Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 110,660 T→A 18.8% I173I (ATT→ATA)  USA300HOU_0109 → staphylococcal tandem lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP000730110,6600TA18.8% 111.8 / 20.9 53I173I (ATT→ATA) USA300HOU_0109staphylococcal tandem lipoprotein
Reads supporting (aligned to +/- strand):  ref base T (19/24);  new base A (5/5);  total (24/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.52e-01

AAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAATT  >  CP000730/110527‑110799
                                                                                                                                     |                                                                                                                                           
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)
                                                                                                                            gagggaTATATCATATAATCAAGAGGTGCCGAATTATTCGGCTAAATAACAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTc          <  1:375366/137‑1 (MQ=17)
                                                                                                                              gagaTATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATCAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGTGTAAAGCTCCAAAGTTATTGTTAAAAGGTTcgg        <  2:306050/141‑3 (MQ=255)
                                                                                                                              gagaTATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGATTCAg        >  2:194837/1‑141 (MQ=255)
                                                                                                                               agaTATTTCATATAATCCAGAGGTGCCGAGATATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATAGGATATACCGACGAGTAAAGCCCCAAAGTTATAGTTAAAAGGTTCAgg       >  2:144860/1‑141 (MQ=255)
                                                                                                                               agaTATTTCATATAATCCAGAGGGGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAgg       <  2:263594/141‑1 (MQ=255)
                                                                                                                               agaTATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAAAAATTACGCAAAAGATATGGTATACAGACGAGTAAAGCGCTAAAGTTATCGTTAAAAGGttaggg       >  1:150870/1‑137 (MQ=17)
                                                                                                                                  tatTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGGTAAAAGGTTCAGGGaa    >  1:107394/1‑141 (MQ=255)
                                                                                                                                    tttCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAAtt  >  2:414558/1‑141 (MQ=255)
                                                                                                                                     |                                                                                                                                           
AAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAATT  >  CP000730/110527‑110799

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: ‑