Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 111,516 C→A 38.5% Q196K (CAA→AAA)  USA300HOU_RS00520 → putative lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE111,5160CA38.5% 49.5 / 41.0 52Q196K (CAA→AAA) USA300HOU_RS00520putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (15/17);  new base A (15/5);  total (30/22)
Fisher's exact test for biased strand distribution p-value = 8.23e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.05e-01

CTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAAT  >  USA300TCH1516_ALE/111376‑111652
                                                                                                                                            |                                                                                                                                        
cTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTc                                                                                                                                          <  2:126113/141‑1 (MQ=255)
       aGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCa                                                                                                                                   <  1:141729/141‑1 (MQ=255)
        gTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCaa                                                                                                                                  <  1:340291/141‑1 (MQ=255)
            aagaagAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTaa                                                                                                                              >  1:13963/1‑141 (MQ=255)
             agaagaAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAAc                                                                                                                             <  1:291260/141‑1 (MQ=255)
             agaagaAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCAAGAGGTGCCGAGTTATTGGGCTAAATATCAATTaat                                                                                                                             >  2:20195/1‑140 (MQ=255)
              gaagaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAAGTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACt                                                                                                                            >  1:280255/1‑141 (MQ=255)
               aagaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTa                                                                                                                           <  1:368574/141‑1 (MQ=255)
                  aaaaCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatg                                                                                                                        <  2:340516/141‑1 (MQ=255)
                    aaCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTTTTTTTTATAGCAATTTTAAAGATTTAATGAATTATAATTATGGAGATATATCATATAATCCAGAGTTGCCGATTTATTCGGCTAAATATCAATTAACTAatgat                                                                                                                      >  2:213185/1‑141 (MQ=17)
                    aaCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAGAGATGTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTCaagat                                                                                                                      >  2:196412/1‑141 (MQ=18)
                    aaCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAatgat                                                                                                                      >  1:254928/1‑141 (MQ=255)
                        tAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGAtt                                                                                                                  >  1:304336/1‑141 (MQ=255)
                        tAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGAtt                                                                                                                  >  2:208466/1‑141 (MQ=255)
                         aaaaaaaGAAATCGAAAACTTTAAGTTTTTTTTTTTTTTTATCAATTTTAAAGATTTAATGAATTATAAAGATGTAGATATATCATATAATCCAGAGGTTCCGAGTTATTCGGCTAAATATCAATTAACTAATGAttatta                                                                                                                 >  2:338181/1‑141 (MQ=14)
                         aaaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCCATTGACTAAggaagaaga                                                                                                                 >  1:10928/1‑138 (MQ=18)
                          aaaaaaGAAATCGAAAACTTTAAGTTTTTTGCTCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATtat                                                                                                                <  2:152442/141‑1 (MQ=255)
                          aaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCACATCATTCATAGGTGCCGAGTTATACGGCTAAATATCAATTAACTAATTATGATtat                                                                                                                >  2:44159/1‑141 (MQ=18)
                                 aaaTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTat                                                                                                         >  2:253446/1‑140 (MQ=255)
                                       aaaaCTTTAAGTTTGTTGCGCAAGATAGCAATTTTAAAGAATTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAAt                                                                                                   <  1:171158/141‑1 (MQ=17)
                                         aaCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATAATGATTATAATGTAAAACAATTa                                                                                                 >  2:225115/1‑141 (MQ=255)
                                         aaCTATAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTa                                                                                                 <  1:26082/141‑1 (MQ=255)
                                               aaGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAACACAATTACGCaaa                                                                                           >  2:40120/1‑141 (MQ=255)
                                               aaGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATGAACTAATGATGAATATAATGTAAAACGATTAcccaaa                                                                                           >  1:89286/1‑136 (MQ=18)
                                                aGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTaaaa                                                                                          >  1:299398/1‑141 (MQ=255)
                                                  ttttttGCGTAATATAGCAATTTTAAAGATTTAATGAATTAGAAAGATGGAGATATATTATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATAACAATTAAATAATGATGATTATAATGTAAAACGATTACGCAAAAGa                                                                                        <  2:21049/141‑1 (MQ=17)
                                                   tttttGAGTAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGat                                                                                       <  2:228977/141‑1 (MQ=255)
                                                       tGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGa                                                                                   <  1:114034/141‑1 (MQ=255)
                                                           cAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTAAGCAACAGATATGAtata                                                                               >  2:9826/1‑141 (MQ=14)
                                                           aaaaataGAAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATa                                                                               <  2:307927/137‑1 (MQ=255)
                                                                 aGCAATTTTAAAGATTTAATGAATTATAAAGATGGGGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAAAAGCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATAccgacg                                                                         <  1:354687/141‑5 (MQ=11)
                                                                 aGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATAcacaca                                                                         >  2:319071/1‑136 (MQ=255)
                                                                  gCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTAGGCTACACATAGAAGAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACcgacga                                                                        >  1:290007/1‑139 (MQ=11)
                                                                  gCAATTTTAAAGAGTGAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACcaacaa                                                                        <  2:138168/141‑1 (MQ=255)
                                                                  gCAATTTTAAAGAATTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACcaacaa                                                                        <  2:38331/141‑1 (MQ=255)
                                                                         tAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAgc                                                                 <  2:254928/141‑1 (MQ=255)
                                                                         tAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACATAAAAGATATGACATACAAACAAATAAAgc                                                                 >  2:255197/1‑141 (MQ=255)
                                                                          aaaGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAgcg                                                                >  2:121284/1‑141 (MQ=255)
                                                                                  aaTGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCt                                                        <  2:179470/141‑1 (MQ=255)
                                                                                   aTGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtg                                                       <  1:328507/141‑1 (MQ=255)
                                                                                        ttATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTgttgtt                                                  >  1:160084/1‑141 (MQ=255)
                                                                                           taAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGaa                                               <  1:111929/141‑1 (MQ=255)
                                                                                               gATAGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGt                                           <  2:126758/141‑1 (MQ=255)
                                                                                                    agaTATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGCTTATAATGTAAAACAATTACGTAAAACATATGACATACCAACAAATAAAGCACCGAAACTGTTGTCTAAAGGTACAga                                      >  2:26258/1‑140 (MQ=14)
                                                                                                      atatatCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAAATAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGa                                    >  1:355976/1‑141 (MQ=255)
                                                                                                                 aaTCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTCAAACAATTACGTAACAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGCGAATTTCAAAggc                         >  2:14678/1‑140 (MQ=255)
                                                                                                                 aaTCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGt                         <  1:76181/141‑1 (MQ=255)
                                                                                                                 aaTCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGt                         <  1:208466/141‑1 (MQ=255)
                                                                                                                        agGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAAGAAATAAAGCGCCGAAGCTGTTGTTGATAGGTACATGGAATTTAAACAGTTCATCAg                  >  1:371575/1‑141 (MQ=17)
                                                                                                                        agGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGAGTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACCAGGAATTCAAAAGGTTAATCAg                  >  2:312570/1‑141 (MQ=17)
                                                                                                                                    aTTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaaaa      >  1:67418/1‑141 (MQ=255)
                                                                                                                                     ttCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaaaaa     >  1:234496/1‑141 (MQ=255)
                                                                                                                                        aGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAAt  >  2:222833/1‑141 (MQ=255)
                                                                                                                                            |                                                                                                                                        
CTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAAT  >  USA300TCH1516_ALE/111376‑111652

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑