Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 2,454,626 A→T 100% L48L (CTA→CTT USA300HOU_2315 → hypothetical membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,454,6260AT96.6% 169.2 / ‑3.3 57L48L (CTA→CTTUSA300HOU_2315hypothetical membrane protein
Reads supporting (aligned to +/- strand):  ref base A (0/2);  new base T (31/24);  total (31/26)
Fisher's exact test for biased strand distribution p-value = 2.04e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.89e-01
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ATAAAATTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTAGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTAATTAT  >  CP000730/2454493‑2454760
                                                                                                                                     |                                                                                                                                      
ataaaaaaacTGGATTTCAATGGGCAATGAAGATATTCGTCTTCTTGGTCTTTAAATTTGCGTAATCCATTATGCTCAGAGATTTCGAGTCTATACTTGGTGTCAAACACTTTCTATTTCGAGTTACACATCTTGCCCCa                                                                                                                                  >  2:6659/10‑140 (MQ=255)
 tAAAATTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCAt                                                                                                                                 <  2:103351/140‑1 (MQ=255)
  aaaaTTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTTTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCAtt                                                                                                                                <  1:110255/140‑1 (MQ=255)
     aTTTCTGGTTTTCAATGGGCAATGACGATTTTTGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAAt                                                                                                                             <  1:258538/140‑1 (MQ=255)
          tGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCCGTGTATAATTAGGGTCAAACCCTTTATATCTGAACTTCCAGATCTTGCACCATTACTtcctg                                                                                                                        >  2:430109/1‑140 (MQ=255)
          tGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTAAATAATTGGTGTCAAAAACTTTATATTTGAAGTTACAGATCTTGCACCATTAATtgctg                                                                                                                        >  2:35373/1‑140 (MQ=255)
            gTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCa                                                                                                                      <  1:221684/140‑1 (MQ=255)
                         aaTGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATAc                                                                                                         <  2:183137/140‑1 (MQ=255)
                           tGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTAGCACCATTAATTGCTGCAATCATTTGTATACTc                                                                                                       <  2:455675/140‑1 (MQ=255)
                              cGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCAATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGtt                                                                                                    >  2:265511/1‑140 (MQ=255)
                                 ttttCGTCTTCTTTGTCATCACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCAATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTc                                                                                                 >  1:330960/1‑140 (MQ=255)
                                 ttttCGTCTTCTTTCTCGTTACAATGGCGCTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTc                                                                                                 >  1:294417/1‑140 (MQ=255)
                                 gtttCGTCTTCTTTTTTATTAACATGGAGTTATCCATTATGCTCAGTTATTTCCTGTCTATAATTTGTGTCAAACACTTTATATTTGAAGTTACATATCTTGCACCATTAATTAATTAAAGCATTTTTATACTCGTTTTc                                                                                                 <  2:530170/139‑1 (MQ=255)
                                      gttttcttTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAata                                                                                            <  2:52011/137‑1 (MQ=255)
                                             ttGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAg                                                                                     >  1:413087/1‑140 (MQ=255)
                                                   ttACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGGACCATTACTTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCaa                                                                               >  1:405886/1‑140 (MQ=255)
                                                   taaCAATGGCGTTATCCAGTATGCTAACAAGTAGCCAGTCTATAAATGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTCCGGCAATCATTTGTATACTAGTTTTCAATTATAAAAAgggcaaa                                                                               >  2:503655/3‑135 (MQ=255)
                                                     acaatgcgcttAGCCATTATGCTCACAGATTTCCAGTCTATCATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAACCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACt                                                                             <  2:146353/131‑1 (MQ=255)
                                                            cGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGt                                                                      <  1:23511/140‑1 (MQ=255)
                                                              ttATCCCTTATTCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGttt                                                                    <  2:282625/140‑1 (MQ=255)
                                                              ttATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGttt                                                                    >  1:229964/1‑140 (MQ=255)
                                                              gtATCCATTATGCTCAGAGTTTTCCATTTTATAATTGGTGTCAAACAATACAAATGTGAAGTTACATATCTTTCACGATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGttt                                                                    <  2:73349/139‑1 (MQ=255)
                                                                 tCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTaaa                                                                 >  1:413250/1‑140 (MQ=255)
                                                                   cATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTCAAAt                                                               >  2:365829/1‑140 (MQ=255)
                                                                     ttATGCTGACAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATtc                                                             <  2:92011/140‑1 (MQ=255)
                                                                     ttATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAAtac                                                             >  1:133157/1‑138 (MQ=255)
                                                                        ttcttatataTTTCCTGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCa                                                          <  2:54587/131‑1 (MQ=255)
                                                                        tGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCa                                                          <  1:321564/140‑1 (MQ=255)
                                                                          cTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATCTTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAACATTCTCAAt                                                        >  2:132439/1‑140 (MQ=255)
                                                                           tCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATc                                                       <  2:244602/140‑1 (MQ=255)
                                                                           tCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTAGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATc                                                       <  1:268502/140‑1 (MQ=255)
                                                                             agagATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAg                                                     >  2:494304/1‑140 (MQ=255)
                                                                                gaTTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCt                                                  >  2:174654/1‑140 (MQ=255)
                                                                                  ttgccAGGCTAGAATTGGTGTCAAACGCTTTATATTTGAAGTTACAGTTCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGGCCAGCGTGCAGGTTTAAGATTCTCAAGCAGGCTGa                                                <  2:109099/137‑1 (MQ=255)
                                                                                      cAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGt                                            >  2:371338/1‑140 (MQ=255)
                                                                                      cAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGt                                            >  1:215682/1‑140 (MQ=255)
                                                                                      cAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAAATGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGt                                            >  1:171089/1‑140 (MQ=255)
                                                                                       aGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCACGTTTAAAATTCTCCATCAGCCCGAAAGTa                                           >  2:234862/1‑140 (MQ=255)
                                                                                           tataATTGGTGTCATACACTTTATACTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGCCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTg                                       <  1:334395/140‑1 (MQ=255)
                                                                                                ttGGTGGCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGt                                  >  2:304886/1‑140 (MQ=255)
                                                                                                    tgtCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTAt                              <  1:190432/140‑1 (MQ=255)
                                                                                                     gtCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTAtt                             >  1:208268/1‑140 (MQ=255)
                                                                                                          acacTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCGTGAAAGTAATTGAACGTCTATTGCTAg                        >  2:492136/1‑140 (MQ=255)
                                                                                                          acacTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAg                        >  2:547497/1‑140 (MQ=255)
                                                                                                           cacTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGc                       >  2:151175/1‑140 (MQ=255)
                                                                                                            acTTTATATTTGAAGTTACTGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCt                      <  2:336143/140‑1 (MQ=255)
                                                                                                            acTTTATATTTGAAGTTACAGATCTTTCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCt                      <  2:508783/140‑1 (MQ=255)
                                                                                                              tttATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAGTAATTTGTATACGCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCttt                    <  1:260196/140‑1 (MQ=255)
                                                                                                                tataTTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTCTATTAGTTAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTaa                  <  1:400541/140‑1 (MQ=255)
                                                                                                                 atatTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAAt                 >  1:235664/1‑140 (MQ=255)
                                                                                                                       gAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTATATTGCTAACTTTAATTTTAcc           >  2:147749/1‑140 (MQ=255)
                                                                                                                          gTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATAGTCGTTTTCGATTATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTAAACGTCTATTGCTAGCTTTAATTTTACCttt        >  1:211322/1‑140 (MQ=255)
                                                                                                                          gTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAAGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCttt        >  1:443420/1‑140 (MQ=255)
                                                                                                                           ttACAGATTTTGCACTATTAATTGCTGCAATCATTTTTATACTCGTTTTTAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTa       <  1:78526/140‑1 (MQ=255)
                                                                                                                               aGATCTTGCACCATTAATAGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTAatta   >  2:233096/1‑140 (MQ=255)
                                                                                                                                gATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTAattat  <  2:511316/140‑1 (MQ=255)
                                                                                                                                gATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCAAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTCCCTTTActtct  >  2:134958/1‑138 (MQ=255)
                                                                                                                                     |                                                                                                                                      
ATAAAATTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTAGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTAATTAT  >  CP000730/2454493‑2454760

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: