Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,028,124 G→A 72.5% P174L (CCG→CTG)  USA300HOU_RS10230 ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,028,1240GA72.5% 36.2 / 19.7 33P174L (CCG→CTG) USA300HOU_RS10230hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (2/7);  new base A (15/9);  total (17/16)
Fisher's exact test for biased strand distribution p-value = 5.70e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.34e-01

GTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTC  >  USA300TCH1516_ALE/2027985‑2028248
                                                                                                                                           |                                                                                                                            
gaaGATGTTAACCGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCgg                                                                                                                             <  1:106592/139‑1 (MQ=255)
gTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCgg                                                                                                                             <  1:9716/141‑1 (MQ=255)
  atatatTAACTTTATAGTTATCCGTTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCa                                                                                                                           <  2:305004/139‑1 (MQ=255)
         aaCTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAAc                                                                                                                    >  2:54360/1‑141 (MQ=255)
             gTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGc                                                                                                                >  1:134038/1‑141 (MQ=255)
               ataGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTACTTAACCAGCAATATAACCTGCAc                                                                                                              >  2:265508/1‑141 (MQ=255)
               ataGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCAc                                                                                                              >  1:30173/1‑141 (MQ=255)
                       ccGGTTTCATCATTTCTTTAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTa                                                                                                      <  2:271884/141‑1 (MQ=255)
                        cGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTaa                                                                                                     <  1:99768/141‑1 (MQ=255)
                        cGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTaa                                                                                                     >  1:124417/1‑141 (MQ=255)
                         ggTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTaaa                                                                                                    >  2:221444/1‑141 (MQ=255)
                         ggTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAAACTGCACTTTACCTaaa                                                                                                    >  2:108263/1‑141 (MQ=255)
                           tttCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAAt                                                                                                  >  2:230781/1‑141 (MQ=255)
                            ttCATCATTTCTTCAATATGAATATTGTTATTGTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAAtg                                                                                                 >  1:208736/1‑141 (MQ=255)
                                     tcttcAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTaaca                                                                                        <  1:239646/141‑1 (MQ=255)
                                      cttcAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAATGTGTCTaacaa                                                                                       >  2:156082/1‑141 (MQ=255)
                                              tGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGta                                                                               <  1:336934/141‑1 (MQ=255)
                                                  tagtGTTATTGTCAACTTTATATGATTTTGCAGTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGtattat                                                                           <  1:153605/138‑1 (MQ=255)
                                                         aTTTTCAAATTAATATGATATTTCATTCACGTAAGTACTTCAATAAAAAGCAGCTACATGTAAATGAACATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCtt                                                                    <  1:59611/141‑1 (MQ=255)
                                                              ctaCTTTATATGATTTTTCATTCACGTAAGGACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCCGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAatat                                                               >  2:390789/3‑141 (MQ=255)
                                                                aCTTTATATGATTTTTCATACACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATAttt                                                             <  1:220672/141‑1 (MQ=255)
                                                                    tataTGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTACTATTAGAACTCACCAGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAg                                                         <  1:290336/141‑1 (MQ=255)
                                                                       agcaTTTTTCCTTCACGTAAGTGTTTCCATCAACATCAGTTACATGTAAATTAATATTGTAATTACCCGGGAAGATAACCGGCACCTTGCCTCTATTGTTTCTACGAATTATGGTATTATTTTCCTTAATATTTGCAGCtt                                                      <  2:162606/138‑1 (MQ=255)
                                                                                          aGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAg                                   >  1:180125/1‑141 (MQ=255)
                                                                                          aGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAg                                   <  1:156082/141‑1 (MQ=255)
                                                                                          aGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAAAATAGACATTAGGGTGAATGCCAGCGGCTATTATAGTATTATTTTCATTAATATTTGCAGCTTTTGTTAAGTCAAtatatat                                   >  2:386119/1‑140 (MQ=255)
                                                                                           gTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAgg                                  >  1:320880/1‑141 (MQ=255)
                                                                                               ttCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGc                              <  2:57757/141‑1 (MQ=255)
                                                                                                tCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTATAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGcc                             <  1:54360/141‑1 (MQ=255)
                                                                                                    tAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTTCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAAGATGTAGGTCGCCAAtt                         >  1:317730/1‑141 (MQ=255)
                                                                                                      aaaaGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTcc                       <  1:230781/141‑1 (MQ=255)
                                                                                                       aaaGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCa                      >  1:189697/1‑141 (MQ=255)
                                                                                                             gcTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTCAGTCAATATGTAGGTCGCCAATTCCATGTTGa                >  2:259007/1‑141 (MQ=255)
                                                                                                                         ttAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCt    <  2:180125/141‑1 (MQ=255)
                                                                                                                           aaTATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTc  <  2:188330/141‑1 (MQ=255)
                                                                                                                                           |                                                                                                                            
GTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTC  >  USA300TCH1516_ALE/2027985‑2028248

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: ‑