Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 111,512 A→G 36.1% S194S (TCA→TCG)  USA300HOU_RS00520 → putative lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE111,5120AG36.1% 49.2 / 39.0 47S194S (TCA→TCG) USA300HOU_RS00520putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base A (13/17);  new base G (7/10);  total (20/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.70e-01

TACTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAA  >  USA300TCH1516_ALE/111374‑111648
                                                                                                                                          |                                                                                                                                        
tACTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAg                                                                                                                                         <  1:161508/140‑1 (MQ=255)
  cTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCt                                                                                                                                       >  1:289416/1‑140 (MQ=255)
   tGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTACCGAGTTATTCGGCta                                                                                                                                      <  1:176925/140‑2 (MQ=255)
      ggAAGTTAAACAAGAAAACATAAAAAAAGAAGTAGTATACTTTAAGTTTTTGGCGCAATACAGCAATATTACATATTTAATGACCAATAAACACTGAGATTTTTCATGTAATCCAGGGGTGCCCATTTATTCGGCTAAat                                                                                                                                   <  2:119733/140‑1 (MQ=255)
        aaGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGAGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATAGAATCAAAAGGTGCCGAGTTATTCAGCTCCataa                                                                                                                                 >  2:42533/1‑139 (MQ=21)
             aaaGAAATAAACAAAAATAAAGAAATCGAAATCTTTAAGTTTTATGCGCAATATAGCAATTTTAAAGATTTAATGCATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAAtt                                                                                                                            <  2:233368/140‑1 (MQ=17)
              aagaagATAACATAGAAAAAGAAATCGGAAACTTTAAGTTTTTTGCGAAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTa                                                                                                                           >  2:354018/1‑140 (MQ=18)
               agaagaAAACATCAAAATAGAAATCGAAAACATTAAGTTTTGTGCGCAATATAGCAATTTGAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTaa                                                                                                                          <  1:109264/140‑1 (MQ=18)
                 aagacAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACt                                                                                                                        <  1:160720/140‑1 (MQ=255)
                 aagaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAAc                                                                                                                         <  2:88432/139‑1 (MQ=255)
                 aagaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAAc                                                                                                                         >  1:88432/1‑139 (MQ=255)
                  agaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTa                                                                                                                       <  2:128161/140‑1 (MQ=255)
                        cATAAAAAAAGCAATCGAAAACCTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAatgatg                                                                                                                 <  2:322137/140‑1 (MQ=255)
                            aaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCCATTTTAACGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTTAGTAATGTTGGTta                                                                                                             >  1:70875/1‑140 (MQ=21)
                            aaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATta                                                                                                             >  2:166616/1‑140 (MQ=255)
                              aaaaGTAATCGTAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATtata                                                                                                           <  1:58705/140‑1 (MQ=17)
                                aaGAAATCGAAAACATTAAGTTTTTTGCGGAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAAt                                                                                                         <  1:171337/140‑1 (MQ=255)
                                   aaaTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTa                                                                                                      >  1:280118/1‑140 (MQ=255)
                                          aaaCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGCATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAAATAATGATGATTATAATGTaaacaaat                                                                                               >  2:226834/1‑135 (MQ=18)
                                           aagtttAAGTTTGGTGCGGAATATAGCAATTTGAAAGATTTAATGAATTACAACTATGGAGATATATCATATACTCCAGAGGTGCCGTTTTATTTAGCTCAATATCAATTAACTTATTATGATTATAATGTAAAACAAtt                                                                                              <  2:317235/137‑1 (MQ=18)
                                             cTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTAc                                                                                            <  1:343802/140‑1 (MQ=255)
                                              tttAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACg                                                                                           <  2:294171/140‑1 (MQ=255)
                                               ttAAGGTTTTTGGTGAATATAGAAAGTTTAAAGATTAAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACgc                                                                                          <  2:183465/140‑2 (MQ=14)
                                                 aaGTTTTTTGCGGAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGTTATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTaa                                                                                        <  2:65794/140‑1 (MQ=255)
                                                    ttttttGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAAATACGCAAAAg                                                                                     >  2:50201/1‑140 (MQ=17)
                                                     tttttGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGa                                                                                    <  1:354481/140‑1 (MQ=255)
                                                          gcgcAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGa                                                                               <  1:166616/140‑1 (MQ=255)
                                                                 ataGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACca                                                                        <  1:136175/140‑1 (MQ=255)
                                                                    gCAATTTTAAAGATTGAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACcgacg                                                                     >  1:265022/1‑139 (MQ=11)
                                                                       aTTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACcgacgagt                                                                  >  1:105890/1‑136 (MQ=11)
                                                                        ttttAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGAAATGACAAACCAACAAATa                                                                 >  1:255533/1‑140 (MQ=255)
                                                                                    aatgaatgATAAAGATGGAGATATAACATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGACTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGc                                                     <  1:218096/140‑1 (MQ=255)
                                                                                         aTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtgttg                                                >  1:208584/1‑140 (MQ=255)
                                                                                         aTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtgttg                                                >  1:208617/1‑140 (MQ=255)
                                                                                               aaGAGGGAGATATAGCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGaaa                                          <  1:44933/140‑1 (MQ=255)
                                                                                                aGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAg                                         <  2:2335/140‑1 (MQ=255)
                                                                                                     gagaTATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACa                                    <  1:298175/140‑1 (MQ=255)
                                                                                                             tCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAAttt                            >  2:64839/1‑140 (MQ=255)
                                                                                                              cATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTa                           <  1:116249/140‑1 (MQ=255)
                                                                                                               atatAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAGGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTaa                          <  2:65627/140‑1 (MQ=255)
                                                                                                                          agGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtcatca               >  1:43324/1‑140 (MQ=255)
                                                                                                                           ggTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAACTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAg              >  1:218069/1‑140 (MQ=255)
                                                                                                                             tGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGtt            >  2:348711/1‑140 (MQ=255)
                                                                                                                                cGAGTTGTTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAAATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGa         >  2:224579/1‑140 (MQ=255)
                                                                                                                                   gTTATTCATCTCAATTTTGATAAACAAATGATGATTATAATGTAAAACAACTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGatat      <  1:7156/140‑1 (MQ=17)
                                                                                                                                      aTTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaaa   <  2:66121/140‑1 (MQ=255)
                                                                                                                                       ttCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaaaa  >  2:105271/1‑140 (MQ=255)
                                                                                                                                          |                                                                                                                                        
TACTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAA  >  USA300TCH1516_ALE/111374‑111648

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: ‑