Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 111,516 C→A 33.4% Q196K (CAA→AAA)  USA300HOU_RS00520 → putative lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE111,5160CA33.4% 57.3 / 34.2 48Q196K (CAA→AAA) USA300HOU_RS00520putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (16/16);  new base A (9/7);  total (25/23)
Fisher's exact test for biased strand distribution p-value = 7.65e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.29e-01

GGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGA  >  USA300TCH1516_ALE/111380‑111655
                                                                                                                                        |                                                                                                                                           
aaaaGTTAAAAAAGAAAACAAAAAAAAATAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATACATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAata                                                                                                                                         <  2:2593/139‑1 (MQ=18)
   aGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCa                                                                                                                                      >  1:183923/1‑141 (MQ=255)
      tAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATCAAGAGCAAGACATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAAtt                                                                                                                                   >  1:70547/1‑141 (MQ=18)
          gaagaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGATATTCGGCTAAATATCAATTAACt                                                                                                                               >  1:55826/1‑141 (MQ=255)
          gaagaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCAAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACt                                                                                                                               >  2:212735/1‑141 (MQ=255)
            agaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTAAATATCAATTAAATaa                                                                                                                             >  1:83550/1‑141 (MQ=255)
               aaaCATAAAAAAAGAAATCGAAACAGTGAAGTTTTTTGCGCAATATAGCAAGTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATACAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatga                                                                                                                          >  2:264685/1‑141 (MQ=17)
                aaCAAAAAAACAGAAATCGAAAACTTTAAGTTTTGTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAatgat                                                                                                                         <  1:297468/141‑1 (MQ=255)
                 aCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGCCTAAATATAAAATAACTactaata                                                                                                                        >  2:120100/1‑135 (MQ=17)
                  cATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAAagatga                                                                                                                       >  2:194781/1‑141 (MQ=255)
                   aTAAAAATAGAAATCGAAAACTTTAAGTTTTTTACGCAATATTGCAATTTTAAAGATTTAATGAATTAAAAAGATGGATAAATATCATATAATCCAGACTTGCCGAGTTATTCAGCTCAATATCAACTAACTAATgatgat                                                                                                                      <  1:1519/141‑1 (MQ=18)
                      aaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATtat                                                                                                                   <  1:235453/141‑1 (MQ=255)
                      aaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATtat                                                                                                                   <  1:242326/141‑1 (MQ=255)
                      aaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATtat                                                                                                                   <  2:320855/141‑1 (MQ=255)
                         aaaGAAATCGAAAACTTTAAGTTTTTTTCTTATTTTAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGCTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAAt                                                                                                                >  2:184483/1‑141 (MQ=18)
                         aaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAAt                                                                                                                >  1:17277/1‑141 (MQ=255)
                         aaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAAt                                                                                                                >  2:348885/1‑141 (MQ=255)
                         aaaGAAATCGAAAACTTTAAGTGTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAAt                                                                                                                <  2:334864/141‑1 (MQ=255)
                              aaTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTaaa                                                                                                           >  1:239028/1‑141 (MQ=255)
                               aTCGAGAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTaaaa                                                                                                          <  2:103750/141‑1 (MQ=255)
                               aTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAGGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAACTATCAATTAACTAATAATGATTATAATGTaaaa                                                                                                          >  2:207528/1‑141 (MQ=18)
                                  gAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACaa                                                                                                       <  2:929/141‑1 (MQ=255)
                                     aaCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAAGAGCAATTAACTAATGATGATTATAATGTAAAACAATTa                                                                                                    <  2:87241/141‑1 (MQ=255)
                                        tttAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACgc                                                                                                 <  1:216861/141‑2 (MQ=255)
                                        tttAAGTTTTTTGCGCAATATAGCAATTTTAAAGAGGTAATGACTCAACAGGAGGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACgc                                                                                                 <  1:175494/141‑2 (MQ=17)
                                           aaGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTAAGaaaa                                                                                              >  2:33468/1‑141 (MQ=255)
                                                   tGCGCAATATAGCAATTTTAAAGATGTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGa                                                                                      <  2:201941/141‑1 (MQ=255)
                                                      gcAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACaa                                                                                   >  1:161046/1‑140 (MQ=255)
                                                      gcAAAATAGCAATTTTAAAGATTTAATGAATTCTAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGataa                                                                                   >  1:267053/1‑138 (MQ=17)
                                                                      aaaGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAAATATGACATAACAAAAAATAAAgcg                                                                   >  1:139426/1‑141 (MQ=255)
                                                                           tttAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGaa                                                              <  1:61316/141‑1 (MQ=255)
                                                                             tAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGTCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGc                                                            <  1:237742/141‑1 (MQ=255)
                                                                             tAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGc                                                            <  1:54268/141‑1 (MQ=255)
                                                                                    ttATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGATgttgtt                                                     >  1:2084/1‑141 (MQ=255)
                                                                                                 aatataaCATATAATCCAGAGATGCCTAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAggg                                        <  1:138642/140‑1 (MQ=255)
                                                                                                   tatatCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGAGATTACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGaa                                      >  1:289823/1‑141 (MQ=255)
                                                                                                     tatCATATAATCCAGAGGTGCCGAGGTATTGAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGAATTAACAACAAATAAAGCGTCGAAGATGTTGTTTAAAGGTAAAGGGAAtt                                    >  2:73038/1‑141 (MQ=14)
                                                                                                      atCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAAttt                                   <  2:183923/141‑1 (MQ=255)
                                                                                                       tCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTa                                  >  1:213538/1‑141 (MQ=255)
                                                                                                        aatatAATCCAGAGATTCCGAGTTATTCAGATCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTaa                                 <  2:161046/140‑1 (MQ=255)
                                                                                                                   gagGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtcatca                      <  1:133040/141‑1 (MQ=255)
                                                                                                                     ggTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGt                    >  1:95887/1‑141 (MQ=255)
                                                                                                                     ggTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGt                    >  1:7897/1‑141 (MQ=255)
                                                                                                                         ccGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAGAGGTTCATCAGTTGGa                <  1:184483/141‑1 (MQ=255)
                                                                                                                         ccGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGa                >  2:138469/1‑141 (MQ=255)
                                                                                                                                  tCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATCAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaaaaaa       <  2:17277/141‑1 (MQ=255)
                                                                                                                                  tCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaaaaaa       <  1:348885/141‑1 (MQ=255)
                                                                                                                                   cAGCTCAATATCAATTAACTACTGATGATTATGATGTAAAACAATTACGCAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTAAAGGGAATTTAAAAGGTTCATCAGTTGGATCTaaaaaaa      >  1:34198/1‑141 (MQ=17)
                                                                                                                                       ccAAGATCAATAAAATAATGATGACTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTTGTGAAAGGTACAGGGAATTTAAAATGTTCATCAGTTGGATATAAAAAAATTGa  <  2:306815/140‑1 (MQ=17)
                                                                                                                                        |                                                                                                                                           
GGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGA  >  USA300TCH1516_ALE/111380‑111655

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: ‑