Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 111,516 C→A 27.2% Q196K (CAA→AAA)  USA300HOU_RS00520 → putative lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE111,5160CA27.2% 90.0 / 34.0 59Q196K (CAA→AAA) USA300HOU_RS00520putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (23/20);  new base A (5/11);  total (28/31)
Fisher's exact test for biased strand distribution p-value = 1.53e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.24e-01

AGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATT  >  USA300TCH1516_ALE/111379‑111653
                                                                                                                                         |                                                                                                                                         
aGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAat                                                                                                                                        <  2:58742/141‑1 (MQ=255)
    aGTTAAAGAAGAAAACATAAAAAAAGAAATCGCAAACTTTAAGATTTTTGCGCAATATAGCAATTTTAAAGACATAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCa                                                                                                                                    >  1:309546/1‑141 (MQ=255)
    aGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCa                                                                                                                                    >  1:34920/1‑141 (MQ=255)
      ttAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAAt                                                                                                                                  >  1:301969/1‑141 (MQ=255)
       tAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAAtt                                                                                                                                 <  1:378983/141‑1 (MQ=255)
       tAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAACCCAGAGGTGCCGTGTTATTCAGCTCAATATCAAtt                                                                                                                                 <  1:304835/141‑1 (MQ=255)
        aaaGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTa                                                                                                                                <  2:306430/141‑1 (MQ=255)
         aagaagAAAACATAAAAAAAGAAATCGAGCGCTTTAAGTTTTTTGCGCAATATAGCAATCTTAAAGATTTAAGGAATTATAAAGATGGAGATATATCATATAATCAAGAGGTGCCGAGTTATTCAGCTCAATATCAATTaa                                                                                                                               >  2:313074/1‑141 (MQ=21)
         aagaagAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTaa                                                                                                                               >  2:173589/1‑141 (MQ=255)
         aagaagAAAACATAAAAAAAGAAAGCGAAAACTTTAAGTTTTTTGCGAAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTaa                                                                                                                               <  2:93710/141‑1 (MQ=255)
           aaagaaAACATAAAAAAAGAAATCAAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACt                                                                                                                             <  1:282774/140‑1 (MQ=255)
             agaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTaa                                                                                                                           <  1:147993/141‑1 (MQ=255)
              gaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGAAATTTTAAAGATTTAATGTATTATAAAGATGGAGATATATAATATAATACAGAGGTGCCGAGTTATTCAGCTAAATATACATTAaataat                                                                                                                          >  2:312351/1‑141 (MQ=18)
               aaaaCATAAAAAAAGAAATCTAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTGAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatg                                                                                                                         <  1:344260/141‑1 (MQ=255)
                  aCATAGAAAAAGAAAGCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatgatg                                                                                                                      <  1:125779/141‑1 (MQ=255)
                  aCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatgatg                                                                                                                      <  1:329064/141‑1 (MQ=255)
                       aaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATtat                                                                                                                 >  2:231240/1‑141 (MQ=255)
                       aaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATtat                                                                                                                 >  1:260432/1‑141 (MQ=255)
                       aaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATtat                                                                                                                 <  1:71161/141‑1 (MQ=255)
                       aaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATtat                                                                                                                 <  2:200214/141‑1 (MQ=255)
                           aaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATg                                                                                                             <  1:290397/141‑1 (MQ=255)
                              aaaTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTACCTAATGATTTTTATTATGTaa                                                                                                          >  2:99875/1‑141 (MQ=255)
                              aaaTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTAAATTATTTATAAAGATGGAGATATATCATATAATCCATAGTTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTaa                                                                                                          <  2:67453/141‑1 (MQ=18)
                                aTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATATaaaa                                                                                                        >  2:347718/1‑141 (MQ=255)
                                 tCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTAGGCTCAATATCAATTAACTAATGATGATTATATTGTAAAAc                                                                                                       >  2:228396/1‑141 (MQ=255)
                                  cGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGACATATATCATATAATAAAAAGGTGACGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAcaca                                                                                                      >  2:309736/1‑141 (MQ=21)
                                  agAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACa                                                                                                      <  2:95495/140‑1 (MQ=255)
                                   gAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCGGAGATTATCTGTAAAATATCAATTAACTACTGATGATTATAATTTAaaaaaa                                                                                                     >  2:185333/1‑141 (MQ=18)
                                      aaCTTTAAGTTTTTTGGGAAAGATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTa                                                                                                  <  2:74553/141‑1 (MQ=17)
                                      aaCTTTAAGTATTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTa                                                                                                  <  2:168284/141‑1 (MQ=255)
                                        cTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGGTATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACg                                                                                                <  2:355158/141‑1 (MQ=255)
                                        cTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACg                                                                                                <  1:341568/141‑1 (MQ=255)
                                           tAAGTTTTTTGCGCAATATAGCAATTTTAAAGATGTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTaa                                                                                             <  2:67369/141‑1 (MQ=255)
                                                          atatAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAAGTAACTAATGAGGATGATAATGTAAGACAATTACGTAAAAGATATGACATAcc                                                                              >  1:81495/1‑141 (MQ=255)
                                                               gCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATAccgacga                                                                         <  1:9226/141‑6 (MQ=11)
                                                                      tAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAgc                                                                  >  2:276897/1‑141 (MQ=255)
                                                                          gATTTAATGAGTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCg                                                              <  2:139685/141‑1 (MQ=255)
                                                                           aTTTAATGATTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGa                                                             <  2:198392/141‑1 (MQ=255)
                                                                                gtatgttATAAAGATGGAGATATATCATATAATCCAGAGGTGCAGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATCACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtg                                                        <  2:81495/136‑1 (MQ=255)
                                                                                aagAAGTATAAAGATGTAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtg                                                        <  2:263433/139‑1 (MQ=255)
                                                                                aTGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtg                                                        >  1:363348/1‑141 (MQ=255)
                                                                                    atgataAAGATGGAGATACATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtgttgt                                                    <  1:200423/138‑1 (MQ=255)
                                                                                            gATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATCACGTAAAAGTTATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGt                                            <  2:227818/141‑1 (MQ=255)
                                                                                            gATGGAGAGATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGt                                            <  2:186220/141‑1 (MQ=255)
                                                                                                    tatatCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAgtgca                                    >  1:3921/1‑137 (MQ=255)
                                                                                                              aaTCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGGATTTAAAAGGt                          >  1:276828/1‑141 (MQ=255)
                                                                                                               aTCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGtt                         <  2:301969/141‑1 (MQ=255)
                                                                                                                tCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGCTACAGGGAATTTAAAAGGTtc                        >  2:300839/1‑141 (MQ=255)
                                                                                                                 ccAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGAAATAACAACAAATAAAGCGCCGCAGCTGTTGTTGAAAGGTACAGGGAATTTAAACGGTtcc                       >  2:6243/1‑140 (MQ=255)
                                                                                                                   agagGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtcatc                     <  1:10089/141‑1 (MQ=255)
                                                                                                                   agagGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAAGAAATTTAAAAGCTtcatc                     >  2:347297/1‑141 (MQ=255)
                                                                                                                   acagGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtcatc                     <  1:313074/139‑1 (MQ=255)
                                                                                                                    gagGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtcatca                    >  1:329680/1‑141 (MQ=255)
                                                                                                                    gagGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCACAGAAACTGTTGTAGAAAGCTACAGGGAAATAAAAACGCtcataa                    >  2:391256/1‑139 (MQ=14)
                                                                                                                      ggTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGt                  >  1:7550/1‑141 (MQ=255)
                                                                                                                      ggTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGATGTTGAAAGGTACAGGGCATTTAAACGGTTCATCAgc                  >  2:272234/1‑140 (MQ=255)
                                                                                                                       gTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGtt                 >  1:291332/1‑141 (MQ=255)
                                                                                                                                     aGCTCAATATCAATTAACTAAAGATGATTATCATGTAAAACAATTACATAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAAt   >  2:61655/1‑141 (MQ=255)
                                                                                                                                      gCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAAtt  >  1:38510/1‑141 (MQ=255)
                                                                                                                                         |                                                                                                                                         
AGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATT  >  USA300TCH1516_ALE/111379‑111653

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: ‑