Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 111,516 C→A 32.3% Q196K (CAA→AAA)  USA300HOU_RS00520 → putative lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE111,5160CA32.3% 63.9 / 40.6 54Q196K (CAA→AAA) USA300HOU_RS00520putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (17/19);  new base A (7/10);  total (24/30)
Fisher's exact test for biased strand distribution p-value = 7.72e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.26e-01

GGAAGTTAAAGAAGAAAACATAAAAAAAG‑AAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAAT  >  USA300TCH1516_ALE/111380‑111652
                                                                                                                                         |                                                                                                                                        
gaaaGTTAAAGAAGAAAACATAAAAAAAGAAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAat                                                                                                                                       <  2:254049/139‑1 (MQ=255)
 gAAGTTAAAGAAGAAAACATAAAAAAAG‑AAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAatat                                                                                                                                     <  1:394102/141‑1 (MQ=255)
     ttAAAGAAGAAAACATAAAAAAAG‑AAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAAt                                                                                                                                 <  1:46934/141‑1 (MQ=255)
       aaaGAAGAAAACATAAAAAAAG‑AAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTa                                                                                                                               <  1:112380/141‑1 (MQ=255)
        aagaagAAAACATAAAAAAAG‑AAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGGGTTATTCGGCTAAATATCAATTaa                                                                                                                              >  1:161834/1‑141 (MQ=255)
        aagaagAAAACATAAAAAAAG‑AAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTaa                                                                                                                              <  1:119281/141‑1 (MQ=255)
          gaagaaAACATAAAAAAAG‑AAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACt                                                                                                                            >  1:168365/1‑141 (MQ=255)
          gaagaaAAAAAAAAAAAAG‑AAATAGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACt                                                                                                                            <  2:64341/141‑1 (MQ=17)
           aagaaAACATAAAAAAAG‑AAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTa                                                                                                                           <  1:51118/141‑1 (MQ=255)
            agaaAACATAAAAAAAG‑AAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTaa                                                                                                                          >  1:214316/1‑141 (MQ=255)
             gaaAACATAAAAAAAG‑AAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAat                                                                                                                         <  1:38532/141‑1 (MQ=255)
             gaaAACATAAAAAAAG‑AAATCGAAAAATTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAat                                                                                                                         <  2:119686/141‑1 (MQ=255)
                aaCATAAAAAAAG‑AAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatgat                                                                                                                      >  1:255976/1‑141 (MQ=255)
                aaCATAAAAAAAG‑AAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatgat                                                                                                                      <  1:34520/141‑1 (MQ=255)
                    tAAAAAAAG‑AAATCGAAAACTTTAAGTTTTTTGCGCAGTATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGAtt                                                                                                                  <  1:363823/141‑1 (MQ=255)
                     aaaaaaaG‑AAAACAAAAACTTTAAGTTTTTTGAGAAATATAGCAATTTTAAAGATTTAATGAATTATAAAGAGGGAGAGAAATCATATAATCCAGAGGTGCCCAGTTATTCAAATAAATATCAATTAACTAatgataaaaa                                                                                                                 <  2:154680/141‑6 (MQ=17)
                            aaaaaCCGAATACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGt                                                                                                           <  2:340270/139‑1 (MQ=17)
                                 tCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAAc                                                                                                      >  1:179171/1‑141 (MQ=255)
                                    aaacCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAAt                                                                                                   <  1:317038/141‑1 (MQ=255)
                                        cTTTAAGTTTTTTCCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACg                                                                                               <  1:262147/141‑1 (MQ=255)
                                         tatAAGGTTTGTGCTCAATATTGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACgc                                                                                              <  2:114445/139‑2 (MQ=14)
                                          ttAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTa                                                                                             >  2:331630/1‑141 (MQ=255)
                                           tAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACgcaa                                                                                            <  1:371614/141‑4 (MQ=255)
                                            aaGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTCTAATGTAACACAATTACCTaaa                                                                                           >  2:129328/1‑141 (MQ=255)
                                               ttttttGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGa                                                                                        <  1:389552/141‑1 (MQ=255)
                                                tttttGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATACACAACATTAGCCGGATTTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGat                                                                                       <  1:100215/141‑1 (MQ=17)
                                                  tttGCGCAATATAGCACTTTTAAAGATTTAATGACTTATACAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCCAAAGatat                                                                                     >  2:116590/1‑141 (MQ=17)
                                                    tcagcAAAATAATAATTTTAAAGATTTAATAAATTATAAAGATGGAGATATATCATATAAGCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGa                                                                                   <  1:219758/138‑1 (MQ=17)
                                                     gcgcAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGat                                                                                  >  1:7434/1‑140 (MQ=255)
                                                     gcgcAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGAc                                                                                  >  2:110227/1‑141 (MQ=255)
                                                      cgcAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGata                                                                                 >  1:277304/1‑139 (MQ=255)
                                                           aataGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACca                                                                            <  1:288933/140‑1 (MQ=255)
                                                                   ttttAAAGATGTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATaa                                                                    <  1:149168/141‑1 (MQ=255)
                                                                   tcttACAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCAGCGGTATTCAACTCAATATCAATTAACTAATGCTGATTATAATGTAAAACAATTACGTAAAAGATAAGACATACCAACaaaaaa                                                                    >  2:341275/3‑141 (MQ=18)
                                                                        aaGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTAAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACCATTACGTAAAAGATATGACATACCAACAaaaaaacctc                                                               >  2:107674/1‑137 (MQ=255)
                                                                                aTGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtg                                                       >  2:391037/1‑141 (MQ=255)
                                                                                     ttATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTgttgtt                                                  <  2:219106/141‑1 (MQ=255)
                                                                                        taAAGATAGAGATATATCATATAATCCAGAGGTGCCGAGTTATTATATATGATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGaa                                               <  1:312953/141‑1 (MQ=17)
                                                                                          aaGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAg                                             >  1:166533/1‑141 (MQ=255)
                                                                                               ggAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACa                                        >  1:335133/1‑141 (MQ=255)
                                                                                                 agaTATATAATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAgg                                      <  2:301215/141‑1 (MQ=255)
                                                                                                    tatatCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTGGGAAGGTACAGGGaa                                   <  1:279337/141‑1 (MQ=255)
                                                                                                     atatCATATAATACAGAGGTGCCGAGTTATTCAGCTCCATATCAATTCACTAATGATGATTATAATGTACAACAATTACGTAAAAGATATGACATACCAACAAATCCACCGCCCAAGCTGTTGTTGAAAGGTACAGGGAAt                                  <  1:430056/141‑1 (MQ=17)
                                                                                                      tatCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAAtt                                 >  1:66472/1‑141 (MQ=255)
                                                                                                                    gagGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtcatca                   >  1:341270/1‑141 (MQ=255)
                                                                                                                     agGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAg                  >  1:214170/1‑141 (MQ=255)
                                                                                                                        tGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCGTCAGTTg               >  2:102901/1‑141 (MQ=255)
                                                                                                                            gAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGata           >  1:299023/1‑141 (MQ=255)
                                                                                                                             aGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGatat          <  1:110227/141‑1 (MQ=255)
                                                                                                                                 aTTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaaaa      <  1:373674/141‑1 (MQ=255)
                                                                                                                                  atCAGCTCAAAATCAATTAACTAATGATGAATATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaaaaa     <  2:311388/140‑1 (MQ=255)
                                                                                                                                   tCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaaaaaa    >  1:95745/1‑141 (MQ=255)
                                                                                                                                    cAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAAACGGCCTGGTATCGTTGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaaaaaaa   >  1:314843/1‑141 (MQ=14)
                                                                                                                                     aGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAAt  >  1:86788/1‑141 (MQ=255)
                                                                                                                                         |                                                                                                                                        
GGAAGTTAAAGAAGAAAACATAAAAAAAG‑AAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAAT  >  USA300TCH1516_ALE/111380‑111652

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: ‑