Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 35,817 A→T 28.6% intergenic (+48/+60) USA300HOU_0025 → / ← USA300HOU_0026 hypothetical protein/IS431mec transposase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP00073035,8170AT28.6% 93.1 / 40.0 54intergenic (+48/+60)USA300HOU_0025/USA300HOU_0026hypothetical protein/IS431mec transposase
Reads supporting (aligned to +/- strand):  ref base A (20/17);  new base T (8/7);  total (30/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.48e-01

GCAAATTATTCTGAATTTAAAGATGTAGATGATCTCATTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCTTTTTATATA  >  CP000730/35677‑35956
                                                                                                                                            |                                                                                                                                           
gCAAATTATTCTGAATTTAAAGATGTAGATGATCTCATTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGaa                                                                                                                                             >  1:99669/1‑141 (MQ=255)
 cAAATTATTCTGCATTTAAAGAAGTAGATGATCTCATTGACAACGTCTTTAATGTAGAAGCTATTCAGTCTCACGTTTTTGGCGCAAAATGTTGACTTCAAAAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAg                                                                                                                                            >  2:43007/1‑141 (MQ=255)
        ttCTGAATTTAAAGATGTAGATGATCTCATTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGt                                                                                                                                     <  2:148062/141‑1 (MQ=255)
        ttCCGAATTTAAAGATGTAGATGATCTCATTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGt                                                                                                                                     <  2:18531/141‑1 (MQ=255)
                ttAAAGATGTAGGTGATCTCATTGACAAAGTTTTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAACATTTAGGTTCTGTTGCAAAGt                                                                                                                             <  2:144172/141‑1 (MQ=255)
                             tgatCTCATTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGc                                                                                                                >  1:87670/1‑141 (MQ=255)
                              gatCTCATTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCt                                                                                                               <  1:329892/141‑1 (MQ=255)
                                 ctcATTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAAc                                                                                                            <  1:385926/141‑1 (MQ=255)
                                          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)
                                                                                                                 acaaaagagtattttaataaAAAT‑GATGGTTCTGTTGCAAAGT‑AAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGaa                          >  1:321338/15‑141 (MQ=11)
                                                                                                                 acaaaagagtattttaataaAAAT‑GAGGGTTCTGTTGCAAAGT‑AAAAAATATAGCTAATAACTAATATATCATGTAAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGaa                          >  2:351610/15‑141 (MQ=11)
                                                                                                                  caaaagagtattttaataaAAAT‑GATGGTTCTGTTGCAAAGT‑AAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAag                         >  2:341785/14‑141 (MQ=11)
                                                                                                                  caaaagagtattttaataaAAAT‑GATGGTTCTGTTGCAAAGT‑AAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAag                         >  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)
                                                                                                                     aagagtattttaataaAAAT‑GATGGTTCTGTTGCAAAGT‑AAAAAATATTGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAgaga                      <  1:206345/131‑1 (MQ=11)
                                                                                                                     aagagtattttaataaAAAT‑GATGGTTCTGTTGCAAAGT‑AAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCAGGGCGACAATCCGTTGATCTGAagagg                      >  2:63273/11‑140 (MQ=11)
                                                                                                                      agagtattttaataaAAAT‑GATGGTTCTGTTTCAAAGT‑AAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGAc                     <  1:171186/132‑1 (MQ=11)
                                                                                                                       ttGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGCTGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAgaga                      >  1:215425/1‑141 (MQ=255)
                                                                                                                       gagtattttaataaAAAT‑GATGGTTCTGTTGCAAAGT‑AAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGAcc                    <  1:68142/133‑1 (MQ=11)
                                                                                                                        agtattttaataaAAAT‑GATGGTTCTGTTGCAAAGT‑AAAAAATATAGCTTATCACTAATATATCATGTCAGTGTTCGTTTCACTTGCTAGCATGATGCTAATTTCGTGGCATGGCTAAAATCCGTAGATCTGAAGAGACCt                   <  2:165901/134‑1 (MQ=11)
                                                                                                                        agtattttaataaAAAT‑GATGGTTCCGTTGCAAAGT‑AAAAAATATAGCTACTCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCt                   <  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)
                                                                                                                           attttaataaAAAT‑GATGGTTCTGTTGCAAAGT‑AAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCg                <  1:371216/137‑1 (MQ=11)
                                                                                                                           attttaataaAAAT‑GATGGTTCTGTTGCAAAGT‑AAAAAATAGAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCg                >  1:273905/5‑141 (MQ=11)
                                                                                                                            ttttaataaAAAT‑GATGGTTCTGTTGCAAAGT‑AAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCgg               >  1:22050/4‑141 (MQ=11)
                                                                                                                            ttttaataaAAAT‑GATGGTTCTGTTGCAAAGT‑AAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCgg               >  1:394194/4‑141 (MQ=11)
                                                                                                                             tttaataaAAAT‑GATGGTTCTGTTGCAAAGT‑AAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCgct              >  2:50946/3‑139 (MQ=11)
                                                                                                                              cTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCgg               >  1:228686/1‑141 (MQ=40)
                                                                                                                                  taaAAAT‑GATGGTTCTGTTGCAAAGT‑AAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCttt         <  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)
                                                                                                                                            |                                                                                                                                           
GCAAATTATTCTGAATTTAAAGATGTAGATGATCTCATTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCTTTTTATATA  >  CP000730/35677‑35956

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: ‑