Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 35,814 Δ1 bp 17.4% intergenic (+45/+63) USA300HOU_0025 → / ← USA300HOU_0026 hypothetical protein/IS431mec transposase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP00073035,8140A.17.4% 104.8 / 24.6 46intergenic (+45/+63)USA300HOU_0025/USA300HOU_0026hypothetical protein/IS431mec transposase
Reads supporting (aligned to +/- strand):  ref base A (19/18);  new base . (3/5);  total (22/24)
Fisher's exact test for biased strand distribution p-value = 6.99e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.88e-01

TGCAAATTATTCTGAATTTAAAGATGTAGATGATCTCATTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCTTTTT  >  CP000730/35676‑35951
                                                                                                                                          |                                                                                                                                         
tGCAAATTATTCTGAATTTAAAGATGTAGATGATCTCATTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAACATAGa                                                                                                                                         >  1:65858/1‑141 (MQ=255)
 gCAAATTATTCTGAATTTAAAGATGTAGATGATCTCATTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAACATAGaa                                                                                                                                        >  2:49308/1‑141 (MQ=255)
     attattCTGAATTTAAAGATGTAGATGATCTCATTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGtt                                                                                                                                    <  2:176659/141‑1 (MQ=255)
      ttattCTGAATTTAAAGATGTAGATGATCTCATTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGATAAAATAAAATTGTGATCTAATAAAAATAAAAGGtta                                                                                                                                   >  1:106749/1‑140 (MQ=255)
            tGAATTTAAAGATGTAGATGATCTCATTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGc                                                                                                                             <  2:54178/141‑1 (MQ=255)
             gAATTTAAAGATGTAGATGATCTCATTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCa                                                                                                                            >  2:105924/1‑141 (MQ=255)
               aTTTAAAGATGTAGATGATCTCATTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGAGTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCaaa                                                                                                                          <  2:246676/141‑1 (MQ=255)
               aTTTAAAGATGTAGATGATCTCATTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAg                                                                                                                         <  1:102635/141‑1 (MQ=255)
               aTTTAAAGATGGAGAGGATCTCAGTGAACAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTGGCGAAAAATGATTAGTTGAACAAGAGCTAAAATAAAATGGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAg                                                                                                                         <  1:102582/141‑1 (MQ=255)
                    aaGATGTACATGATCTCATTGACAAAGTATTTAATGTAGAAGCTATTCAGAATAAAGTTTTTGGCGAAAAATGATTACTTGAACAACAGCGAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTGTGTTGAAAAGTaaa                                                                                                                     >  2:246192/1‑141 (MQ=255)
                          tAGATGATCTCATTGACAAAGTATTTAAGGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAata                                                                                                               <  1:50118/141‑1 (MQ=255)
                             gtgatCTCATTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTGTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATATAAGGTTCTGAAAAAAAATAAAAAAACATAg                                                                                                            <  2:202748/140‑1 (MQ=255)
                              tgatCTCATTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGc                                                                                                           >  2:305847/1‑141 (MQ=255)
                                   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                         >  2:1121/1‑141 (MQ=255)
                                                                                                                aaataaaatTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATc                         <  1:305847/141‑1 (MQ=255)
                                                                                                                aaataaaatTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATc                         <  1:18041/141‑1 (MQ=255)
                                                                                                                 aataaaatTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACAACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGAGGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCt                        >  2:76765/1‑141 (MQ=255)
                                                                                                                  acaaaagagtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGaa                     >  1:138666/15‑141 (MQ=11)
                                                                                                                  acaaaagagtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGaa                     >  1:133051/15‑141 (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)
                                                                                                                                          |                                                                                                                                         
TGCAAATTATTCTGAATTTAAAGATGTAGATGATCTCATTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCTTTTT  >  CP000730/35676‑35951

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: