Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP000730111,5160CA28.9% 80.7 / 30.9 47Q196K (CAA→AAA) USA300HOU_0110possible staphylococcal tandem lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (13/19);  new base A (6/7);  total (21/26)
Fisher's exact test for biased strand distribution p-value = 7.51e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.13e-01
Rejected as consensus: Frequency below/above cutoff threshold.

AGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATT  >  CP000730/111379‑111653
                                                                                                                                         |                                                                                                                                         
aGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAat                                                                                                                                        <  1:346490/141‑1 (MQ=255)
 ggAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTAGCGCAATATAGCAATATTAAAAAATTAATGAACTATAACGATGGAGATATATCATATAACCAAGAGGTGCCGAGTTATTCGGCTAAata                                                                                                                                       <  1:144874/141‑1 (MQ=18)
    aGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTATTGCGCAATATAGCACTTTTAAAGATTTAATGAATTATAAAGATGGAGATATATAATATAATCCAGAGGTGACGAGTTATTCAGCTCAATATCa                                                                                                                                    >  2:89201/1‑141 (MQ=255)
       tAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTTTTTATTTTTGCAATTTTAAAGATTTAATGAATTATAAATATGGAGATATATCATATAATCCAGAGGTTCCGAGTTATTCGGCTAAATATCAAtt                                                                                                                                 >  2:311031/1‑141 (MQ=17)
         aagaagAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTaa                                                                                                                               >  1:152391/1‑141 (MQ=255)
          agaagaAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGTTCATTATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGTTGCCGAGTTATTCGGCTAAATATCAATTAAc                                                                                                                              >  2:47589/1‑141 (MQ=17)
              gaaAACATAAAAAAAGGAATCGAAAACTTTAAGTTTTTTGCGCAAGATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAat                                                                                                                          <  1:111570/141‑1 (MQ=255)
               aaaaCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAatg                                                                                                                         <  1:146727/141‑1 (MQ=255)
                aaaCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatga                                                                                                                        >  1:314456/1‑141 (MQ=255)
                  aCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAatgatg                                                                                                                      <  2:251011/141‑1 (MQ=255)
                    aTAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATgatgat                                                                                                                    >  1:272823/1‑141 (MQ=255)
                    aTAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGCTGCCGAGATATTCGGCTAAATATCAATTAACTAATgatgat                                                                                                                    >  1:183192/1‑141 (MQ=255)
                     tAAAAAAAGAAATCGAAAACTTTAAGTTTTTCGAGAAATAAAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTAGTCTGCTTAATATCAATTAACTAATGAGGAtt                                                                                                                   >  2:154942/1‑141 (MQ=18)
                             gAAATCGAAAACTTTAAGTTTTTTTTTTTTTATAGCAATTTTAAAGATTTAATGAATTATAAATATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTa                                                                                                           >  2:148347/1‑141 (MQ=17)
                              aaaTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGCTATCTAATATAATCCAGCGGTGCCGTGTTATTCGGCTCAATCTCAATTCACTTATGATGATTATAATGTaa                                                                                                          <  1:238477/141‑1 (MQ=255)
                                    aaaaCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAAt                                                                                                    <  1:309131/141‑1 (MQ=255)
                                    aaaaCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAAt                                                                                                    <  2:67083/141‑1 (MQ=255)
                                      aaCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTa                                                                                                  >  1:192655/1‑141 (MQ=255)
                                        cTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACg                                                                                                <  1:18183/141‑1 (MQ=255)
                                        cTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGCGGAGATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACg                                                                                                <  1:114578/141‑1 (MQ=255)
                                        atttAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACg                                                                                                <  1:184882/140‑1 (MQ=255)
                                          ttAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTa                                                                                              <  1:56800/141‑1 (MQ=255)
                                           tAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTaa                                                                                             <  2:73955/141‑1 (MQ=255)
                                            aaGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCaaa                                                                                            <  2:274475/141‑1 (MQ=255)
                                                 ttttGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGata                                                                                       >  1:25913/1‑141 (MQ=255)
                                                 ttttGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGata                                                                                       >  1:25904/1‑141 (MQ=255)
                                                    ttttttttttttcAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTTCCGAGTTATTCGGCTTTATTTCAATTTACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGa                                                                                    >  2:24777/13‑141 (MQ=14)
                                                     gcgcAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGATATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGAc                                                                                   >  1:267133/1‑141 (MQ=255)
                                                            ataGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATAccga                                                                            <  2:347528/141‑3 (MQ=14)
                                                             taGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATAccgac                                                                           <  1:94156/141‑4 (MQ=11)
                                                              aggaaTTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACcgacg                                                                          <  2:82461/138‑2 (MQ=11)
                                                              aGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACcgacg                                                                          >  2:195035/1‑140 (MQ=11)
                                                                          gATTTAACGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCg                                                              >  1:325385/1‑141 (MQ=255)
                                                                            tttAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGaa                                                            <  1:282342/141‑1 (MQ=255)
                                                                             ttAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAg                                                           >  2:80862/1‑141 (MQ=255)
                                                                              tAATGAATGATAAAGATAGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGc                                                          <  2:50368/141‑1 (MQ=255)
                                                                                 tGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtgt                                                       <  2:21008/141‑1 (MQ=255)
                                                                                   aaTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtgttg                                                     <  2:265597/141‑1 (MQ=255)
                                                                                         aaaGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGaaa                                               >  1:82899/1‑141 (MQ=255)
                                                                                              ttgagaTATATCATATAATCCAGAGGTGCTGAGTTATTCAGCTCAATATCCATTAACTAATTATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTAc                                          <  2:57771/139‑1 (MQ=255)
                                                                                                   atatatCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGa                                     <  1:208053/141‑1 (MQ=255)
                                                                                                        tCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTa                                <  1:148347/141‑1 (MQ=255)
                                                                                                          atatAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTaaa                              <  1:169421/141‑1 (MQ=255)
                                                                                                                               ttATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaa         <  2:192655/141‑1 (MQ=255)
                                                                                                                                    cAGCTCAATATCAATTAACTAATGATGAGGATAAGGTAAAACAATTATGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAACTGTTGTTGAAAGGCACAGGGAATTTAAAAGGTTCATCAGTTGGATATaaaaaaa    >  2:355475/1‑141 (MQ=17)
                                                                                                                                     aGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAAt   >  1:217183/1‑141 (MQ=255)
                                                                                                                                      gCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAAtt  >  1:25635/1‑141 (MQ=255)
                                                                                                                                         |                                                                                                                                         
AGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATT  >  CP000730/111379‑111653

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑