Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 111,516 C→A 21.8% Q196K (CAA→AAA)  USA300HOU_RS00520 → putative lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE111,5160CA21.8% 59.2 / 13.8 37Q196K (CAA→AAA) USA300HOU_RS00520putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (12/17);  new base A (3/5);  total (15/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.89e-01

GAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAA  >  USA300TCH1516_ALE/111390‑111651
                                                                                                                              |                                                                                                                                       
gaagaaAACATAAAAAAAGAAATAGAAAACTTTAAGTTTTTTGCGAAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACt                                                                                                                           <  2:83099/141‑1 (MQ=255)
  agaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTaa                                                                                                                         <  2:298129/141‑1 (MQ=255)
     aaaaATTAAAAAAGAAATAGAAAACTTTAAGTTTTTTGCGTAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATTCATAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAatga                                                                                                                      <  2:135122/141‑1 (MQ=18)
     aaaCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTTTCGAGTTATTCAGCTCAATATCAATTAACTAatga                                                                                                                      <  1:66600/141‑1 (MQ=255)
      aaCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGGTATTCGGCGCAATATCAGTTAACTAatgat                                                                                                                     >  1:29360/1‑141 (MQ=255)
       aCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAatgatg                                                                                                                    >  1:215525/1‑141 (MQ=255)
        cATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAAtgatga                                                                                                                   >  1:41383/1‑141 (MQ=255)
         aTAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATgatgat                                                                                                                  >  1:242633/1‑141 (MQ=255)
           aaaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGCATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATta                                                                                                                <  2:207712/141‑1 (MQ=255)
                 aGAAAGCGAAAACATTAAGGTTTTTGCGCAATATAGAAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGt                                                                                                          <  2:250587/141‑1 (MQ=255)
                   aaaTAGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTaa                                                                                                        <  1:36438/141‑1 (MQ=255)
                    aaTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTaaa                                                                                                       <  1:84241/141‑1 (MQ=255)
                    aaTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTaaa                                                                                                       >  1:186764/1‑141 (MQ=255)
                       cGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACa                                                                                                    >  1:326053/1‑141 (MQ=255)
                         aaaaCAATAAGTTTATTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAAt                                                                                                  <  1:171496/141‑1 (MQ=255)
                           aaCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTa                                                                                                >  2:55604/1‑141 (MQ=255)
                              tttAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACgc                                                                                             <  1:299944/141‑2 (MQ=255)
                                tAAGTTTGTTGCGTAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTaa                                                                                           <  1:228290/141‑1 (MQ=255)
                                        tagcgcAATAAAGCAAATTTAAAGATTTAAACTGTAATACAGATTGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATg                                                                                   <  1:145665/139‑1 (MQ=17)
                                              aaTATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATAc                                                                             <  1:125837/141‑1 (MQ=255)
                                                     cAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACcgacgag                                                                      >  2:91525/1‑138 (MQ=11)
                                                                aTTTAATGAATTATAAAGAGGGAGACAAATCAAATAATCCAGATGTGCCGAGTTATTCAGCTCAATATCAACTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGa                                                           <  1:79121/141‑1 (MQ=17)
                                                                        aaatataAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTACAAGATATGACATACCAACAAATAAAGCGCCGAAGCtgttg                                                   <  1:180506/138‑1 (MQ=255)
                                                                             aaaaGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGaa                                              <  2:254726/140‑1 (MQ=255)
                                                                                   tGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAAAAATTACGTAAAAGATATGACATACAAACAAATAAAACGAAGAAGATGTTGTTGAAAGGTaa                                        >  2:220619/1‑140 (MQ=17)
                                                                                     gagaTATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAg                                      >  2:187181/1‑141 (MQ=255)
                                                                                             tCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTa                              >  1:166679/1‑141 (MQ=255)
                                                                                                    aTCCAGAGGTGCCGAGTAATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGtt                       <  2:46370/141‑1 (MQ=255)
                                                                                                      ccAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAATAGATATTACATACCAACAACTAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtca                     <  1:288320/141‑1 (MQ=255)
                                                                                                      ccAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtca                     <  1:17802/141‑1 (MQ=255)
                                                                                                      ccAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtca                     <  2:326053/141‑1 (MQ=255)
                                                                                                       cAGAGGTGCCGAGTTATTCAGCTCAATATCAATTACCTAATGATCCTTATAATGTCACACAATTCCCCCCGTGATCCGGCATACCAACAAATAAAGCGCCGAAGCTGATGCGAAGAGGCGGATGGTATTTAAAAGGTtcat                    <  2:89441/141‑1 (MQ=255)
                                                                                                        agagGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATAACAACAAATAAAGCACCGAAGCTGTTGTTGAAAGATACAGGGAATTTAAACAGTtaatc                   >  2:334512/1‑141 (MQ=14)
                                                                                                            gTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGtt               >  1:137337/1‑141 (MQ=255)
                                                                                                              gCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTgg             >  1:138249/1‑141 (MQ=255)
                                                                                                                 gAGTTATACAGATCAATCGAAATCAACAAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGata          <  2:295157/141‑1 (MQ=14)
                                                                                                                         cAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaaaaaaa  >  1:170524/1‑141 (MQ=255)
                                                                                                                              |                                                                                                                                       
GAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAA  >  USA300TCH1516_ALE/111390‑111651

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: