Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 111,512 A→G 32.2% S194S (TCA→TCG)  USA300HOU_0110 → possible staphylococcal tandem lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP000730111,5120AG32.2% 58.8 / 36.3 53S194S (TCA→TCG) USA300HOU_0110possible staphylococcal tandem lipoprotein
Reads supporting (aligned to +/- strand):  ref base A (16/19);  new base G (13/4);  total (30/23)
Fisher's exact test for biased strand distribution p-value = 4.33e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.72e-01

ACTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAAT  >  CP000730/111375‑111652
                                                                                                                                         |                                                                                                                                            
aCTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTGTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATAGCATATAATCCAGAGGTGCCGAGTTATTCGGcg                                                                                                                                           >  1:381321/1‑140 (MQ=255)
 cTGAGGAAGTTAAAGAAGAAAACATAAAAAGAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTc                                                                                                                                          <  2:362450/141‑1 (MQ=255)
   gAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTaaa                                                                                                                                        >  2:529704/1‑141 (MQ=255)
        aGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAGTTTTAAAGATGGAGATATATCATATAATCCAGAGGTGCCGGGGTATTCAGCTCAGTATCa                                                                                                                                   >  1:558907/1‑141 (MQ=21)
        aGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCa                                                                                                                                   >  1:492576/1‑141 (MQ=255)
           tAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTTTTTTTTTTTTCAATTGTAAAGATGTAATGAATTATAAAGATGGAGATAGATGACATAATCGAGGGGTGCCGAGTTATTCAGGTCAATAACAAtt                                                                                                                                >  2:529958/1‑141 (MQ=16)
           tAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTCTTCCGCTAAATATCAAtt                                                                                                                                >  1:222052/1‑141 (MQ=255)
             aagaagAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTaa                                                                                                                              <  1:261146/141‑1 (MQ=255)
             aagaagAAAACAAAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATACCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTaa                                                                                                                              <  1:161844/141‑1 (MQ=255)
               gaagaaAACATAAATGAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTGAAGATTTGATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTATCt                                                                                                                            >  2:431417/1‑141 (MQ=17)
                    aaaCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAatga                                                                                                                       <  1:544155/141‑1 (MQ=255)
                     aaCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGGTATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAatgat                                                                                                                      >  1:415820/1‑141 (MQ=255)
                         tAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGAtt                                                                                                                  >  2:65270/1‑141 (MQ=255)
                           aaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTCACTAATGATGATtaa                                                                                                                >  2:75372/1‑140 (MQ=255)
                             aaaaGAAATCTAAAAATTTAAGTTTTTTGCGCAACATACCAATTTTAAAGATTTAAAGAATTATAAAGATGTAGATAGATTATATAAACCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATaa                                                                                                              <  1:45244/141‑1 (MQ=18)
                                aGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGt                                                                                                           <  1:200046/141‑1 (MQ=255)
                                        aaaaCTTTAAGTTTTTTGCGCAATGTAGCAATTTTAAAGATTTAATGAATTATAAAGATGGCGATCTCTCATATCATACAGCGGTGCCGCGTTATTCGGCCAAATATCCCGTAACTACTGATGATTATAATGTATAACAAt                                                                                                   <  2:476426/141‑1 (MQ=255)
                                         aaaCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAAtt                                                                                                  >  1:447133/1‑141 (MQ=255)
                                          aaCTGTAAGTTTTTTGAGCAATATATAAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTa                                                                                                 <  2:554037/141‑1 (MQ=255)
                                             tttAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGt                                                                                              <  1:472603/141‑1 (MQ=255)
                                                    tttttGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTAGGCAAAAGat                                                                                       >  1:83205/1‑141 (MQ=255)
                                                       ttGCGGAATATAGCAATTTTAGAGATTGAATGAATTATAAAGATGGAGACATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACATTTACGCAAAAGATATg                                                                                    <  2:231966/141‑1 (MQ=14)
                                                       ttGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATg                                                                                    >  2:452935/1‑141 (MQ=255)
                                                       ttGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATAATTATAATGTAAAACAATTACGCAAAAGATATg                                                                                    >  2:319534/1‑141 (MQ=255)
                                                        tGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGa                                                                                   >  2:125191/1‑141 (MQ=255)
                                                          cgcAAGATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACa                                                                                 <  2:446994/141‑1 (MQ=255)
                                                            cAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATGTCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATCTAAATTAACTAATGAGGATTATCATGTAAGACAATTAGGTAAAGGATATGACATa                                                                               >  1:56902/1‑141 (MQ=18)
                                                             aaTATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTGAAACAATTACGCAAAAGATATGATATAc                                                                              <  2:54066/141‑1 (MQ=14)
                                                               tataGCAATTTTAAAGATTTAATGAATTATAAGGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATAccg                                                                            >  1:409693/1‑140 (MQ=14)
                                                               tataGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATAccg                                                                            <  2:60891/141‑2 (MQ=14)
                                                                ataGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACcaa                                                                           <  1:202326/141‑1 (MQ=255)
                                                                ataGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACcaa                                                                           <  2:194443/141‑1 (MQ=255)
                                                                   gCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACcaacaa                                                                        <  2:384034/141‑1 (MQ=255)
                                                                     aaTTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAAt                                                                      >  1:426072/1‑141 (MQ=255)
                                                                      aTTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACcgacgagta                                                                     >  1:552115/1‑136 (MQ=11)
                                                                      aTTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACcaacgagta                                                                     >  2:275915/1‑136 (MQ=11)
                                                                           aaaGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAgcg                                                                >  1:127623/1‑141 (MQ=255)
                                                                           aaaGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAgcg                                                                >  1:460918/1‑141 (MQ=255)
                                                                               aTTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGa                                                            <  2:530419/141‑1 (MQ=255)
                                                                                    aTGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtg                                                       >  1:471151/1‑141 (MQ=255)
                                                                                            taAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGaa                                               >  2:493352/1‑141 (MQ=255)
                                                                                              aaGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAg                                             <  2:306071/141‑1 (MQ=255)
                                                                                                       aaagatCCTATAATCCAGAGGTGCCGAGTTATGCAGCTTAATATCCATTAACTAATGATGATTATAATGTAAAACCATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGa                                    <  2:95246/137‑1 (MQ=14)
                                                                                                        tatatCATAGAATCCAGAGGTGCCGAGTTATTCAGGTCAATATCAAGTAACTAATGATGATTATAATGTAAAACAATTACGACAAAGATATGACATACCAACAAAGAAAGCGCCACAGCTGTTGTTGAAGGGTGAAGGGaa                                   >  2:156864/1‑141 (MQ=14)
                                                                                                           atCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAAttt                                <  1:157110/141‑1 (MQ=255)
                                                                                                           atCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAAttt                                <  2:299612/141‑1 (MQ=255)
                                                                                                             cATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTaa                              >  2:245504/1‑141 (MQ=255)
                                                                                                             cATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTaa                              >  2:245530/1‑141 (MQ=255)
                                                                                                             cATATAATCCAGAGGGGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTaa                              <  1:5479/141‑1 (MQ=255)
                                                                                                              atagAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAAAAAAGCGACGAAGCAGTTGTGAAAAGGAACAGGGAATTTaaa                             >  2:222722/1‑141 (MQ=17)
                                                                                                                     ccAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtca                      <  1:529958/141‑1 (MQ=255)
                                                                                                                         agGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGAAAAACAATTCCGTAACAGATATGACATACCAACAAATAAAGCGCCGCAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtcatccg                  >  2:112799/1‑139 (MQ=255)
                                                                                                                           gTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTAGAATGTAAAACAATTACGTAACAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGTAATTTAAAAGGTtcatccgcg                >  2:285815/1‑137 (MQ=255)
                                                                                                                                         aGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAAt  <  1:190504/141‑1 (MQ=255)
                                                                                                                                         aGCTCAAAATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAAt  <  1:77527/141‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                            
ACTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAAT  >  CP000730/111375‑111652

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: ‑