Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 995,747 C→T 9.9% intergenic (+24/‑27) appA → / → oppD_3 Oligopeptide‑binding protein AppA/Oligopeptide transport ATP‑binding protein OppD

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE995,7470CT 9.9% 118.1 / 3.2 40intergenic (+24/‑27)appA/oppD_3Oligopeptide‑binding protein AppA/Oligopeptide transport ATP‑binding protein OppD
Reads supporting (aligned to +/- strand):  ref base C (14/22);  new base T (2/2);  total (16/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.70e-01

CCTGGATTACCAATGTTCCAAGGTAAATCGATAACTATTGTTAACGATAAAGTACGAAACTTAGACATTGAAATTGGAACTGATCAAAGTTTATATAATTTAACTAAAGAAGCTTAGTAATGTAACCTCGACGATTTTGTCGAGGTTTACTTATATGGGGGGATGTTATGAATAATGTATTGTTAGAGGTTAAAGATTTAGAAACATCATTAAAAATAAATAATGAATGGTTAGCAACTGTTGAAAATATTTCTTTTGAATTATCTAAAGGAG  >  USA300TCH1516_ALE/995607‑995879
                                                                                                                                            |                                                                                                                                    
ccTGGATTACCAATGTTCCAAGGTAAATCGATAACTATTGTTAACGATAAAGTACGAAACTTAGACATTGAAATTGGAACTGATCAAAGTTTATATAATTTAACTAAAGAAGCTTAGTAATGTAACCTCGACGATTTTGTc                                                                                                                                      <  1:431684/141‑1 (MQ=255)
ccTGGATTACCAATGTTCCAAGGTAAATCGATAACTATTGTTAACGATAAAGTACGAAACTTAGACATTGAAATTGGAACTGATCAAAGTTTATATAATTTAACTAAAGAAGCTTAGTAATGTAACCTCGACGATTTTGTc                                                                                                                                      <  1:42496/141‑1 (MQ=255)
ccTGGATTACCAATGTTCCAAGGTAAATCGATAACTATTGTTAACGATAAAGTACGAAACCTAGACATTGAAATTGGAACTGATCAAAGTTTATATAATTTAACTAAAGAAGCTTAGTAATGTAACCTCGACGATTTTGTc                                                                                                                                      >  1:413223/1‑141 (MQ=255)
 cTGGATTACCAATGTTCCAAGGTAAATCGATAACTATTGTTAACGATAAAGTACGAAACTTAGACATTGAAATTGGAACTGATCAAAGTTTATATAATTTAACTAAAGAAGCTTAGTAATGTAACCTCGACGATTTTGTCg                                                                                                                                     <  2:303080/141‑1 (MQ=255)
 cTGGATTACCAATGTCCCAAGGTAAATCGATAACTATTGTTAACGATAAAGTACGAAACTTAGACATTGAAAGTGGAACTGATCAAAGTTTATATAATTTAACTAAAGAAGCTTAGTAATGTAACCTCGCCGATTTTGTCg                                                                                                                                     <  2:384803/141‑1 (MQ=255)
                                        ttAACNATAAAGTACGAAACTTAGACATTGAAATTGGAACTGATCAAAGTTTATATAATTTAACTAAAGAAGCTTAGTAATGTAACCTCGACGATTTTGTCGAGGTTNACTTATATGGGGGGATGTTATGAATAATGTAtt                                                                                              <  1:70023/141‑1 (MQ=255)
                                         tAACGATAAAGTACGAAACTTAGACATTGAAATTGGAACTGATCAAAGTTTATATAATTTAACTAAAGAAGCTTAGTAATGTAACCTCGACGATTTTGTCGAGGTTTACTTATATGGGGGGATGTTATGAATAATGTATTg                                                                                             >  2:206809/1‑141 (MQ=255)
                                           aCGATAAAGTACGAAACTTAGACATTGAAATTGGAACTGATCAAAGTTTATATAATTTAACTAAAGAAGCTTAGTAATGTAACCTCGACGATTTTGTCGAGGTTTACTTATATGGGGGGATGTTATGAATAATGTATTGtt                                                                                           <  1:278340/141‑1 (MQ=255)
                                                 aaGTACGAAACTTAGACATTGAAATTGGAACTGATCAAAGTTTATATAATTTAACTAAAGAAGCTTAGTAATGTAACCTCGACGATTTTGTCGAGGTTTACTTATATGGGGGGATGTTATGAATAATGTATTGTTAGAggg                                                                                     >  1:204641/1‑140 (MQ=255)
                                                 aaGTACGAAACTTAGACATTGAAATTGGAACTGATCAAAGTTTATATAATTTAACTAAAGAAGCTTAGTAATGTAACCTCGACGATTTTGTCGAGGTTTACTTATATGGGGGGATGTTATGAATAATGTATTGTTAGAGGt                                                                                     >  1:137461/1‑141 (MQ=255)
                                                 aaGTACGAAACTTAGACATTGAAATTGGAACTGATCAAAGTTTATATAATTTAACTAAAGAAGCTTAGTAATGTAACCTCGACGATTTTGTCGAGGTTTACTTATATGGGGGGATGTTATGAATAATGTATTGTTAGAGGt                                                                                     <  1:460165/141‑1 (MQ=255)
                                                 aaGTACGAAACTTAGACATTGAAATTGGAACTGATCAAAGTTTATATAATTTAACTAAAGAAGCTTAGTAATGTAACCTCGACGATTTTGTCGAGGTTTACTTATATGGGGGGATGTTATGAATAATGTATTGTTAGAGGt                                                                                     >  1:392736/1‑141 (MQ=255)
                                                 aaGTACGAAACTTAGACATTGAAATTGGAACTGATCAAAGTTTATATAATTTAACTAAAGAAGCTTAGTAATGTAACCTCGACGATTTTGTCGAGGTTTACTTATATGGGGGGATGTTATGAATAATGTATTGTTAGAGGt                                                                                     <  1:33319/141‑1 (MQ=255)
                                                 aaGTACGAAACTTAGACATTGAAATTGGAACTGATCAAAGTTTATATAATTTAACTAAAGAAGCTTAGTAATGTAACCTCGACGATTTTGTCGAGGTTTACTTATATGGGGGGATGTTATGAATAATGTATTGTTAGAGGt                                                                                     <  1:304242/141‑1 (MQ=255)
                                                 aaGTACGAAACTTAGACATTGAAATTGGAACTGATCAAAGTTTATATAATTTAACTAAAGAAGCTTAGTAATGTAACCTCGACGATTTTGTCGAGGTTTACTTATATGGGGGGATGTTATGAATAATGTATTGTTAGAGGt                                                                                     >  1:140037/1‑141 (MQ=255)
                                                             tAGACATTGAAATTGGAACTGATCAAAGTTTATATAATTTAACTAAAGAAGCTTAGTAATGTAACCTCGACGATTTTGTCGAGGTTTACTTATATGGGGGGATGTTATGAATAATGTATTGTTAGAGGTTAAAGATTTAGa                                                                         <  1:439202/141‑1 (MQ=255)
                                                                         ttGGAACTGATCAAAGTTTATATAATTTAACTAAAGAAGCTTAGTAATGTAACCTCGACGATTTTGTTGAGGTTTACTTATATGGGGGGATGTTATGAATAATGTATTGTTAGAGGTTAAAGATTTAGAAACATCATTaaa                                                             >  2:252129/1‑141 (MQ=255)
                                                                         ttGGAACTGATCAAAGTTTATATAATTTAACTAAAGAAGCTTAGTAATGTAACCTCGACGATTTTGTTGAGGTTTACTTATATGGGGGGATGTTATGAATAATGTATTGTTAGAGGTTAAAGATTTAGAAACATCATTaaa                                                             >  2:390792/1‑141 (MQ=255)
                                                                                   taaaaGTTTATATAATTTAACTAAAGAAGCGTAGTAATATAACATCGACGATTTTGTCGATGTTTACATATATGGAGGGATGTTATGAATAATATATTGTTAGAAATTAAAGATTTAGAAACATCATTAAAAATAaataat                                                   <  2:215609/139‑1 (MQ=255)
                                                                                   tCAAAGTTTATATAATTTAACTAAAGAAGCTTAGTAATGTAACCTCGACGATTTTGTCGAGGTTTACTTATATGGGGGGATGTTATGAATAATGTATTGTTAGAGGTTAAAGATTTAGAAACATCATTAAAAATAaataat                                                   <  2:138247/141‑1 (MQ=255)
                                                                                                aaTTTAACTAAAGAAGCTTAGTAATGTAACCTCGACGATTTTGTCGAGGTTTACTTATAT‑GGGGGATGTTATGAATAATGTATTGTTAGAGGTTAAAGATTTAGAAACATCATTAAAAATAAATAATGAATGGTTAGCAAc                                     <  2:149810/141‑1 (MQ=255)
                                                                                                 aTTTAACTAAAGAAGCTTAGTAATGTAACCTCGACGATTTTGTCGAGGTTTACTTATATGGGGGGATGTTATGAATAATGTATTGTTAGAGGTTAAAGATTTAGAAACATCATTAAAAATAAATAATGAATGGTTAGCAAc                                     <  2:339262/141‑1 (MQ=255)
                                                                                                   ttAACTAAAGAAGCTTAGTAATGTAACCTCGACGATTTTGTCGAGGTTTACTTATATGGGGGGATGTTATGAATAATGTATTGTTAGAGGTTAAAGATTTAGAAACATCATTAAAAATAAATAATGAATGGTTAGCAACTg                                   <  1:186747/141‑1 (MQ=255)
                                                                                                         aaaGAAGCTTAGTAATGTAACCTCGACGATTTTGTCGAGGTTTACTTATATGGGGGGATGTTATGAATAATGTATTGTTAGAGGTTAAAGATTTAGAAACATCATTAAAAATAAATAATGAATGGTTAGCAACTGTTGaaa                             <  1:105719/141‑1 (MQ=255)
                                                                                                                   aGTAATGTAACCTCGACGATTTTGTTGAGGTTTACTTATATGGGGGGATGTTATGAATAATGTATTGTTAGAGGTTAAAGATTTAGAAACATCATTAAAAATAAATAATGAATGGTTAGCAACTGTTGAAAATATTTCttt                   <  1:252129/141‑1 (MQ=255)
                                                                                                                   aGTAATGTAACCTCGACGATTTTGTTGAGGTTTACTTATATGGGGGGATGTTATGAATAATGTATTGTTAGAGGTTAAAGATTTAGAAACATCATTAAAAATAAATAATGAATGGTTAGCAACTGTTGAAAATATTTCttt                   <  1:390792/141‑1 (MQ=255)
                                                                                                                      aaagTAACCTCGACGATTTTGTCGAGGTTTAATTATATGGGGGGATGTTATAAATAATGTATTGTTAGAAGTTAAAGATTTAGAAACATCATTAAAAATAAATAATGAATGGTTAGCTACAGTTTAAAATATTTCTTTTGa                <  2:309699/138‑1 (MQ=255)
                                                                                                                      aaTGTAACCTCGACGATTTTGTCGAGGTTTACTTATATGGGGGGATGTTATGAATAATGTATTGTTAGAGGTTAAAGATTTAGAAACATCATTAAAAATAAATAATGAATGGTTAGCAACTGTTGAAAATATTTCTTTTGa                <  2:167925/141‑1 (MQ=255)
                                                                                                                      aaTGTAACCTCGACGATTTTGTCGAGGTTTACTTATATGGGGGGATGTTATGAATAATGTATTGTTAGAGGTTAAAGATTTAGAAACATCATTAAAAATAAATAATGAATGGTTAGCAACTGTTGAAAATATTTCTTTTGa                <  2:143692/141‑1 (MQ=255)
                                                                                                                        tGTAACCTCGACGATTTTGTCGAGGTTTACTTATATGGGGGGATGTTATGAATAATGTATTGTTAGAGGTTAAAGATTTAGAAACATCATTAAAAATAAATAATGAATGGTTAGCAACTGTTGAAAATATTTCTTTTGAAt              <  1:423173/141‑1 (MQ=255)
                                                                                                                        tGTAACCTCGACGATTTTGTCGAGGTTTACTTATATGGGGGGATGTTATGAATAATGTATTGTTAGAGGTTAAAGATTTAGAAACATCATTAAAAATAAATAATGAATGGTTAGCAACTGTTGAAAATATTTCTTTTGAAt              <  1:372002/141‑1 (MQ=255)
                                                                                                                        tGTAACCTCGACGATTTTGTCGAGGTTTACTTATATGGGGGGATGTTATGAATAATGTATTGTTAGAGGTTAAAGATTTAGAAACATCATTAAAAATAAATAATGAATGGTTAGCAACTGTTGAAAATATTTCTTTTGAAt              <  1:261989/141‑1 (MQ=255)
                                                                                                                         gTAACCTCGACGATTTTGTCGAGGTTTACTTATATGGGGGGATGTTATGAATAATGTATTGTTAGAGGTTAAAGATTTAGAAACATCATTAAAAATAAATAATGAATGGTTAGCAACTGTTGAAAATATTTCTTTTGAAtt             <  1:285788/141‑1 (MQ=255)
                                                                                                                             ccTCGACGATTTTGTCGAGGTTTACTTATATGGGGGGATGTTATGAATAATGTATTGTTAGAGGTTAAAGATTTAGAAACATCATTAAAAATAAATAATGAATGGTTAGCAACTGTTGAAAATATTTCTTTTGAATTATCt         >  1:872/1‑141 (MQ=255)
                                                                                                                             ccTCGACGATTTTGTCGAGGTTTACTTATATGGGGGGATGTTATGAATAATGTATTGTTAGAGGTTAAAGATTTAGAAACATCATTAAAAATAAATAATGAATGGTTAGCAACTGTTGAAAATATTTCTTTTGAATTATCt         >  1:313159/1‑141 (MQ=255)
                                                                                                                             ccTCGACGATTTTGTCGAGGTTTACTTATATGGGGGGATGTTATGAATAATGTATTGTTAGAGGTTAAAGATTTAGAAACATCATTAAAAATAAATAATGAATGGTTAGCAACTGTTGAAAATATTTCTTTTGAATTATCt         >  1:263251/1‑141 (MQ=255)
                                                                                                                             ccTCGACGATTTTGTCGAGGTTTACTTATATGGGGGGATGTTATGAATAATGTATTGTTAGAGGTTAAAGATTTAGAAACATCATTAAAAATAAATAATGAATGGTTAGCAACTGTTGAAAATATTTCTTTTGAATTATCt         >  1:238788/1‑141 (MQ=255)
                                                                                                                             ccTCGACGATTTTGTCGAGGTTTACTTATATGGGGGGATGTTATGAATAATGTATTGTTAGAGGTTAAAGATTTAGAAACATCATTAAAAATAAATAATGAATGGTTAGCAACTGTTGAAAATATTTCTTTTGAATTATCt         >  1:197008/1‑141 (MQ=255)
                                                                                                                             ccTCGACGAATATGTCGAGGTTTACTTATATGGGGGGATGCTATGAATAATGTATTGATAGTGGTTAAAGATTTAGAAACATCATTAAAAATAAATAATGAATGGCTAGAAACCGTTGAAAATATTTCTTTTGAATTATCt         >  2:457365/1‑141 (MQ=255)
                                                                                                                              cTCGACGATTTTGTCGAGGTTTACTTATATGGGGGGATGTTATGAATAATGTATTGTTAGAGGTTAAAGATTTAGAAACATCATTAAAAATAAATAATGAATGGTTAGCAACTGTTGAAAATATTTCTTTTGAATTATCTa        >  1:86699/1‑141 (MQ=255)
                                                                                                                              cTCGACGATTTTGTCGAGGTTTACTTATATGGGGGGATGTTATGAATAATGTATTGTTAGAGGTTAAAGATTTAGAAACATCATTAAAAATAAATAATGAATGGTTAGCAACTGTTGAAAATATTTCTTTTGAATTATCTa        >  1:379897/1‑141 (MQ=255)
                                                                                                                                   cgaTTTTGTCGAGGTTTACTTATATGGGGGGATGTTATGAATAATGTATTGTTAGAGGTTAAAGATTTAGAAACATCATTAAAAATAAATAATGAATGGTTAGCAACTGTTGAAAATATTTCTTTTGAATTATCTAAAGga   >  2:134767/1‑141 (MQ=255)
                                                                                                                                    gaTTTTGTCGAGGTTTACTTATATGGGGGGATGTTATGAATAATGTATTGTTAGAGGTTAAAGATTTAGAAACATCATTAAAAATAAATAATGAATGGTTAGCAACTGTTGAAAATATTTCTTTTGAATTATCTAAAGgag  <  1:319215/141‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                    
CCTGGATTACCAATGTTCCAAGGTAAATCGATAACTATTGTTAACGATAAAGTACGAAACTTAGACATTGAAATTGGAACTGATCAAAGTTTATATAATTTAACTAAAGAAGCTTAGTAATGTAACCTCGACGATTTTGTCGAGGTTTACTTATATGGGGGGATGTTATGAATAATGTATTGTTAGAGGTTAAAGATTTAGAAACATCATTAAAAATAAATAATGAATGGTTAGCAACTGTTGAAAATATTTCTTTTGAATTATCTAAAGGAG  >  USA300TCH1516_ALE/995607‑995879

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