAATTTATCATGTCGGTGTTCgat                                                                                         >  2:268054/1‑139 (MQ=255)
                 cTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCtt                                                                                       <  1:289245/141‑1 (MQ=255)
                 cTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCtt                                                                                       >  2:275276/1‑141 (MQ=255)
                   atgcAGTAGAAAGTTTTTGGCGACAAATGATTACTTGAACAAGAGCTAAAATAAAATCGGGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATCTAGCTACCCAATAATTGAACAGGGCAGCATACGCTTaa                                                                                     >  2:193245/4‑141 (MQ=25)
                            aaaGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGc                                                                            >  1:121688/1‑141 (MQ=255)
                                     ggCGAAAAATGATTACTTGAACAAGAGCTACAATAAAATTGTGATATCATCAAAATCGACGATACTGTCGCAAAGTAAAAAAATATAGTTAACCACTAATTAATCAGGTCACGGTTCGCTTAACTGGCTAGCATGATGATa                                                                   >  2:262252/1‑141 (MQ=18)
                                           aaaTGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCg                                                             >  2:118006/1‑141 (MQ=255)
                                                cttACTTGAACACGAGCTAAAATAAAATTGTGATCTACTAAAAATAGAAGGCTGTGTGGCGAGGTCAACACATATACATAGCCAATAATTTATAAGGTTAGTGTTCGCTTAACTTCGTTGCATGACGCTAATTTctgggcc                                                        >  2:154662/2‑135 (MQ=255)
                                                     ttGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCg                                                   <  2:276320/141‑1 (MQ=255)
                                                             gagCTAAAATAAACATGTGATCTAATAAAAAAAGAAGGTTCTGTTGCAAAGTAAAAAAAGATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAAATTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCg                                           >  2:12374/1‑141 (MQ=17)
                                                                cTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAg                                        >  2:356805/1‑141 (MQ=255)
                                                                 taaaataaaaTTGTGATCCAATAAAAATAGAAGGTTCTGTTGCAAAATAAAAAAATATAGCTAGCCACTAATTTATCATGTCAGTGTTAGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGa                                       >  1:158792/1‑141 (MQ=255)
                                                                  aaaataaaatTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGTGCTACCATGTACCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGAt                                      >  1:116326/1‑141 (MQ=17)
                                                                  aaaataaaatTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGAt                                      <  2:121688/141‑1 (MQ=255)
                                                                       aaaagagtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGTCGAAAATCCACACATCTGAaga                               >  2:142730/13‑141 (MQ=11)
                                                                         aagagtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAgaga                             <  1:289486/131‑1 (MQ=11)
                                                                         aagagtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAgaga                             >  1:43498/11‑141 (MQ=11)
                                                                          agattattttaataaAAATGATGGTTCTGTTGCAAAGTAAAATCTATCGATACTATTTTATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGAc                            <  2:343690/132‑1 (MQ=2)
                                                                          agagtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAagaggc                            >  1:97609/10‑139 (MQ=11)
                                                                          agagtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGAc                            <  2:156940/132‑1 (MQ=11)
                                                                          agagtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGAc                            >  1:68271/10‑141 (MQ=11)
                                                                          agagtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGAc                            <  2:191624/132‑1 (MQ=11)
                                                                          agagtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTACTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGAc                            >  2:195761/10‑141 (MQ=11)
                                                                           gagtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGAcc                           <  2:336269/133‑1 (MQ=11)
                                                                           gagtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGAcc                           <  2:346702/133‑1 (MQ=11)
                                                                            tgtgATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGAc                            <  1:29741/141‑1 (MQ=255)
                                                                            tgtgATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGAc                            <  1:246851/141‑1 (MQ=255)
                                                                            tgtgATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCAAAATTGTTTCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGAc                            <  1:352139/141‑1 (MQ=14)
                                                                            agtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCt                          <  2:42724/134‑1 (MQ=11)
                                                                            agtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGCCGAAAAGCCGTAGATCTGAAGAGACCt                          <  2:164678/134‑1 (MQ=11)
                                                                             gtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTg                         >  1:166320/7‑141 (MQ=11)
                                                                             gtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTg                         <  1:83195/135‑1 (MQ=11)
                                                                              tattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATGACTAATATATAATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCCTGGCGAAGAGCCGTAGATCTGAAGTGACATgg                        >  2:271487/6‑140 (MQ=11)
                                                                              tattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGc                        <  1:295848/136‑1 (MQ=11)
                                                                               attttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCg                       >  1:254896/5‑141 (MQ=11)
                                                                                ttttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCgg                      <  1:140873/138‑1 (MQ=11)
                                                                                ttttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCgg                      >  2:184893/4‑141 (MQ=11)
                                                                                ttttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGACCTGAAGAGACCTGCgg                      >  1:86939/4‑141 (MQ=11)
                                                                                 tttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGt                     >  1:229285/3‑141 (MQ=11)
                                                                                 tCTAATAAAAATAGAAGGTTTTGTTGAAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCg                       <  2:1698/141‑1 (MQ=255)
                                                                                 tCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCg                       <  1:106863/141‑1 (MQ=255)
                                                                                  ttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCGCTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGtt                    >  2:269101/2‑141 (MQ=11)
                                                                                  ttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCTTGTTAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGTAAATTCGTAGGTTTGATGAGACCTGCgggt                    >  2:296495/2‑139 (MQ=11)
                                                                                  ttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTGGATCTGAAGAGACCTGCGGtt                    >  2:144807/2‑141 (MQ=11)
                                                                                  ttaataaAAATGATGGTTCTGTTACAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGtt                    >  2:319691/2‑141 (MQ=11)
                                                                                   taataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTc                   <  2:295532/141‑1 (MQ=11)
                                                                                            ttaaaGTTTCTGATGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCTTTTtat            <  2:134037/138‑1 (MQ=0)
                                                                                            tAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCTTTTtat            >  2:152680/1‑141 (MQ=32)
                                                                                              gctgggtCTGTTGCAAAGGAAAAAAATATAGCTAACCACTAATTTATCATATCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCTTTTtatat          >  2:263720/7‑141 (MQ=0)
                                                                                              aaaGGTTCTGTTGCAAAGTAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCTTTTtttata         <  2:217198/140‑1 (MQ=2)
                                                                                                      tgttaaaaaGTAAAAAAATATAGCTAACCACTAATTTAGCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCTTTTTATATAGAGCGTa  <  2:114869/135‑1 (MQ=0)
                                                                                                                                         |                                                                                                          
AGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCTTTTTATATAGAGCGTA  >  CP000730/35721‑35963

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: