Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 110,651 C→T 13.5% D170D (GAC→GAT)  USA300HOU_0109 → staphylococcal tandem lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP000730110,6510CT13.5% 114.0 / 7.2 50D170D (GAC→GAT) USA300HOU_0109staphylococcal tandem lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (18/25);  new base T (3/4);  total (21/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.48e-01

AAGATATCCGGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGT  >  CP000730/110513‑110789
                                                                                                                                          |                                                                                                                                          
aaGATATCCGGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACgg                                                                                                                                          <  1:289458/141‑1 (MQ=255)
 aGATATCCGGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGga                                                                                                                                         <  1:347749/141‑1 (MQ=255)
  aatatACAGTTAAAAAGGACAATAATAAAATAATTCCAACAAAAGAAAAAAAAAAAAAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTAAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGgag                                                                                                                                        <  2:190300/140‑1 (MQ=17)
    tatCCGGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCTACTTTAAAAATTTGAAAAATTATAAAGACTgagaa                                                                                                                                      >  1:95725/1‑140 (MQ=255)
              aaaTGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCAtata                                                                                                                            >  1:371804/1‑141 (MQ=255)
                aTGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGACCACATTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAAt                                                                                                                          >  1:198184/1‑141 (MQ=255)
                aTGGTCGATAATAAAATCATGCCAACAAAAGAAATTAAAGATGAAAAAATAAAATAAGAAATCGAAAACTTTAAGTTCTGTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAAt                                                                                                                          >  1:299256/1‑141 (MQ=255)
                  ggTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAGAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATTGCGACTTTAAAAATTTGAAGAATTAAAAAGACGGAGATATTTCATATAATca                                                                                                                        >  2:378435/1‑140 (MQ=255)
                  ggTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAATACGGAGATATTTCATATAATcc                                                                                                                        >  2:272621/1‑141 (MQ=255)
                    tctataatataatGATTCCAACAATACAAATTAAAGCTGAAAAAATAAAAAAATAAATCGAAAACTGTAAGTTCTTTGTGCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCag                                                                                                                      <  1:160441/138‑1 (MQ=17)
                            aaaaTCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTAAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCg                                                                                                              >  2:421239/1‑141 (MQ=255)
                                     ccAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGCTAtcgg                                                                                                     >  2:225766/1‑138 (MQ=255)
                                      caacaaAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCAAGAGGTGCCGAGTTATTCgg                                                                                                    >  2:220025/1‑141 (MQ=255)
                                      caacaaAAGAAAGTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCgg                                                                                                    <  1:352684/141‑1 (MQ=255)
                                             aaaaaaaaaaaATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAata                                                                                             <  2:365518/134‑1 (MQ=255)
                                             aGAAATTAAAGATAAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAata                                                                                             <  2:184164/141‑1 (MQ=255)
                                               aaaTTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGATGCCGAGTTATTCGGCTAAATATc                                                                                           >  1:42229/1‑141 (MQ=255)
                                                       gATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACt                                                                                   <  2:391995/141‑1 (MQ=255)
                                                         tGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTaa                                                                                 <  2:371628/141‑1 (MQ=255)
                                                             acaaTAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTCAAAAATTTGAAAAATTATAAAGACGGACATATTTCATATAAACCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatgat                                                                             <  1:413449/139‑1 (MQ=255)
                                                             aaaataaaaaaataaaTCGAACACTTTAAGTTCTTTGTTCAATTTGGCGACTTTAAAAATTTGAAAAATTATAAAGACTGAATTATTTGATGTTATCTTTATCTGCCGAGTTAGTCGGCTAAATATCAATTAACTAatgat                                                                             <  2:166190/141‑1 (MQ=17)
                                                                    aaaaaGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATtata                                                                      <  2:192956/141‑1 (MQ=255)
                                                                     aaaaGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCTGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATaa                                                                     <  1:306773/141‑1 (MQ=255)
                                                                      aaaGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAAt                                                                    <  1:163561/141‑1 (MQ=255)
                                                                      aaaGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAAATTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAAGGAGGATTATaaa                                                                    >  1:153400/1‑140 (MQ=255)
                                                                                 aaaCTTTAAGTTCTTTGTTCAATATGGAGACTTAAAAAATTGAAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACagtt                                                         <  2:95725/141‑4 (MQ=17)
                                                                                    cTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACg                                                      <  1:327382/141‑1 (MQ=255)
                                                                                     tttAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGc                                                     <  2:126845/141‑1 (MQ=255)
                                                                                       tAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCaa                                                   <  1:421239/141‑1 (MQ=255)
                                                                                         aGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCaaaa                                                 >  2:352255/1‑141 (MQ=255)
                                                                                              tttGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGACTATAATGTAAAACAATTACGCAAAAgatat                                            >  2:111926/1‑141 (MQ=255)
                                                                                                  ttCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAgatatgata                                        <  1:206543/141‑1 (MQ=255)
                                                                                                    cAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGAtata                                      >  1:348567/1‑141 (MQ=255)
                                                                                                    cAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGAgata                                      >  1:191119/1‑141 (MQ=255)
                                                                                                           gCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTACCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACcgacga                               >  2:69679/1‑141 (MQ=255)
                                                                                                                tttAAAGATTTAAATAATTACAAAGATGGAGACATATCATATAAGCCATATGTGTCGAGTTATTCGGCTTAAGTTCATTTAACTAACGATGATTATAATGTAATACAATTACGCAATAGATATGATATACCGACGAGttat                          <  2:20064/141‑4 (MQ=255)
                                                                                                                    aagatttaatgaaTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTc                      >  1:311559/12‑141 (MQ=11)
                                                                                                                            atgaaTTATAAAGATGGAGATATATCATATAATCCAGAGGCGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTa              <  1:93600/138‑1 (MQ=255)
                                                                                                                            aaaaaTTATAAAGACGGAGATATTTCATATCATCCAACGGTGCATAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTa              <  1:238994/141‑1 (MQ=18)
                                                                                                                             tgaaTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATAATATACCGACGAGTAAAGCTCCAAAGGTAt             >  2:346616/3‑141 (MQ=14)
                                                                                                                              aaaTTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTAtt            <  1:244406/141‑1 (MQ=255)
                                                                                                                                 ttATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAAATAATGATGATTATAATGTAAAACAATTACGAAAAAGATATGATATACCGACGAGCAACGCTCCaaaaaccctttt         >  2:226567/1‑132 (MQ=17)
                                                                                                                                   ataAAGTCGGAGATATTTCAGATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTaa       <  2:267425/141‑1 (MQ=255)
                                                                                                                                    taAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTaaa      <  2:308738/141‑1 (MQ=255)
                                                                                                                                    aaaaGATGGAATTATATCAGATAATCCAGAGGTGCCGGGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTaaa      <  2:177495/140‑1 (MQ=18)
                                                                                                                                    aaaaGACGGAGATGTTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAATAGATATGATATACCGACGAGTAAAGCTCCCAAGTTATTGTTaaa      <  1:251525/140‑1 (MQ=255)
                                                                                                                                      aaGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATATAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCAAAGGTTATTGTTAAAAg    >  1:311285/1‑141 (MQ=17)
                                                                                                                                      aaGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATAAATTAACTAATGCCGATTATCATGTAAAACAATTACGCAAAAGATATGATATACCCACGAGTAAAGCTCCAAAGTTATTGTTAAAAg    >  2:338321/1‑141 (MQ=18)
                                                                                                                                       aGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAgg   <  1:260786/141‑1 (MQ=255)
                                                                                                                                        gACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGt  <  1:173993/141‑1 (MQ=255)
                                                                                                                                          |                                                                                                                                          
AAGATATCCGGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGT  >  CP000730/110513‑110789

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: ‑