Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 35,817 A→T 22.2% intergenic (+48/+60) rlmH → / ← tpn hypothetical protein/IS431mec transposase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP00073035,8170AT22.2% 115.8 / 18.4 47intergenic (+48/+60)rlmH/tpnhypothetical protein/IS431mec transposase
Reads supporting (aligned to +/- strand):  ref base A (17/19);  new base T (6/5);  total (23/24)
Fisher's exact test for biased strand distribution p-value = 7.40e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTATTCTGAATTTAAAGATGTAGATGATCTCATTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCTTTTTATA  >  CP000730/35682‑35954
                                                                                                                                       |                                                                                                                                         
ttattCTGAATTTAAAGATGTAGATGATCTCATTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTc                                                                                                                                      <  1:1963/141‑1 (MQ=255)
      tGAATTTAAAGATGTAGATGATCTCATTGACAAAGTATTTAATGTAGAAGCTATTCAGAATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGc                                                                                                                                >  1:115432/1‑141 (MQ=255)
        aaTTTAAAGATGTAGATGATCTCATTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCaa                                                                                                                              <  1:305663/141‑1 (MQ=255)
               aGATGTAGATGATCTCATTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTaaaa                                                                                                                       >  1:298652/1‑141 (MQ=255)
                                    cAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTTTTTTTTTTTGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAAtt                                                                                                  >  2:174467/1‑141 (MQ=37)
                                    cAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAGAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAAtt                                                                                                  >  1:4398/1‑141 (MQ=255)
                                    cAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTAAAAAAAAAAAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAAtt                                                                                                  <  2:77630/141‑1 (MQ=38)
                                     aaaGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAAttt                                                                                                 >  2:247013/1‑141 (MQ=255)
                                      aaGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTa                                                                                                >  2:10417/1‑141 (MQ=255)
                                       aGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATACAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTAt                                                                                               <  1:271308/141‑1 (MQ=255)
                                        gTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGTCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCGAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATc                                                                                              >  2:251297/1‑141 (MQ=255)
                                                    gAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTc                                                                                  <  1:209785/141‑1 (MQ=255)
                                                     aaGCCATTCAGTATAAAGATAGAAGAGAAAAATGACTAACAGAACAAGAGCTAAAATAAAATTGAAATCTAATACAAATAGAAGGTTCAGAAAAAAAAAAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCg                                                                                 <  2:64086/141‑1 (MQ=16)
                                                       gCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCt                                                                               >  2:102897/1‑141 (MQ=255)
                                                           ttCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAAc                                                                           <  1:135827/141‑1 (MQ=255)
                                                              aGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTg                                                                        <  1:247013/141‑1 (MQ=255)
                                                                       tttttGGAGAAAAATGATTACTTGAACAAGAGCTAAAATAAAACTGTTATCTAATATACATAGTAGGTTTAATAAAAAAAAAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCatga                                                               <  2:68041/141‑1 (MQ=18)
                                                                          ttGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGc                                                            <  1:165555/141‑1 (MQ=255)
                                                                           tgacataaaaTGATTACGTGAAGAAGAGCTAAAATAAAATTGTGAACAAATAAAAAGAGATTGTGCTGTTGAAAAGTAAAGAAAGATAAATAACCACTTACGTACCATGTCAGTGTGTGCTTAGATTGCAAGTAAGAAGCt                                                           <  2:136756/135‑1 (MQ=255)
                                                                            ggCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTa                                                          >  2:259498/1‑141 (MQ=255)
                                                                             gCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAAGTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTaa                                                         <  2:84671/141‑1 (MQ=255)
                                                                                     tGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTgg                                                 <  2:106618/141‑1 (MQ=255)
                                                                                           cTTGAACAAGAGCTAGAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATTCTAATTTCGTGTCATGGc                                           >  2:26323/1‑141 (MQ=255)
                                                                                            ttGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCg                                          <  2:165007/141‑1 (MQ=255)
                                                                                             tGAACAAGAGATAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGa                                         <  2:242453/141‑1 (MQ=255)
                                                                                                   agagCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATcc                                   >  2:98718/1‑141 (MQ=255)
                                                                                                    gagCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCg                                  >  1:32546/1‑141 (MQ=255)
                                                                                                          aaataaaatTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATc                            <  1:284414/141‑1 (MQ=255)
                                                                                                            acataagcgtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATATCTAATCACTAATATATCTTGTCAGTGTTTGTTTAACTTGCTAGCATTATCCTAATTTCGTGGCATGGCGACATTCCGTAGTCCTGaa                        >  2:34872/15‑141 (MQ=2)
                                                                                                            acaaaagagtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGaa                        >  2:99850/15‑141 (MQ=11)
                                                                                                                 atTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAagag                     >  1:208316/1‑141 (MQ=255)
                                                                                                                    gtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTg                >  2:230409/7‑141 (MQ=11)
                                                                                                                      gATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTg                <  1:55424/141‑1 (MQ=255)
                                                                                                                      attgtaataaAAATGATGATTCTTTTGCAAAGTAAAAAATATAGCTAGTCACTAATATATCTAGTCAGTGTTCGTTTACCTTGCTAGCATGATGATAATTTCGTGCCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCg              <  2:185032/137‑1 (MQ=11)
                                                                                                                       ttttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCgg             <  1:15779/138‑1 (MQ=11)
                                                                                                                       ttttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCgg             >  1:289171/4‑141 (MQ=11)
                                                                                                                         ttaataaAAATGATGGTACTGTTTCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGATGAGACCTGCGGtt           <  2:232123/140‑1 (MQ=11)
                                                                                                                          taataaAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGt            <  1:324997/141‑1 (MQ=40)
                                                                                                                           aataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCt         <  2:57244/141‑1 (MQ=11)
                                                                                                                            ataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCtt        >  1:132431/1‑141 (MQ=11)
                                                                                                                            ataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCtt        >  1:77376/1‑141 (MQ=11)
                                                                                                                                 aaTAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCttttt     <  2:327748/141‑1 (MQ=34)
                                                                                                                                 aaTAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCttttt     <  2:306748/141‑1 (MQ=34)
                                                                                                                                 aaTAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCttttt     >  1:21386/1‑141 (MQ=34)
                                                                                                                                 aaTAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCttttt     >  2:27155/1‑141 (MQ=34)
                                                                                                                                 aaTAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCttttt     >  1:228216/1‑141 (MQ=34)
                                                                                                                                    aGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCTTTTtata  >  1:260123/1‑141 (MQ=32)
                                                                                                                                       |                                                                                                                                         
TTATTCTGAATTTAAAGATGTAGATGATCTCATTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCTTTTTATA  >  CP000730/35682‑35954

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: