Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 2,566,074 C→T 9.5% G20R (GGA→AGA)  USA300HOU_2426 ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,566,0740CT 9.5% 126.0 / 4.1 42G20R (GGA→AGA) USA300HOU_2426hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (15/23);  new base T (2/2);  total (17/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.66e-01

TTACAGTCCAAACATTAAGCAAGACATAACAATACCCCCGTACATATGAGACAAAGTCATTATCATCTCATATGTACGGGGTTTTTATATTCAACATCAAAAAATCAGATTGATGAAAAGTAAATAACCTTTCATCAATCCGATTTGATTATAGAATCTATTTTTTAAGTTTAAATGGAATTGTACATACGTTAACATTCTTTTGATAAATTAAATACAATTTCATACGCAAACTAGTTTGATTGTGTAATAAATTATGCCAACGTTTCTTAGTAA  >  CP000730/2565934‑2566209
                                                                                                                                            |                                                                                                                                       
ttACAGTCCAAACATTAAGCAAGACATAACAATACCCCCGTACATATGAGACAAAGTCATTATCATCTCATATGTACGGGGTTTTTATATTCAACATCAAAAAATCAGATTGATGAAAAGTAAATAACCTTTCATCAATcc                                                                                                                                         <  1:834/141‑1 (MQ=255)
     gTCCAAACATTAAGCAAGACATAACAATACCCCCGTACATATGAGACAAAGTCATTATCATCTCATATGTACGGGGTTTTTATATTCAACATCAAAAAATCAGATTGATGAAAAGTAAATAACCTTTCATCAATCCGAttt                                                                                                                                    <  2:5886/141‑1 (MQ=255)
     gTCCAAACATTAAGCAAGACATAACAATACCCCCGTACATATGAGACAAAGTCATTATCATCTCATATGTACGGGGTTTTTATATTCAACATCAAAAAATCAGATTGATGAAAAGTAAATAACCTTTCATCAATCCGAttt                                                                                                                                    <  2:4942/141‑1 (MQ=255)
     gTCCAAACATTAAGCAAGACATAACAATACCCCCGTACATATGAGACAAAGTCATTATCATCTCATATGTACGGGGTTTTTATATTCAACATCAAAAAATCAGATTGATGAAAAGTAAATAACCTTTCATCAATCCGAttt                                                                                                                                    <  2:27139/141‑1 (MQ=255)
      tCCAAACATTAAGCAAGACATAACAATACCCCCGTACATATGAGACAAAGTCATTATCATCTCATATGTACGGGGTTTTTATATTCAACATCAAAAAATCAGATTGATGAAAAGTAAATAACCTTTCATCAATCCGATTTg                                                                                                                                   >  1:192617/1‑141 (MQ=255)
           aCATTAAGCAAGACATAACAATACCCCCGTACATATGAGACAAAGTCATTATCATCTCATATGTACGGGGTTTTTATATTCAACATCAAAAAATCAGATTGATGAAAAGTAAATAACCTTTCATCAATCCGATTTGATtat                                                                                                                              >  2:90299/1‑141 (MQ=255)
                  gCAAGACATAACAATACCCCCGTACATATGAGACAAAGTCATTATCATCTCATATGTACGGGGTTTTTATATTCAACATCAAAAAATCAGATTGATGAAAAGTAAATAACCTTTCATCAATCCGATTTGATTATAGAATCt                                                                                                                       <  1:108357/141‑1 (MQ=255)
                  gCAAGACATAACAATACCCCCGTACATATGAGACAAAGTCATTATCATCTCATATGTACGGGGTTTTTATATTCAACATCAAAAAATCAGATTGATGAAAAGTAAATAACCTTTCATCAATCCGATTTGATTATAGAATCt                                                                                                                       <  1:152505/141‑1 (MQ=255)
                     aGACATAACAATACCCCCGTACATATGAGACAAAGTCATTATCATCTCATATGTACGGGGTTTTTATATTCAACATCAAAAAATCAGATTGATGAAAAGTAAATAACCTTTCATCAATCCGATTTGATTATAGAATCTAtt                                                                                                                    >  1:24212/1‑141 (MQ=255)
                         aTAACAATACCCCCGTACATATGAGACAAAGTCATTATCATCTCATATGTACGGGGTTTTTATATTCAACATCAAAAAATCAGATTGATGAAAAGTAAATAACCTTTCATCAATCCGATTTGATTATAGAATCTAtttttt                                                                                                                <  2:130787/141‑1 (MQ=255)
                         aTAACAATACCCCCGTACATATGAGACAAAGTCATTATCATCTCATATGTACGGGGTTTTTATATTCAACATCAAAAAATCAGATTGATGAAAAGTAAATAACCTTTCATCAATCCGATTTGATTATAGAATCTAtttttt                                                                                                                <  2:74077/141‑1 (MQ=255)
                         aTAAAAATACCCCCGTACAGATGAGACAAAGTCATTATCAGCAAATATGTACGGGGTTTTTATATTCAACATCAAGAAATAAGATTGATGAAAAGTAAATAACCTTTCATCAATCCGATTTGATTATAGAATCTAtttttt                                                                                                                <  2:26441/141‑1 (MQ=255)
                            aCAATACCCCCGTACATATGAGACAAAGTCATTATCATCTCATATGTACGGGGTTTTTATATTCAACATCAAAAAATCAGATTGATGAAAAGTAAATAACCTTTCATCAATCCGATTTGATTATAGAATCTATTTTTTAAg                                                                                                             >  2:221922/1‑141 (MQ=255)
                                  cccccGTACATATGAGACAAAGTCATTATCATCTCATATGTACGGGGTTTTTATATTCAACATCAAAAAATCAGATTGATGAAAAGTAAATAACCTTTCATCAATCTGATTTGATTATAGAATCTATTTTTTAAGTTTaaa                                                                                                       >  1:79612/1‑141 (MQ=255)
                                  cccccGTACATATGAGACAAAGTCATTATCATCTCATATGTACGGGGTTTTTATATTCAACATCAAAAAATCAGATTGATGAAAAGTAAATAACCTTTCATCAATCTGATTTGATTATAGAATCTATTTTTTAAGTTTaaa                                                                                                       >  1:51669/1‑141 (MQ=255)
                                  cccccGTACATATGAGACAAAGTCATTATCATCTCATATGTACGGGGTTTTTATATTCAACATCAAAAAATCAGATTGATGAAAAGTAAATAACCTTTCATCAATCCGATTTGATTATAGAATCTATTTTTTAAGTTTaaa                                                                                                       >  1:122854/1‑141 (MQ=255)
                                    cccGTACATATGAGACAAAGTCATTATCATCTCATATGTACGGGGTTTTTATATTCAACATCAAAAAATCAGATTGATGAAAAGTAAATAACCTTTCATCAATCCGATTTGATTATAGAATCTATTTTTTAAGTTTAAATg                                                                                                     <  1:250564/141‑1 (MQ=255)
                                    cccGTACATATGAGACAAAGTCATTATCATCTCATATGTACGGGGTTTTTATATTCAACATCAAAAAATCAGATTGATGAAAAGTAAATAACCTTTCATCAATCCGATTTGATTATAGAATCTATTTTTTAAGTTTAAATg                                                                                                     <  1:236122/141‑1 (MQ=255)
                                             atGAGACAAAGTCATTATCATCTCATATGTACGGGGTTTTTATATTCAACATCAAAAAATCAGATTGATGAAAAGTAAATAACCTTTCATCAATCCGATTTGATTATAGAATCTATTTTTTAAGTTTAAATGGAATTGTAc                                                                                            <  1:203643/141‑1 (MQ=255)
                                                 gaCAAAGTCATTATCATCTCATATGTACGGGGTTTTTATATTCAACATCAAAAAATCAGATTGATGAAAAGTAAATAACCTTTCATCAATCCGATTTGATTATAGAATCTATTTTTTAAGTTTAAATGGAATTGTACATAc                                                                                        >  2:135681/1‑141 (MQ=255)
                                                      aGTCATTATCATCTCATATGTACGGGGTTTTTATATTCAACATCAAAAAATCAGATTGATGAAAAGTAGATAACCTTTCATCAATCCGATTTGATTATAGAATCTATTTTTTAAGTTTAAATGGAATTGTACATACGTTaa                                                                                   <  1:126053/141‑1 (MQ=255)
                                                      aGTCATTATCATCTCATATGTACGGGGTTTTTATATTCAACATCAAAAAATCAGATTGATGAAAAGTAAATAACCTTTCATCAATCCGATTTGATTATAGAATCTATTTTTTAAGTTTAAATGGAATTGTACATACGTTaa                                                                                   <  1:126067/141‑1 (MQ=255)
                                                         cATTATCATCTCATATGTACGGGGTTTTTATATTCAACATCAAAAAATCAGATTGATGAAAAGTAAATAACCTTTCATCAATCCGATTTGATTATAGAATCTATTTTTTTTTTTTATTTTGAATTGTACATACGTTAACAt                                                                                >  2:150340/1‑141 (MQ=255)
                                                             atcatcTCATATGTACGGGGTTTTTATATTCAACATCAAAAAATCAGATTGATGAAAAGTAAATAACCTTTCATCAATCCGATTTGATTATAGAATCTATTTTTTAAGTTTAAATGGAATTGTACATACGTTAACATTCtt                                                                            >  2:159385/1‑141 (MQ=255)
                                                             atcatcTCATATGTACGGGGTTTTTATATTCAACATCAAAAAATCAGATTGATGAAAAGTAAATAACCTTTCATCAATCCGATTTGATTATAGAATCTATTTTTTAAGTTTAAATGGAATTGTACATACGTTAACATTCtt                                                                            >  1:161432/1‑141 (MQ=255)
                                                                            cGGGGTTTTTATATTCAACATCAAAAAATCAGATTGATGAAAAGTAAATAACCTTTCATCAATCCGATTTGATTATAGAATCTATTTTTTAAGTTTAAATGGAATTGTACATACGTTAACATTCTTTTGATAAATTAAATa                                                             <  2:77403/141‑1 (MQ=255)
                                                                             ggggTTTTTATATTCAACATCAAAAAATCAGATTGATGAAAAGTAAATAACCTTTCATCAATCTGATTTGATTATAGAATCTATTTTTTAAGTTTAAATGGAATTGTACATACGTTAACATTCTTTTGATAAATTAAATAc                                                            <  2:51669/141‑1 (MQ=255)
                                                                             ggggTTTTTATATTCAACATCAAAAAATCAGATTGATGAAAAGTAAATAACCTTTCATCAATCTGATTTGATTATAGAATCTATTTTTTAAGTTTAAATGGAATTGTACATACGTTAACATTCTTTTGATAAATTAAATAc                                                            <  2:79612/141‑1 (MQ=255)
                                                                                   tttATATTCAACATCAAAAAATCAGATTGATGAAAAGTAAATAACCTTTCATCAATCCGATTTGATTATAGAATCTATTTTTTAAGTTTAAATGGAATTGTACATACGTTAACATTCTTTTGATAAATTAAATACAATTTc                                                      <  1:90299/141‑1 (MQ=255)
                                                                                      atatTCAACATCAACAAATAATATTGATGAAAGGTAAATGACCTTTTATCAAGCCGAATTGATTATAGAATCTATTTTTTAAGTTTAAATGGAAGTGTACATACGTTAACATTCTTTTTATAAATTAAATACAATTTCATa                                                   >  1:25824/1‑141 (MQ=255)
                                                                                           cAACATCAAAAAATCAGATTGATGAAAAGTAAATAACCTTTCATCAATCCGATTTGATTATAGAATCTATTTTTTAAGTTTAAATGGAATTGTACATACGTTAACATTCTTTTGATAAATTAAATACAATTTCATACGCaa                                              <  1:141323/141‑1 (MQ=255)
                                                                                             aCATCAAAAAATCAGATTGATGAAAAGTAAATAACCTTTCATCAATCCGATTTGATTATAGAATCTATTTTTTAAGTTTAAATGGAATTGTACATACGTTAACATTCTTTTGATAAATTAAATACAATTTCATACGCAAAc                                            >  1:208972/1‑141 (MQ=255)
                                                                                              cATCAAAAAATCAGATTGATGAAAAGTAAATAACCTTTCATCAATCCTATTTGATTATAGAATCTATTTTTTAAGTTTAAATGGAATTGTACATACGTTAACATTCTTTTGATAAATTAAATACAATTTCATACGCAAACt                                           <  1:235245/141‑1 (MQ=255)
                                                                                              cATCAAAAAATCAGATTGATGAAAAGTAAATAAACTTTCATCAATCCGATTTGATTATAGAATCTATTTTTTAAGTTTAAATGGAATTGTACATACGTTAACATTCTTTTGATAAATTAAATACAATTTCATACGCAAACt                                           <  2:248519/141‑1 (MQ=255)
                                                                                                  aaaaaaTCAGATTGATGAAAAGTAAATAACCTTTCATCAATCCGATTTGATTATAGAATCTATTTTTTAAGTTTAAATGGAATTGTACATACGTTAACATTCTTTTGATAAATTAAATACAATTTCATACGCAAACTAGtt                                       >  2:61631/1‑141 (MQ=255)
                                                                                                     aaaTCAGATTGATGAANAGTAAATAACCTNTCATCAATCCGATTTGATTATAGAATCTATTTTTTAAGTTTAAATGGAATTGTACATACGTTAACATTCTTTTGATAAATTAAATACAATTTCATACGCAAACTAGTTTgt                                    >  1:178289/1‑140 (MQ=255)
                                                                                                                  gaAAAGTAAATAACCTTTCATCAATCCGATTTGATTATAGAATCTATTTTTTAAGTTTAAATGGAATTGTACATACGTTAACATTCTTTTGATAAATTAAATACAATTTCATACGCAAACTAGTTTGATTGTGTAATAAAt                       <  1:221922/141‑1 (MQ=255)
                                                                                                                        tAAATAACCTTTCATCAATCCGATTTGATTATAGAATCTATTTTTTAAGTTTAAATGGAATTGTACATACGTTAACATTCTTTTGATAAATTAAATACAATTTCATACGCAAACTAGTTTGATTGTGTAATAAATTATGcc                 >  1:170351/1‑141 (MQ=255)
                                                                                                                          aaTAACCTTTCATCAATCCGATTTGATTATAGAATCTATTTTTTAAGTTTAAATGGAATTGTACATACGTTAACATTCTTTTGATAAATTAAATACAATTTCATACGCAAACTAGTTTGATTGTGTAATAAATTATGCCaa               <  2:122854/141‑1 (MQ=255)
                                                                                                                           aTAACCTTTCATCAATCCGATTTGATTATAGAATCTATTTTTTAATTTTAAATTTAATTGTACATACGTTAACATTCTTTTGATAAATTAAATACAATTTCATACGCAAACTAGTTTGATTGTGTAATAAATTATGCCAAc              >  2:177179/1‑141 (MQ=255)
                                                                                                                             aaCCTTTCATCAATCCGATTTGATTATAGAATCTATTTTTTAAGTTTAAATGGAATTGTACATACGTTAACATTCTTTTGATAAATTAAATACAATTTCATACGCAAACTAGTTTGATTGTGTAATAAATTATGCCAACGt            <  1:245494/141‑1 (MQ=255)
                                                                                                                                       caATCCGATTTGATTATAGAATCTATTTTTTAAGTTTAAATGGAATTGTACATACGTTAACATTCTTTTGATAAATTAAATACAATTTCATACGCAAACTAGTTTGATTGTGTAATAAATTATGCCAACGTTTCTTAGtaa  <  2:256807/141‑1 (MQ=255)
                                                                                                                                       caATCCGATTTGATTATAGAATCTATTTTTTAAGTTTAAATGGAATTGTACATACGTTAACATTCTTTTGATAAATTAAATACAATTTCATACGCAAACTAGTTTGATTGTGTAATAAATTATGCCAACGTTTCTTAGtaa  <  1:202496/141‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                       
TTACAGTCCAAACATTAAGCAAGACATAACAATACCCCCGTACATATGAGACAAAGTCATTATCATCTCATATGTACGGGGTTTTTATATTCAACATCAAAAAATCAGATTGATGAAAAGTAAATAACCTTTCATCAATCCGATTTGATTATAGAATCTATTTTTTAAGTTTAAATGGAATTGTACATACGTTAACATTCTTTTGATAAATTAAATACAATTTCATACGCAAACTAGTTTGATTGTGTAATAAATTATGCCAACGTTTCTTAGTAA  >  CP000730/2565934‑2566209

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