Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 111,516 C→A 28.0% 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
*CP000730111,5160CA28.0% 89.7 / 34.0 58Q196K (CAA→AAA) USA300HOU_0110possible staphylococcal tandem lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (17/23);  new base A (11/5);  total (29/29)
Fisher's exact test for biased strand distribution p-value = 1.38e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.86e-01

TGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAAT  >  CP000730/111377‑111652
                                                                                                                                           |                                                                                                                                        
tGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGTAAACTTTATGTTTTTTGCGCAATATTGCAATCTTAAAGATTTAATGAATTATAAAGATGGATATATATCATATACTCCAGAGTTTCTGAGTTAGTCAGCTCa                                                                                                                                         <  2:112711/141‑1 (MQ=21)
  cggAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTACGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAat                                                                                                                                       <  1:251681/140‑1 (MQ=255)
  aGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAat                                                                                                                                       <  1:54885/141‑1 (MQ=255)
       gTTAAGAAAGAAAACATACAACAAGAAATCGCAAACTTTAGGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCaa                                                                                                                                  >  1:263751/1‑141 (MQ=25)
            agaagaAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAAc                                                                                                                             <  1:25292/141‑1 (MQ=255)
                gaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAat                                                                                                                         <  1:24316/141‑1 (MQ=255)
                gaaAACATAAAAAAAGAAATCGAAAAATTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCAAGAGGTGTCGAGTTATTCGGATAAATATCAATTAACTatt                                                                                                                         >  2:308601/1‑139 (MQ=18)
                 aaaaCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatg                                                                                                                        >  2:240424/1‑141 (MQ=255)
                   aaCATAAAAAAAGAAATCGAAAACTTTAAGTTTTGTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTTAGCTCAATGTCAATTAACTAatgat                                                                                                                      >  1:108970/1‑141 (MQ=255)
                    aCATAAATAAAGAAATGTAAAACTTTAAGTGTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatgatg                                                                                                                     <  2:226818/141‑1 (MQ=17)
                    aCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTGAGCTCAATATCAATTAACTAatgagg                                                                                                                     >  2:211897/1‑139 (MQ=255)
                    aCATAAAAAAAGAAATCGAAAAATTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAAAGGTGCCGAATTATTCAGTTCAATATCAATTAACTAatgatg                                                                                                                     >  2:72081/1‑141 (MQ=255)
                      aTAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATgatgat                                                                                                                   >  2:340358/1‑141 (MQ=255)
                      aTAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATgatgat                                                                                                                   >  1:306779/1‑141 (MQ=255)
                      aTAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATgatgat                                                                                                                   >  2:298262/1‑141 (MQ=255)
                       tAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGAtt                                                                                                                  <  1:15582/141‑1 (MQ=255)
                       tAAAAAAAGAAATCCAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGAtt                                                                                                                  <  2:80446/141‑1 (MQ=255)
                       aaaaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGAtt                                                                                                                  <  2:80513/140‑1 (MQ=255)
                         aaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATtat                                                                                                                >  2:272998/1‑141 (MQ=255)
                         aaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATAAATTAACTAATGATGATtat                                                                                                                >  2:241840/1‑141 (MQ=255)
                         aaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAACATTTAAGGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTACTCAGCTCAATATCAATTAACTAATGATGATtat                                                                                                                <  2:236981/141‑1 (MQ=255)
                         aaaaaaGAAATCGAAAACTTTAAGTTCTTTGCGGAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATtat                                                                                                                <  2:251005/141‑1 (MQ=255)
                          aaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATtata                                                                                                               <  1:300771/141‑1 (MQ=255)
                                aaaTCGAAATCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTaa                                                                                                         <  1:92677/141‑1 (MQ=255)
                                  aTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTaaaa                                                                                                       >  2:22816/1‑141 (MQ=255)
                                    cGAAAACTCTAAGTTTTTTTTGTTTTTTAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGGCGAGTTATTAAGCTCAATATCAATTTACTAATGATGTTTATAATTTaaaaaa                                                                                                     >  2:25521/1‑139 (MQ=21)
                                     gAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAAGGCCCGATTTATTCGTCGAACTATCAATTAACTAATGATGATTCTAATGTAAAACaa                                                                                                    >  2:267889/1‑141 (MQ=18)
                                      aaaaCTTTAAGTTTTTTGCGCAATATAGCAGTTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGACTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGCAAAACAAt                                                                                                   <  2:263751/141‑1 (MQ=255)
                                      aaaaCTTTAAGTTTTTTGCGCAATAAAGCAAGTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAAt                                                                                                   <  1:31480/141‑1 (MQ=255)
                                         aCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGGATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATAAc                                                                                                >  2:191069/1‑141 (MQ=255)
                                          cTTCAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGACTTATTAAGCTGGAGATATATCATCTAACCCAGAGGTGCCGAGTTCTTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACg                                                                                               >  2:75806/1‑141 (MQ=17)
                                             tAAGTTTTTTGCGCAATATAGCAATTATAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTaa                                                                                            <  1:356013/141‑1 (MQ=255)
                                               aGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCaaaa                                                                                          >  1:60687/1‑141 (MQ=255)
                                                  tttgtgagtaaTATAGGAATTTTAAAGATTTAAAGAATTATAAAGATGGAGCTATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATGAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGat                                                                                       <  1:109851/132‑1 (MQ=17)
                                                       tttttttttttcAATATTAAAAATTTAATGAATTTTATAGAGGGGGATGTATCATATAATCCAGGTGTTCCGAGTTATTGAGTTTTTTTTTTTTTTTCTAATGATGATTATAATGTAAAACATTTACGTAATACATATGaa                                                                                  >  2:355477/12‑140 (MQ=9)
                                                        cgcAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCAAATGGTCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATACGata                                                                                 <  1:244243/141‑3 (MQ=14)
                                                          cAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATa                                                                               <  1:283242/141‑1 (MQ=255)
                                                                       ttAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAg                                                                  <  1:278880/141‑1 (MQ=255)
                                                                         aaaGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACTTACCAACAAATAAAgcg                                                                >  2:322048/1‑141 (MQ=255)
                                                                            gATTTAATTAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCg                                                             <  1:61784/141‑1 (MQ=255)
                                                                            gATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTCATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAAGTACGTAAAAGATATGACATACTAACAAATAAAGCGCCg                                                             <  1:200107/141‑1 (MQ=255)
                                                                                 aaTGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCt                                                        <  1:220926/141‑1 (MQ=255)
                                                                                              gATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGt                                           <  2:33808/141‑1 (MQ=255)
                                                                                              gATGGAGATATATCATATAAGCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGt                                           <  1:156640/141‑1 (MQ=255)
                                                                                                       atatCATATAATCCAGAGGGGGCGAGTTACTCTGATTTTTCGCATCTTCCAAATTATGATTATAATGTAAAACAATTACGTTAAAGATATGACATACCGACGAATTAAGCGCCTAAGCTGTTGTTGTGAGGTACAGGGAAt                                  <  2:108970/141‑1 (MQ=9)
                                                                                                                aaTCCAGAGGTGCCGAGTTACTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGt                         <  1:22201/141‑1 (MQ=255)
                                                                                                                 aTCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGTTGTTGTTGAAAGGTACAGGGAATTTAAAAGGtt                        >  1:281593/1‑141 (MQ=255)
                                                                                                                     agagGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGCATTTAAAAGGTtcatc                    >  2:14696/1‑141 (MQ=255)
                                                                                                                     agagGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtcctc                    >  2:244545/1‑141 (MQ=255)
                                                                                                                     agagGTGCCGAGTTATTCAGCTCAATATCAATTAAATAATGATGATAATAATATCAAACAAAAACGTAAAAGATATAAAATACAAACAAATAAACCGCCGAAGCCGTTGTTGAAAGGCACAAGGAATGCAAAAAGatcatc                    >  2:335666/1‑141 (MQ=255)
                                                                                                                       agGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAg                  >  1:73147/1‑141 (MQ=255)
                                                                                                                        ggTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGAGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTGAACAGGCTCATCAGt                 >  1:327309/1‑141 (MQ=255)
                                                                                                                            ccGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGa             >  2:235965/1‑141 (MQ=255)
                                                                                                                              gAGTTATTCAGCTCAATATCAATTAACTAATGACGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGata           >  2:236319/1‑141 (MQ=255)
                                                                                                                              gAGTTATTCAGCTCAATATCAATTAACTAATGAAGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGata           <  1:135502/141‑1 (MQ=255)
                                                                                                                                     tCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGCTATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaaaaaa    >  2:69418/1‑141 (MQ=255)
                                                                                                                                     tCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGTTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaaaaaa    >  2:69453/1‑141 (MQ=255)
                                                                                                                                       accTCAATATCAACTAACTAACGATGATTATAATGTAAAACAATTACGTAAAAGATATGACAAAACAACAAATAAAGCCCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAAt  <  1:25521/139‑1 (MQ=14)
                                                                                                                                           |                                                                                                                                        
TGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAAT  >  CP000730/111377‑111652

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: ‑