Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 111,560 T→C 13.0% R210R (CGT→CGC)  USA300HOU_RS00520 → putative lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE111,5600TC13.0% 121.1 / 10.3 53R210R (CGT→CGC) USA300HOU_RS00520putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base T (29/16);  new base C (2/5);  total (31/22)
Fisher's exact test for biased strand distribution p-value = 1.04e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.56e-01

AAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATAT‑AAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAATATTTACTTT  >  USA300TCH1516_ALE/111423‑111695
                                                                                                                                         |                                                                                                                                        
aaGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTaa                                                                                                                                        >  1:164282/1‑140 (MQ=255)
aaGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTaa                                                                                                                                        >  1:374358/1‑140 (MQ=255)
aaGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTaa                                                                                                                                        >  1:245565/1‑140 (MQ=255)
    tttttGCGCAATATAGCAATTTTAAAGATTTAATGAATTAAAAAGATGGAGATATATCATATAATCCAGAGGTGCCGGGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGa                                                                                                                                    <  1:265699/140‑1 (MQ=17)
        tGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTCAGCACAAGATATg                                                                                                                                >  2:76775/1‑140 (MQ=17)
         gcgcAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGa                                                                                                                               <  1:143241/140‑1 (MQ=255)
            cAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAgatatgatat                                                                                                                            <  2:124810/140‑1 (MQ=14)
            cAATAGAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGatat                                                                                                                            <  1:201403/140‑4 (MQ=14)
             aaTATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAACTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGAtata                                                                                                                           <  1:441634/140‑1 (MQ=14)
                  cgCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACcaac                                                                                                                      <  1:143148/139‑1 (MQ=255)
                  aGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCGAAATATCAATTAACTAATGATGATTATAATGTAAAAAAATTACGCAAAAGATATGATATACcgac                                                                                                                      >  1:656125/1‑140 (MQ=14)
                   gCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATTACATACcaaca                                                                                                                     >  2:378077/1‑140 (MQ=255)
                   gCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACcaaaa                                                                                                                     >  1:209305/1‑138 (MQ=255)
                         ttAAAGATTTAATGAATGATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATCATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATaaa                                                                                                               <  2:431184/140‑1 (MQ=255)
                           aaaGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAgc                                                                                                             >  1:353487/1‑140 (MQ=255)
                                tttAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGa                                                                                                        <  1:608898/140‑1 (MQ=255)
                                         ttATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAAATAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtgttgt                                                                                               >  1:65900/1‑140 (MQ=255)
                                            taagggtGGAGGTATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGCTATGACATACCAATAAATAAAGCGCCGAAGTTGTTGTTGa                                                                                            <  2:126328/134‑1 (MQ=14)
                                                gacggAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAACTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAgg                                                                                        <  2:72622/137‑1 (MQ=255)
                                                        tatatCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTATCTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGa                                                                                <  1:299010/140‑1 (MQ=255)
                                                        tatatCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGa                                                                                >  2:351933/1‑140 (MQ=255)
                                                            tCATATAATTCAGGGGTTCCGAATTAGTCAGCTCAATATCAATTAACTAATTATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAAttt                                                                            <  1:283095/140‑1 (MQ=17)
                                                            tCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAAttt                                                                            >  1:202008/1‑140 (MQ=255)
                                                            tCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGATACAGGGAAttt                                                                            >  1:567809/1‑140 (MQ=255)
                                                              atatAATGCCGAGATGCCGAGTTATTCAGCTCGAGAGCAATTCAGTCACCAAACTCAGAAAGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTaa                                                                          >  2:470087/1‑140 (MQ=14)
                                                                  aaTCCAGAGCTGCTGAGTTATTCAGCTCAATATCAATTAACTAATGATGCTTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTGAAAAgg                                                                      <  2:454492/140‑1 (MQ=255)
                                                                   aTCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGt                                                                     <  1:568383/140‑1 (MQ=255)
                                                                    tCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGCAAGGTACAGGGAATTTAAAAGGtt                                                                    >  2:19325/1‑140 (MQ=255)
                                                                      cAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtca                                                                  <  2:533256/140‑1 (MQ=255)
                                                                        gagGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtcatc                                                                >  1:112527/1‑140 (MQ=255)
                                                                        gagGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtcatc                                                                >  1:608998/1‑140 (MQ=255)
                                                                        gagGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtcatc                                                                >  1:500221/1‑140 (MQ=255)
                                                                          ggTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAg                                                              >  1:402483/1‑140 (MQ=255)
                                                                           gTGCCAAGTTATTCAGATCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGGTCATCAGt                                                             <  2:407760/140‑1 (MQ=255)
                                                                              ccGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCACCAGTTgg                                                          >  2:529661/1‑140 (MQ=255)
                                                                                    tATTCAGCTCAATATCAATTAACTAATGATGAATAAAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATAT‑aa                                                   <  1:45381/140‑1 (MQ=255)
                                                                                                tatCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATAT‑AAAAAAATTGAAtt                                       >  1:453836/1‑140 (MQ=255)
                                                                                                tatCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTAGAGGGCTGGAAAATGTAAGATCAAAGGTTCATCAGTTGAATGT‑AAAAAAATTGAAtt                                       >  1:151409/1‑140 (MQ=14)
                                                                                                  tCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAAATTGAAttt                                      >  1:410404/1‑140 (MQ=255)
                                                                                                   cAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAAGTTAAAAGGTTCATCAGTTGGATAT‑AAAAAAATTGAATTTAc                                    <  1:320559/140‑1 (MQ=255)
                                                                                                   cAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAACGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATAT‑AAAAAAATTGAATTTAc                                    >  1:200919/1‑140 (MQ=255)
                                                                                                     aTTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGATGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATAT‑AAAAAAATTGAATTTACtt                                  >  1:47079/1‑140 (MQ=255)
                                                                                                             atgatgATTATAATGTAAAACAATTACGTAAAAGATATGACATGCCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATAT‑AAAAAAATTGAATTTACTTTTTTagag                          >  1:351451/1‑140 (MQ=255)
                                                                                                             atgatgATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTAAAGGGAATTTAAAAGGTTCATCAGTTGGATAT‑AAAAAAATTGAATTTACTTTTTTagag                          >  1:310831/1‑140 (MQ=255)
                                                                                                               gatgatTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATAT‑CAAAAAATTGAATTTACTTTTTTAGaaaa                        >  2:430587/1‑140 (MQ=255)
                                                                                                                  gatTATAATGTAAAACAATTACGTAAAAGATAGAACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATAT‑AAAAAAATTGAATTTACTTTTTTAGAGAATaa                     <  2:652491/140‑1 (MQ=255)
                                                                                                                           gTAAAACAATTACGGAAAAGATATGACATACCAACATATAAACCGCCGAAGCTGTTTTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTCGATAT‑AAAAAAAGTGAATTTACTTTTTTAGAGACTAAAAATCaaaa            <  1:470087/140‑1 (MQ=18)
                                                                                                                              aaaCAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATAT‑AAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAatat         <  2:453836/140‑1 (MQ=255)
                                                                                                                                 cAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATAT‑AAAAAAATTGAATTTACTTTTTTTTATATTTAAAATGAAAATAtttg      >  2:385166/1‑139 (MQ=17)
                                                                                                                                 cAATTACGTAAAAGATATGACATACCAACAAATAAAGCACCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATAT‑AAAAAAATTGAATTTACTTTTTTAGAGAAGAAAAATGAAAATAttta      >  2:437611/1‑140 (MQ=255)
                                                                                                                                    ttACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATAT‑AAAAAAATTTAATTTACTTTTTTAGAGAATAAAAATGAAAATAtttactt   >  2:118649/1‑140 (MQ=255)
                                                                                                                                    ttACGTAAAAGATATGACATACAAACAAATCAAGCGCCGAAGCGGCTGTCGAAAAGAACAGGGAATTTAAAAGGTTCATCAGTGGGATAT‑AAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAATAtatactt   >  2:460768/1‑140 (MQ=18)
                                                                                                                                     tACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATAT‑AAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAATAtttacttt  <  2:245565/140‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                        
AAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATAT‑AAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAATATTTACTTT  >  USA300TCH1516_ALE/111423‑111695

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑