Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 111,516 C→A 29.6% Q196K (CAA→AAA)  USA300HOU_RS00520 → putative lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE111,5160CA29.6% 55.5 / 25.1 43Q196K (CAA→AAA) USA300HOU_RS00520putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (16/14);  new base A (5/8);  total (21/22)
Fisher's exact test for biased strand distribution p-value = 5.10e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.75e-01

CTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAA  >  USA300TCH1516_ALE/111376‑111651
                                                                                                                                            |                                                                                                                                       
atGAGGAAGTGAAAGAAGAAAGGCTAAAAAAAGAAATCGAAAACTTTAAATTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTc                                                                                                                                         <  1:227583/140‑1 (MQ=25)
    ggAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAata                                                                                                                                     <  2:131857/141‑1 (MQ=255)
       aGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCa                                                                                                                                  >  2:108535/1‑141 (MQ=255)
       aGTGAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCa                                                                                                                                  <  2:42659/141‑1 (MQ=255)
              gaagaaAACATAAAAAAAGAAATCGAAAACTTTAAGTGTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACt                                                                                                                           <  2:74531/141‑1 (MQ=255)
                           aaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGCGTTATTCAGCTCAATATCAATTAAATAATGATGataata                                                                                                              >  1:244126/1‑141 (MQ=255)
                            aaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATaa                                                                                                             <  1:240617/141‑1 (MQ=255)
                             aaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTGTAAt                                                                                                            >  1:43907/1‑141 (MQ=255)
                               aGAAGTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCCTATAATCCAGAGGTGCCGAGTTATTTGGCTAAATATCAATTAACTAATGTTGAttttgttat                                                                                                          >  2:102145/1‑134 (MQ=18)
                                 aaaTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATCATGATTATAATGTaa                                                                                                        >  1:58274/1‑141 (MQ=255)
                                     cGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAGTGTAAAACa                                                                                                    >  2:58404/1‑141 (MQ=255)
                                     cGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGAGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACa                                                                                                    >  1:215145/1‑141 (MQ=255)
                                      gAAAAGTTTAAGTTTTTTGGGCAATATAGAAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACaa                                                                                                   <  2:108266/141‑1 (MQ=255)
                                       aaaaCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATTGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAAt                                                                                                  <  1:233624/141‑1 (MQ=255)
                                         aaCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTa                                                                                                <  1:273862/141‑1 (MQ=255)
                                            tttAAGTTTTTTGCGCAATATCGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGt                                                                                             <  1:48050/141‑1 (MQ=255)
                                            tttAAGTTTTTTGCGCAATATAGAAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACgc                                                                                             <  1:157523/141‑2 (MQ=255)
                                            tttAAGCTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACgc                                                                                             <  1:107894/141‑2 (MQ=255)
                                              tAAGTTTTTTGAGCAATATATCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTaa                                                                                           <  1:260995/141‑1 (MQ=255)
                                              tAAGTTTTGTGCGAAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATAGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACgcaa                                                                                           <  2:48403/141‑4 (MQ=17)
                                                aGTTTTTTGCGCAATATAGCAATTTTAAAGCTTTAATGCCAGAAAAAGATGGAGATATATCATATAATTCATAGGTGCCGCGGTATTCGGCTAAATATCAATTAACTAATGCTGTTTATAATGTAAATCACTTACGCaaaa                                                                                         >  2:64295/1‑141 (MQ=17)
                                                              aataGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACca                                                                           <  1:201839/140‑1 (MQ=255)
                                                               ataGCAATTTTAAAGATTTAATGAATTATAAAAATGGAGATATATAAGATAATCCAGAGGTGCCGAGTGATTCGGCTAAATATAAATTAACTAATGATGATTATAACGTAAAACAATTACGCAAAAGATATGATATAccga                                                                          <  2:125118/141‑3 (MQ=14)
                                                                  acAATTTTAAAGATTTAATGAATTATAAAGATGGAAATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATAccgacga                                                                       <  2:27715/140‑6 (MQ=11)
                                                                          aaaGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGACGAGTTCTTCAGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTAAATAATAGAAATAACATACTAAAAAATAAAgag                                                               >  2:183147/1‑139 (MQ=17)
                                                                          aaaGAATTAATGAAGTAAAAAGATGGAGATAAAGGAGATAATCCAGAGGTGGCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAgcg                                                               <  2:28565/141‑1 (MQ=17)
                                                                           aaGATTTAATGAATTATAAAGATTGAGATATATCATATAATCCAGAGGTGCCGAGTTATGCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAgcgc                                                              >  1:211189/1‑141 (MQ=255)
                                                                           aaGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATACAgcgc                                                              >  1:251648/1‑141 (MQ=255)
                                                                           aaGATTTAATGAACTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAgcgc                                                              <  1:253303/141‑1 (MQ=255)
                                                                            aGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTCTAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAACGcc                                                             >  2:96130/1‑141 (MQ=255)
                                                                                    tGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtgt                                                     <  1:231350/141‑1 (MQ=255)
                                                                                     gAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAACGCGCCGAGGCtgtt                                                    >  1:42881/1‑141 (MQ=255)
                                                                                       aTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCagttgt                                                  >  2:112357/1‑141 (MQ=255)
                                                                                        ttATAAAGATGGAGATATATCATATAATCCGGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTgttgtt                                                 >  1:91746/1‑141 (MQ=255)
                                                                                        ttATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTgttgtt                                                 >  1:99477/1‑141 (MQ=255)
                                                                                          ataAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGa                                               <  1:35627/141‑1 (MQ=255)
                                                                                             aaGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATCATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAg                                            >  2:178459/1‑141 (MQ=255)
                                                                                              aGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAgg                                           >  2:119581/1‑141 (MQ=255)
                                                                                                     aatatatTATATAATTCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAggg                                    <  2:235584/140‑1 (MQ=255)
                                                                                                           taatatAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAGAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTa                              <  1:287194/139‑1 (MQ=255)
                                                                                                              tataATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTCTAGAAAGGTACAGGAAATTTaaaa                           >  2:117833/1‑141 (MQ=255)
                                                                                                                    ccAGAGGTGCCGAGTTATTCAGCTCAATATAAATTAAAAAAAGATAATTATAATGTAAAAAAAATACGTAAAAAATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtca                     >  1:280120/1‑141 (MQ=17)
                                                                                                                          gTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGtt               >  1:35275/1‑141 (MQ=255)
                                                                                                                                       cAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaaaaaaa  <  1:149865/141‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                       
CTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAA  >  USA300TCH1516_ALE/111376‑111651

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: