Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 111,512 A→G 22.2% S194S (TCA→TCG)  USA300HOU_RS00520 → putative lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE111,5120AG22.2% 106.6 / 21.0 58S194S (TCA→TCG) USA300HOU_RS00520putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base A (16/28);  new base G (5/8);  total (22/36)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATA  >  USA300TCH1516_ALE/111380‑111645
                                                                                                                                    |                                                                                                                                     
ggAAGTTAAATAAGAGAACAAAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAg                                                                                                                                      <  2:437862/134‑1 (MQ=255)
   aGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTc                                                                                                                                   <  2:118141/134‑1 (MQ=255)
     ttAAAGAAGAAAACATAAAAAAAGAAATCGACAACTCTACGTTTTTTGCGCAGTTTTGCAACTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGCTGCCGAGTTATTCGGCTaaa                                                                                                                                 >  1:229088/1‑134 (MQ=17)
     ttAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCaa                                                                                                                                 <  2:158551/134‑1 (MQ=255)
       aaaGAAGGAAACAGAAAAAAAGAAATCGGAAACTTTAAGTTATTGGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAata                                                                                                                               <  2:333731/134‑1 (MQ=18)
          gaagaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCa                                                                                                                            <  1:510300/134‑1 (MQ=255)
           aagaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCaa                                                                                                                           <  2:382318/134‑1 (MQ=255)
             gaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAAtt                                                                                                                         >  2:527398/1‑134 (MQ=255)
               aaaCATAAAATTAGAAATCGATTTCTTTAATTTTTTTGTGCTATATAGCAATTTTAAAGATTTAATGAATTATAAAGAGGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTaa                                                                                                                       <  1:98223/134‑1 (MQ=14)
               aaaCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTaa                                                                                                                       <  1:265885/134‑1 (MQ=255)
                aaCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAAc                                                                                                                      <  2:605358/134‑1 (MQ=255)
                aaCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGAAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTACCGAGTTATTCGGCTACAGATCAATTAAc                                                                                                                      >  2:598996/1‑134 (MQ=17)
                 aCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACt                                                                                                                     <  1:312582/134‑1 (MQ=255)
                 aCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACt                                                                                                                     <  1:527398/134‑1 (MQ=255)
                 aCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAACTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATAAATTAACt                                                                                                                     >  2:244890/1‑134 (MQ=255)
                  gaTAAAAAAAAAAATCAAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTa                                                                                                                    <  2:436265/133‑1 (MQ=17)
                  cATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTa                                                                                                                    >  2:332945/1‑134 (MQ=255)
                  cATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTATAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTCCCGACGTATTCAGCTCAAAATCAATCAACTa                                                                                                                    >  2:20559/1‑134 (MQ=21)
                   aTAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTaa                                                                                                                   >  1:530477/1‑134 (MQ=255)
                   aTAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTaa                                                                                                                   <  1:401353/134‑1 (MQ=255)
                             aaaTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATtat                                                                                                         <  2:72254/134‑1 (MQ=255)
                             aaaTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATtat                                                                                                         <  1:87918/134‑1 (MQ=255)
                                  gAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGt                                                                                                    <  2:82143/134‑1 (MQ=255)
                                     aaatttAAGTTATTTGCGCAAGATAGCAATTTTAAAGATTCAATGAACTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTaaa                                                                                                 <  2:262961/131‑1 (MQ=18)
                                        tttAAGTTTTTTGCGCAATATAGAAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGAGCCGAGCTATTCCGCTCAATATCCGTTACCCAATGCGGATTATAATGTcaaaaa                                                                                              >  1:405721/1‑132 (MQ=21)
                                             attttttGCTCGATATAATAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGTTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTAc                                                                                         <  2:309873/133‑1 (MQ=14)
                                               tttttGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCAGATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGt                                                                                       <  1:171983/134‑1 (MQ=255)
                                               tttttGAGCAATAGAGCAATTTTAAAGATGTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGt                                                                                       <  1:579146/134‑1 (MQ=255)
                                                ttttGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTa                                                                                      >  1:514070/1‑134 (MQ=255)
                                                    tggcAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAg                                                                                  <  1:145839/132‑1 (MQ=255)
                                                      gtaaTATATCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAAACCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGat                                                                                <  1:20417/132‑1 (MQ=255)
                                                      gcAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGat                                                                                >  1:299248/1‑134 (MQ=255)
                                                      gcAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGat                                                                                <  2:339349/134‑1 (MQ=255)
                                                       cAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGata                                                                               <  1:332945/134‑1 (MQ=255)
                                                        aaTATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGatat                                                                              <  2:90217/134‑1 (MQ=255)
                                                          tataGCAATTTTAAAGATTTAAGGAAGTATAAAGATGAAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGa                                                                            <  2:394119/134‑1 (MQ=255)
                                                              gCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGAGAtt                                                                        >  1:205911/1‑133 (MQ=255)
                                                              gCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAAAAAAAACGAAAAAGAAATGACaaa                                                                        >  1:454924/1‑132 (MQ=18)
                                                                 aTTTTAAATATTTAATGAATTAAAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACca                                                                     <  1:244657/134‑1 (MQ=255)
                                                                    ttAAAGATTTAATGAATTATAAAGAAGGCGATATTTCATATAATCCAGATGTGCCGTGTTATTCAGCTCATTATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACcaaca                                                                  <  1:163643/134‑1 (MQ=17)
                                                                               attatttATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGcc                                                       <  1:303008/129‑1 (MQ=255)
                                                                               aTGAATTATAAATATGGAGATATATTATATAATGCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGcc                                                       <  1:525382/134‑1 (MQ=255)
                                                                               aTGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATAACAACAAATAAAgcgca                                                       >  2:171423/1‑133 (MQ=255)
                                                                                tGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCg                                                      <  2:144443/134‑1 (MQ=255)
                                                                                       taAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGCAAAACAATTACGTAAAAGATCTGACGTACCAACAAACAAAACACCGAAGAtgt                                               >  2:28213/1‑134 (MQ=14)
                                                                                        aaaGATGGAGATATATCATATAATCCAGAGGGGCCGAGTTATTCAGCTCAATATCCATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtgtt                                              >  1:169709/1‑134 (MQ=255)
                                                                                          aGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtgttgt                                            >  2:398402/1‑134 (MQ=255)
                                                                                              ggAGATATATCATATTATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAGTTAGGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGaa                                        <  2:400126/134‑1 (MQ=255)
                                                                                                      atCATACAATGCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAg                                <  1:429420/134‑1 (MQ=255)
                                                                                                       tCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAgg                               <  1:409445/134‑1 (MQ=255)
                                                                                                        cATATACTCCAGAGGTGCCGAGTTATTCAGCCCAATATCAATTCACTGATGGTGACTCTCATGTTCAACAGTTACGTAAATGATATGACATACCAACCACTCTGGATATGCAGGTGTTGTTGAAAGGTACAggg                              <  2:299248/134‑1 (MQ=9)
                                                                                                                ccAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATACTGTAAAACAATTACGTACAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAAATTaaa                      >  1:104995/1‑134 (MQ=255)
                                                                                                                ccAGAGGTGCCGAGTTATTCAGCTCAATAACAATTAGCTAGTGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCAGAAGCTGTTGTTGAAAGGTACAGGGCATTTaca                      >  2:333800/1‑132 (MQ=17)
                                                                                                                ccAGAGCTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGGTGAAAGGTACAGGGAATTTaaa                      >  2:510637/1‑134 (MQ=255)
                                                                                                                   gagGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAgg                   <  1:373158/134‑1 (MQ=255)
                                                                                                                     ggTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGACTTTAAAAGGtt                 >  1:426325/1‑134 (MQ=255)
                                                                                                                        gCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtcat              >  1:290101/1‑134 (MQ=255)
                                                                                                                        gCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtcat              >  1:394751/1‑134 (MQ=255)
                                                                                                                                    aGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGAtata  >  2:520931/1‑134 (MQ=255)
                                                                                                                                    |                                                                                                                                     
GGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATA  >  USA300TCH1516_ALE/111380‑111645

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑