Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 35,858 T→A 35.3% 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
*CP00073035,8580TA35.3% 71.0 / 45.5 48intergenic (+89/+19)USA300HOU_0025/USA300HOU_0026hypothetical protein/IS431mec transposase
Reads supporting (aligned to +/- strand):  ref base T (18/13);  new base A (9/8);  total (27/21)
Fisher's exact test for biased strand distribution p-value = 7.69e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.31e-01

AAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCTTTTTATATAGAGCGTAAATACATTCAATACCTTTTAAAGTA  >  CP000730/35719‑35988
                                                                                                                                           |                                                                                                                                  
aaaGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTGAttt                                                                                                                                   >  1:148082/1‑141 (MQ=255)
    tATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCa                                                                                                                               <  1:49733/141‑1 (MQ=255)
         aaTGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCa                                                                                                                          >  2:350471/1‑141 (MQ=255)
          aTGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAg                                                                                                                         <  1:382873/141‑1 (MQ=255)
          aTGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAg                                                                                                                         <  1:351426/141‑1 (MQ=255)
             tAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAgtgt                                                                                                                      >  1:389032/1‑141 (MQ=255)
                       tCAATAAAAAGTTTTTAGCGAAAAATAATTACCTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACt                                                                                                            <  1:48836/141‑1 (MQ=25)
                               aaGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCa                                                                                                    >  1:177507/1‑141 (MQ=255)
                               aaGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCa                                                                                                    >  2:337828/1‑141 (MQ=255)
                               aaGTGTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCa                                                                                                    >  1:271118/1‑141 (MQ=255)
                                        gCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTaa                                                                                           >  2:45561/1‑141 (MQ=255)
                                         cGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGACGGTTCTGTTGCACAGTACACAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACATCCCACCATGCTGCAAAt                                                                                          >  2:208616/1‑141 (MQ=25)
                                         cGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAACATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAAt                                                                                          >  1:162743/1‑141 (MQ=255)
                                          gAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGGTATAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATGAAGCTAACCACTAATTTATCATGAACGTGTTTCCTTGACTTGCTAGCATGATGCTAAtt                                                                                         >  2:68814/1‑141 (MQ=21)
                                          gAAAAATGATTACTTGAAAACGCCTTAATGGAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAAtt                                                                                         >  1:95583/1‑141 (MQ=17)
                                               aTGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTg                                                                                    >  1:399790/1‑141 (MQ=255)
                                                     aCTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATgg                                                                              <  1:85231/141‑1 (MQ=255)
                                                      catGAACAAGAGCTAAAATAAAATTGGGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGc                                                                             <  2:132097/139‑1 (MQ=255)
                                                       gtaaaCAAGAGCTAAAATAAAATTTTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATTGTAGTGTTCGCTTAACTGGCTAGCTTGATGCTAATTTCGtttcaggtcc                                                                            <  2:105293/138‑10 (MQ=18)
                                                               gagCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCg                                                                    >  2:187136/1‑141 (MQ=255)
                                                                       acaaaagagtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGaa                                                          >  1:321338/15‑141 (MQ=11)
                                                                       acaaaagagtattttaataaAAATGAGGGTTCTGTTGCAAAGTAAAAAATATAGCTAATAACTAATATATCATGTAAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGaa                                                          >  2:351610/15‑141 (MQ=11)
                                                                        caaaagagtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAag                                                         >  2:341785/14‑141 (MQ=11)
                                                                        caaaagagtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAag                                                         >  2:321060/14‑141 (MQ=11)
                                                                          agatTGTGAACTAATAACAATAAGAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCCCTTAACTTGCTAGCACGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAag                                                         <  2:66191/139‑1 (MQ=11)
                                                                          aaatTGTGATCTAATAAAAATAGAATGTTCTGTTGCAAAGTAAAAAAATATACCTCAACACCAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAag                                                         <  1:289840/141‑1 (MQ=17)
                                                                          aaatTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTCAag                                                         >  2:120009/1‑141 (MQ=255)
                                                                           aatTGTGATCTAATACAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAaga                                                        >  2:385595/1‑141 (MQ=255)
                                                                           aagagtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATTGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAgaga                                                      <  1:206345/131‑1 (MQ=11)
                                                                           aagagtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCAGGGCGACAATCCGTTGATCTGAagagg                                                      >  2:63273/11‑140 (MQ=11)
                                                                            agagtattttaataaAAATGATGGTTCTGTTTCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGAc                                                     <  1:171186/132‑1 (MQ=11)
                                                                             ttGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGCTGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAgaga                                                      >  1:215425/1‑141 (MQ=255)
                                                                             gagtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGAcc                                                    <  1:68142/133‑1 (MQ=11)
                                                                              agtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTTATCACTAATATATCATGTCAGTGTTCGTTTCACTTGCTAGCATGATGCTAATTTCGTGGCATGGCTAAAATCCGTAGATCTGAAGAGACCt                                                   <  2:165901/134‑1 (MQ=11)
                                                                              agtattttaataaAAATGATGGTTCCGTTGCAAAGTAAAAAATATAGCTACTCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCt                                                   <  1:303397/134‑1 (MQ=11)
                                                                               gtgATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGAcg                                                    >  1:35013/1‑140 (MQ=255)
                                                                                tgATCTAATAAAAATAGAAGGTTCGGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATTATGCTATTTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCt                                                   <  2:258688/141‑1 (MQ=255)
                                                                                 gATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTg                                                  <  1:259481/141‑1 (MQ=255)
                                                                                 attttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCg                                                <  1:371216/137‑1 (MQ=11)
                                                                                 attttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATAGAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCg                                                >  1:273905/5‑141 (MQ=11)
                                                                                  ttttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCgg                                               >  1:22050/4‑141 (MQ=11)
                                                                                  ttttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCgg                                               >  1:394194/4‑141 (MQ=11)
                                                                                   tttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCgct                                              >  2:50946/3‑139 (MQ=11)
                                                                                    cTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCgg                                               >  1:228686/1‑141 (MQ=40)
                                                                                        taaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCttt                                         <  2:94873/141‑1 (MQ=11)
                                                                                              tAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCTTTTtat                                     <  1:380302/141‑1 (MQ=32)
                                                                                              tAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACATGCGGTTCTTTTgat                                     >  1:275739/1‑141 (MQ=17)
                                                                                                 aaGGTTCTGGTGAAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCTTTTtatata                                  <  2:238344/141‑1 (MQ=11)
                                                                                                                                 aatcACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGGGAAAATCCGTAGATCTGAAGAGACCTACGGTTCTTTTTATATAGAGCGTAAATACATTCAATACCTTTTAAAGTa  <  1:2052/138‑1 (MQ=1)
                                                                                                                                           |                                                                                                                                  
AAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCTTTTTATATAGAGCGTAAATACATTCAATACCTTTTAAAGTA  >  CP000730/35719‑35988

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: