Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 35,850 C→T 23.6% intergenic (+81/+27) USA300HOU_0025 → / ← USA300HOU_0026 hypothetical protein/IS431mec transposase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP00073035,8500CT23.6% 63.7 / 11.7 33intergenic (+81/+27)USA300HOU_0025/USA300HOU_0026hypothetical protein/IS431mec transposase
Reads supporting (aligned to +/- strand):  ref base C (12/13);  new base T (3/5);  total (15/18)
Fisher's exact test for biased strand distribution p-value = 6.99e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.86e-01

TCATTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCTTTTTATATAGAGCGTAAA  >  CP000730/35711‑35965
                                                                                                                                           |                                                                                                                   
tcATTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGAATACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTTTGTTGCAATGAAAAAAAATATAGCTAAcc                                                                                                                    >  1:136584/1‑141 (MQ=255)
         aaGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTa                                                                                                           >  1:145485/1‑141 (MQ=255)
                tAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTc                                                                                                    >  2:312004/1‑141 (MQ=255)
                     tAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGATAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATAATGTCAgtga                                                                                               >  2:203481/1‑140 (MQ=255)
                       gAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTc                                                                                             >  2:70902/1‑141 (MQ=255)
                         aGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGc                                                                                           >  1:216508/1‑141 (MQ=255)
                                          tttttGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTCATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCatga                                                                          >  2:276640/1‑141 (MQ=255)
                                             ttGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGc                                                                       <  1:23039/141‑1 (MQ=255)
                                              tGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCt                                                                      <  1:252774/141‑1 (MQ=255)
                                               tgataaaaaTGATTACTTGAACAATAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTa                                                                     <  2:65442/137‑1 (MQ=255)
                                                    aaaaTGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAACAATAGAAGGTTCTGTTGCAAAGTAAAATAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTc                                                                >  1:329679/1‑141 (MQ=255)
                                                      aaTGATTACTTGAACAAGGGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTGAAAAAATATAGCTACCCACTAATTTATCATGTCAGTGTTAGCTTAGCTTGCTAGCATGAGGCTAATTTCGt                                                              >  2:38533/1‑141 (MQ=21)
                                                               ttGAAAAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGTAATGGct                                                     <  2:289270/141‑2 (MQ=255)
                                                                    cAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAAt                                                <  1:58720/141‑1 (MQ=255)
                                                                    cAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAAt                                                <  1:323583/141‑1 (MQ=255)
                                                                        agCTAAAATAAAATTGTGATCTAATAGAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGACACTCCGt                                            >  2:306491/1‑141 (MQ=255)
                                                                             aaataaaatTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATc                                       <  1:305847/141‑1 (MQ=255)
                                                                             aaataaaatTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATc                                       <  1:18041/141‑1 (MQ=255)
                                                                             aaataaaatTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATc                                       >  2:1121/1‑141 (MQ=255)
                                                                              aataaaatTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACAACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGAGGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCt                                      >  2:76765/1‑141 (MQ=255)
                                                                               acaaaagagtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGaa                                   >  1:133051/15‑141 (MQ=11)
                                                                               acaaaagagtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGaa                                   >  1:138666/15‑141 (MQ=11)
                                                                                  aaatTGTGATCTAATAAGAATAGAAGGTGCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCCTGTCAGTGTTCCTTTAACTTGCTAGCATGATGCTAATGTCGTGGCATGGCGAAAATCCGTAGATCTGAag                                  <  2:113847/141‑1 (MQ=14)
                                                                                    atagtattttaataaAAATGATGGTTCCGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGAc                              <  1:247329/132‑1 (MQ=11)
                                                                                    agagtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGAc                              <  1:247202/132‑1 (MQ=11)
                                                                                    agagtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGAc                              <  1:56848/132‑1 (MQ=11)
                                                                                     gagtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGAcc                             <  1:276739/133‑1 (MQ=11)
                                                                                      tgtgATCTAATAAAAATCGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGAc                              <  2:106749/141‑1 (MQ=255)
                                                                                        tgAGCTAATAAAAATAAAAGGTTCTTTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAagaccaca                            <  2:252766/141‑6 (MQ=255)
                                                                                          ttttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATGATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCGTGGCGAAAATCAGTAGATCTGAAGAGGCCTGCgg                        >  1:133254/4‑141 (MQ=11)
                                                                                             taataaAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACGTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGt                       >  2:167419/1‑141 (MQ=255)
                                                                                              aataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTGGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCt                    <  2:53817/141‑1 (MQ=11)
                                                                                                    aaTAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCttttt                <  1:133753/141‑1 (MQ=34)
                                                                                                                  ttacAAAGTAAAAAAATATAGATAACCACTAATTTATCATGTCAGTGTTCGCTTAACTGGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCTTTTTATATAGAGCGTaaa  <  2:170172/138‑1 (MQ=0)
                                                                                                                                           |                                                                                                                   
TCATTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCTTTTTATATAGAGCGTAAA  >  CP000730/35711‑35965

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: