Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 111,516 C→A 36.1% Q196K (CAA→AAA)  USA300HOU_0110 → possible staphylococcal tandem lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP000730111,5160CA36.1% 56.5 / 37.4 47Q196K (CAA→AAA) USA300HOU_0110possible staphylococcal tandem lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (14/16);  new base A (6/11);  total (20/27)
Fisher's exact test for biased strand distribution p-value = 5.46e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.49e-01

AGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAA  >  CP000730/111379‑111656
                                                                                                                                         |                                                                                                                                            
aGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAat                                                                                                                                           <  1:7031/141‑1 (MQ=255)
    aGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCa                                                                                                                                       >  1:62135/1‑141 (MQ=255)
     gTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCaa                                                                                                                                      >  2:409515/1‑141 (MQ=255)
     attAAATAAAGAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCaa                                                                                                                                      <  2:75004/140‑1 (MQ=17)
          agaagaAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAAc                                                                                                                                 <  2:426653/141‑1 (MQ=255)
           aaagaaAACATAAAAAAAGAAATCGAAAACTTGAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACt                                                                                                                                <  2:419000/140‑1 (MQ=255)
            aagaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATGTGGCGATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTa                                                                                                                               <  1:358231/141‑1 (MQ=255)
            aagaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTa                                                                                                                               <  1:325505/141‑1 (MQ=255)
            aagaaAACATAAAAAAAGAAATCGAAAACGTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTa                                                                                                                               <  1:119614/141‑1 (MQ=255)
                   cATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTTTTTTTTTTTTCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTTCCGAGTTATTCGGCTAAATATAAAATAAGAAatgaaaa                                                                                                                        >  2:323264/1‑138 (MQ=14)
                   cATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAAtgatga                                                                                                                        <  1:152171/141‑1 (MQ=255)
                    aaaaaaaaaaaaACCGAAAACTTTAAGTTTTTTGCCCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATgatgat                                                                                                                       <  1:234079/139‑1 (MQ=17)
                             gAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATAAAATCCAGAGGTGCCGAATTATTAGGCTAAATATAAATTAACTAATGATGATTATAATGTa                                                                                                              >  2:216838/1‑141 (MQ=18)
                               aaTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATCTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTaaa                                                                                                            <  2:434718/141‑1 (MQ=255)
                                aTCGAAAACTTTAAGTTTTTTGCGCACTCAATCAGTTGTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAAGGATGATTATAATGTaaaa                                                                                                           >  1:110049/1‑141 (MQ=21)
                                aTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTaaaa                                                                                                           >  2:16338/1‑141 (MQ=255)
                                aTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATGTAATGAATTATAAAGATGGAGATATATAATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTaaaa                                                                                                           >  2:199268/1‑141 (MQ=255)
                                    aaaaCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAAt                                                                                                       <  2:91731/141‑1 (MQ=255)
                                    aaaaCTTTAAGTGTTTGGCGCAATATAGCAATTGTAAAGAGTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAAt                                                                                                       <  2:49884/141‑1 (MQ=17)
                                     aaaCTTTAAGTTTTTTGCGCAATATAGCAATTTGAAAGAGTTAATGAATTATAAAGATTGAGATATATCATATAATGCAGAGGTGCCGAGTTATTAGGCTAAATATAAATTAAATAATGATGATTATAATGTAAAAGAAtt                                                                                                      >  2:160634/1‑141 (MQ=18)
                                       aCTTGAAGTTTTTTGCGAAATATAGAAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTAc                                                                                                    <  1:36104/141‑1 (MQ=255)
                                        cTTTACGCTTTTTTCTCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGACGGATATATATTATATAATCCAGAGGTGCCGAGTTATTCAGATCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACg                                                                                                   <  1:31238/141‑1 (MQ=17)
                                         tttAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGATATATATCATATAATCCAGAGGGGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACgc                                                                                                  <  2:115438/141‑2 (MQ=255)
                                         tttAAGTTGTTTCAGCAATATATCAATTTTAAAGATTTAATGAATTAGAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACgc                                                                                                  <  2:453678/141‑2 (MQ=17)
                                            aaGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCaaa                                                                                               >  1:3356/1‑141 (MQ=255)
                                             aGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTaaaa                                                                                              >  1:160544/1‑141 (MQ=255)
                                               ttttttGAGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGa                                                                                            <  2:381989/141‑1 (MQ=255)
                                                tttttGGACAATATAGTAATTTTAAATATTCAAGTAATTTTAAAGATGTATTTATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAACATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAgtt                                                                                           <  2:86902/141‑3 (MQ=17)
                                                tttgtGAGCAATATAGCAATTTTAAATATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGat                                                                                           <  2:376437/141‑1 (MQ=14)
                                                             taGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACcaac                                                                              >  2:194503/1‑141 (MQ=255)
                                                              aGCAATTTTAAAGAGTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACcgacg                                                                             <  2:257539/141‑2 (MQ=11)
                                                               gCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATAccgacga                                                                            <  1:66206/141‑6 (MQ=11)
                                                               gCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAAAAATTACGAAAACGATTTGATATACcgacga                                                                            >  2:69291/1‑139 (MQ=14)
                                                                       aaaGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAACAGATATGACCTACCAACAAATAAAgcc                                                                    >  2:90681/1‑140 (MQ=255)
                                                                         acaTTTAATGAATTATAAAGATGGACATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGcc                                                                  <  2:133931/139‑1 (MQ=255)
                                                                              tAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGc                                                             <  2:454637/141‑1 (MQ=255)
                                                                                       ataAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGa                                                    <  2:329536/141‑1 (MQ=255)
                                                                                                   atatatCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGa                                        <  2:160544/141‑1 (MQ=255)
                                                                                                                accAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtc                           <  2:19554/140‑1 (MQ=255)
                                                                                                                 ccAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTTTAATGTAAGACAATTACGTAAAAGATATGGCATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtca                          <  1:335465/141‑1 (MQ=255)
                                                                                                                  cAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAGATAAAGCGCCGAAGCTGTTGTTGGAAGGTACAGGGAATTTAAAAGGTtcat                         >  1:118523/1‑141 (MQ=255)
                                                                                                                    gagGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtcatca                       >  1:388212/1‑141 (MQ=255)
                                                                                                                       gTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACTAATAAAGCGCCGCGGCTGTTGTTGAGAGGTACCGGGAATTTAAAAGGTTCGTCAGtt                    >  1:132687/1‑141 (MQ=17)
                                                                                                                       gTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAGAGTTCATCAggt                    >  1:123755/1‑139 (MQ=255)
                                                                                                                         gCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTgg                  >  2:46410/1‑141 (MQ=255)
                                                                                                                                  ttCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGAACAGGGAAGTTAAAGGGTTCATCAGTTGGATATaaaaa         >  1:322440/1‑141 (MQ=255)
                                                                                                                                     aGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAAt      >  1:319851/1‑141 (MQ=255)
                                                                                                                                         cAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGaa  <  2:300024/141‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                            
AGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAA  >  CP000730/111379‑111656

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: ‑