Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 148,138 A→G 8.4% intergenic (+296/‑49) butA → / → wbgU Diacetyl reductase [(S)‑acetoin forming]/UDP‑N‑acetylglucosamine 4‑epimerase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE148,1380AG 8.4% 109.1 / 3.2 48intergenic (+296/‑49)butA/wbgUDiacetyl reductase [(S)‑acetoin forming]/UDP‑N‑acetylglucosamine 4‑epimerase
Reads supporting (aligned to +/- strand):  ref base A (22/22);  new base G (2/2);  total (24/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.35e-01

GCATTATTAGTATTAACACACCCAAGATATTATAAAACATCACAAAAACACCACTATCTAATTTATCTCAATAAAAATTCACAAAGTTATCTCATTTTATTTTTATAAATAAAAAATATCGATAAAAAGCTTACAATACTTTATGTTTTTATGATATATTTTTAATGTATAAATGAGGTGGAAGATTTGGAAAGAGTTTTGATAACTGGTGGGGCTGGTTTTATTGGGTCGCATTTAGTAGATGATTTACAACAAGATTATGATGTTTATGTT  >  USA300TCH1516_ALE/148001‑148273
                                                                                                                                         |                                                                                                                                       
gCATTATTAGTATTAACACACCCAAGATATTATAAAACATCACAAAAACACCACTATCTAATTTATCTCAATAAAATCTCACAAAGTAATCTCATTTTATTTTTATAAATAAAAAATATGGATAAAAAGCTTACAATGCtt                                                                                                                                      >  1:260643/1‑141 (MQ=255)
gCATTATTAGTATTAACACACCCAAGATATTATAAAACATCACAAAAACACCACTATCTAATTTATCTCAATAAAAATTCACAAAGTTATCTCATTTTATTTTTATAAATAAAAAATATCGATAAAAAGCTTACAATGCtt                                                                                                                                      >  1:161474/1‑141 (MQ=255)
gCATTATTAGTATTAACACACCCAAGATATTATAAAACATCACAAAAACACCACTATCTAATTTATCTCAATAAAAATTCACAAAGTTATCTCATTTTATTTTTATAAATAAAAAATATCGATAAAAAGCTTACAATACtt                                                                                                                                      >  1:248864/1‑141 (MQ=255)
   ttattaGTATTAACACACCCAAGATATTATAAAACATCACAAAAACACCACTATCTCATTTATCTCAATAAAAATTCACAAAGTTATCTCATTTTATTTTTATAAATAAAAAATATCGATAAAAAGCTTACAATACttttt                                                                                                                                   >  2:298749/1‑139 (MQ=255)
     attaGTATTAACACACCCAAGATATTATAAAACATCACAAAAACACCACTATCTAATTTATCTCAATAAAAATTCACAAAGTTATCTCATTTTATTTTTATAAATAAAAAATATCGATAAAAAGCTTACAATACTTTATGt                                                                                                                                 >  1:48256/1‑141 (MQ=255)
     attaGTATTAACAAACCCAAGATATTATAAAACATCACAAAAACACCACTATCTAATTTATCTCAATAAAAATTCACAAAGTTATCTCATTTTATTTTTATAAATAAAAAATATCGATAAAAAGCTTACAATACTTTATGt                                                                                                                                 >  1:158706/1‑141 (MQ=255)
          tATTAACACACCCAAGATATTATAAAACATCACAAAAACACCACTATCTAATTTATCTCAATAAAAATTCACAAAGTTATCTCATTTTATTTTTATAAATAAAAAATATCGATAAAAAGCTTACAATACTTTATGTTTTTa                                                                                                                            >  1:138598/1‑141 (MQ=255)
              aaCACACCCAAGATATTATAAAACATCACAAAAACACCACTATCTAATTTATCTCAATAAAAATTCACAAAGTTATCTCATTTTATTTTTATAAATAAAAAATATCGATAAAAAGCTTACAATACTTTATGTTTTTATGat                                                                                                                        <  1:79666/141‑1 (MQ=255)
                cacacCCAAGATATTATAAAACATCACAAAAACACCACTATATAATTTATCTCATTAAAAATTCACAAAGTTATCTCATTTTATTTTTATAAATAAAAAATATTGATAAAAAGCTTACAATACTTTATGTTGTTATGatct                                                                                                                      >  2:96917/1‑139 (MQ=255)
                 acacCCAAGATATTATAAAACATCACAAAAACACCACTATCTAATTTATCTCAATAAAAATTCACAAAGTTATCTCATTTTATTTTTATAAATAAAAAATATCGATAAAAAGCTTACAATACTTTATGTTTTTATGatata                                                                                                                     <  1:176843/141‑1 (MQ=255)
                 acacCCAAGATATTATAAAACATCACAAAAACACCACTATCTAATTTATCTCAATAAAAATTCACAAAGTTATCTAATTTTATTTTTATAAATAAAAAATATCGATAAAAAGCTTACAATACTTTATGTTTTTATGatata                                                                                                                     <  2:16059/141‑1 (MQ=255)
                             ttatAAAACATCACAAAAACACCACTATCTAATTTATCTCAATAAAAATTCACAAAGTTATCTCATTTTATTTTTATAAATAAAAAATATCGATAAAAAGCTTACAATACTTTATGTTTTTATGATATATTTTTAATGtat                                                                                                         >  1:59650/1‑141 (MQ=255)
                              tataAAACATCACAAAAACACCACTATCTAATTTATCTCAATAAAAATTCACAAAGTTATCTCATTTTATTTTTATAAATAAAAAATATCGATAAAAAGCTTACAATACTTTATGTTTTTATGATATATTTTTAATGtata                                                                                                        >  1:60024/1‑141 (MQ=255)
                                  aaaCATCACAAAAACACCACTATCTAATTTATCTCAATAAAAATTCACAAAGTTATCTCATTTTATTTTTATAAATAAAAAATATCGATAAAAAGCTTACAATACTTTATGTTTTTATGATATATTTTTAATGTATAAATg                                                                                                    >  2:303988/1‑141 (MQ=255)
                                          caAAAACACAACTATCTAATTTATCTAAACAAAAATTCACAAAGTTATCTAATTTTATTTTTATAAATAAAAAATATCGATAAAAAGCTTACAATACTTTATGTTTTTATGATCTATTTTTAATGTATAAATGAGGTGGag                                                                                            >  2:328252/1‑140 (MQ=255)
                                            aaaaCACCACTATCTAATTTATCTCAATAAAAATTCACAAAGTTATCTCATTTTATTTTTATAAATAAAAAATATCGATAAAAAGCTTACAATACTTTATGTTTTTATGATATATTTTTAATGTATAAATGAGGTGGAAGa                                                                                          >  2:190851/1‑141 (MQ=255)
                                                caccacTATCTAATTTATCTCAATAAAAATTCACAAAGTTATCTCATTTTATTTTTATAAATAAAAAATATCGATAAAAAGCTTACAATACTTTATGTTTTTATGATATATTTTTAATGTATAAATGAGGTGGAAGATTTg                                                                                      >  2:97946/1‑141 (MQ=255)
                                                caccacTATCTAATTTATCTCAATAAAAATTCACAAAGTTATCTCATTTTATTTTTATAAATAAAAAATATCGATAAAAAGCTTACAATACTTTATGTTTTTATGATATATTTTTAATGTATAAATGAGGTGGAAGATTTg                                                                                      >  2:327258/1‑141 (MQ=255)
                                                  ccacTATCTAATTTATCTCAATAAAAATTCACAAAGTTATCTCATTTTATTTTTATAAATAAAAAATATCGATAAAAAGCTTACAAAACTTTATGTTTTTATGATATATTTTTAATGTATAAAAGAGGTGGAGGATTTGGa                                                                                    >  1:195407/1‑141 (MQ=255)
                                                      tATCTAATTTATCTCAATAAAAATTCACAAAGTTATCTCATTTTATTTTTATAAATAAAAAATATCGATAAAAAGCTTACAATACTTTATGTTTTTATGATATATTTTTAATGTATAAATGTAGTGGAAGATTTGGTAaga                                                                                >  2:82316/1‑141 (MQ=255)
                                                       aTCTAATTTATCTCAATAAAAATTCACAAAGTTATCTCATTTTATTTTTATAAATAAAAAATATCGATAAAAAGCTTACAATGCTTTATGTTTTTATGATATATTTTTAATGTATAAATGAGGTGGAAGATTTGGAAagag                                                                               <  2:161474/141‑1 (MQ=255)
                                                       aTCTAATTTATCTAAATAAAAATTCACAAAGTTATCTCATTTTATTTTTATAAATAAAAAATATCGATAAAAAGCTTACAATGCTTTATGTTTTTATGATATATTTTTAATGTATAAATGAGGTGGAAGATTTGGAAagag                                                                               <  2:260643/141‑1 (MQ=255)
                                                                    cAATAAAAATTCACAAAGGTATCTCATTAAATCTTTATAAATAAAAAATATCGATAAAAAGCTTACAATACTTTATGTTTTTATGATATATTTTTAATGTATAAATGAGGTGGAAGATTTGGAAAGAGTTTTGATAACtgg                                                                  >  2:237273/1‑141 (MQ=255)
                                                                       tAAAAATTCACAAAGTTATCTCATTTTATTTTTATAAATAAAAAATATCGATAAAAAGCTTACAATACTTTATGTTTTTATGATATATTTTTAATGTATAAATGAGGTGGAAGATTTGGAAAGAGTTTTGATAACttgtgg                                                               <  2:23893/141‑1 (MQ=255)
                                                                       aaaaaaTTCATAAAGTTATCTCATTTTATTTTTATAAATAAAAAATATCGATAAAAAGCTTACAATACTTTATGTTTTTATGATATATTTTTAATGTATAAATGAGGTGGAAGATTTGGAAAGAGTTTTGATAACtggtgg                                                               <  2:341898/140‑1 (MQ=255)
                                                                          aaaTTCACAAAGTTATCTCATTTTATTTTTATAAATAAAAAATATCGATAAAAAGCTTACAATACTTTATGTTTTTATGATATATTTTTAATGTATAAATGAGGTGGAAGATTTGGAAAGAGTTTTGATAACTGGTGGGGc                                                            >  2:97348/1‑141 (MQ=255)
                                                                             tgcatcaaGTTATCTCATTTTATTTTTATAAATAAAAAATATCGATAAAAAGCTTACAATACTTTATGTTTTTATGATAGATTTTTAATGTATAAATGAGGTGGAAGATTTGGAAAGAGTTTTGATAACTGGTGGGGCTgg                                                         <  1:146553/135‑1 (MQ=255)
                                                                                acaAAGTTATCTCATTTTATTTTTATAAATAAAAAATATCGATAAAAAGCTTACAATACTTTATGTTTTTATGATATATTTTTAATGTATAAATGAGGTGGAAGATTTGGAAAGAGTTTTGATAACTGGTGGGGCTGGttt                                                      >  1:230304/1‑141 (MQ=255)
                                                                                acaAAGTTATCTCATTTTATTTTTATAAATAAAAAATATCGATAAAAAGCTTACAATACTTTATGTTTTTATGATATATTTTTAATGTATAAATGAGGTGGAAGATTTGGAAAGAGTTTTGATAACTGGTGGGGCTGGttt                                                      <  1:264205/141‑1 (MQ=255)
                                                                                  aaaataaTCTCATGTTATTTTTATAAATAAAAAATATCGATAAAAAGCTTACAATACTTTATGTTTTTATGATATATTTTTAATGTATAAATGAGGTGGAAGATTGGGAAAGAGTTTTGATAACTGGTGGGGCTGGTTTTa                                                    <  1:18809/135‑1 (MQ=255)
                                                                                  aaaGTTATCTCATTTTATTTTTATAAATAAAAAATATCGATACAACGACTCCCTCATAAGATGGGGCTATGATATATTTTTCATGTATAAATTAGGTGGAAGATTTGGAAAGAGTTTTGATAACTGGTGGGGCTGGTTTTa                                                    <  2:163122/141‑1 (MQ=255)
                                                                                   aaGTTATCTCAGTTTATTTTCATAAATAAAAAATATCGATAAAAAGCTTACAATACTTTATGTTTTTATGATATATTTTTAATGTATAAATGAGGTGGAAGATTTGGAAAGAGTTTTGATAACTGGTGGGGCTGGTTTTAt                                                   <  1:126072/141‑1 (MQ=255)
                                                                                     gTTATCTCATTTTATTTTTCTAGTTGCGAATTATCGATAAAAAGCTTACAATACTTTATGTTTTTATGATATATTTTTAATGTATAAATGAGGTGGAAGATTTGGAAAGAGTTTTGATAACTGGTGGGGCTGGTTTTATTg                                                 >  1:85737/1‑141 (MQ=255)
                                                                                     gTTATCTCATTTTATTTTTATAAATAAAAAATATCGATAAAAAGCTTACAATACTTTATGTTTTTATGATATATTTTTAATGTATAAATGAGGTGGAAGATTTGGAAAGAGTTTTGATAACTGGTGGGGCTGGTTTTATTg                                                 <  1:190851/141‑1 (MQ=255)
                                                                                        aTCTCATTTTATTTTTATAAATAAAAAATATCGATAAAAAGCTTACAATACTTTATGTTTTTATGATATATTTTTAATGTATAAATGAGGTGGAAGATTTGGAAAGAGTTTTGATAACTGGTGGGGCTGGTTTTATTGGGt                                              <  1:97348/141‑1 (MQ=255)
                                                                                          ttcATTTTATTTTTATAAACAAAAAATATCGATAAAAAACTTACAATACTTTATGTTTTTATGATATATTTTTAATGTATAAATGAGGTGTAAGATTTGGAAAGAGTTTTGATAACTGGTGGGGCTGGTTTTATTGGGTCg                                            <  1:42289/140‑1 (MQ=255)
                                                                                                    ttttatAAATAAAAAATATCGATAAAAAGCTTACAATACTTTATGTTTTTATGATATATTTTTAATGTATAAATGAGGTGGAAGATTTGGAAAGAGTTTTGATAACTGGTGGGGCTGGTTTTATTGGGTCGCATTtagtag                                  <  2:204474/141‑1 (MQ=255)
                                                                                                    ttttatAAATAAAAAATATCCATAAAAAGGTTACAATACTTTATGTTTTTATGATATAGTTTTAATGTATAAATGAGGTGGAAGATTTGGAAAGAGTTTTGATAACTGGTGGGGCTGGTTTTATTGGGTCGCATTtagtag                                  <  2:58227/141‑1 (MQ=255)
                                                                                                           aataaaAAATATCGATAAAAAGCTTACAATACTTTATGTTTTTATGATATATTTTTAATGTATAAATGAGGTGGAAGATTTGGAAAGAGTTTTGATAACTGGTGGGGCTGGTTTTATTGGGTCGCATTTAGTAGATGAttt                           <  1:291642/141‑1 (MQ=255)
                                                                                                            ataaaAAATATCGATAAAAAGCTTACAATACTTTATGTTTTTATGATATATTTTTAATGTATAAATGAGGTGGAAGATTTGGAAAGAGTTTTGATAACTGGTGGGGCTGGTTTTATTGGGTCGCATTTAGTAGATGATTTa                          <  1:303988/141‑1 (MQ=255)
                                                                                                            ataaaAAATATCGATAAAAAGCTTACAATACTTTATGTTTTTATGATATATTTTTAATGTATAAATGAGGTGGAAGAGTTGGAAAGAGTTTTGATAACGGGGGTGGCTGGTTTTATTGGGTCGCAGTTAGTAGATGATTTa                          >  1:320358/1‑141 (MQ=255)
                                                                                                             aaaaaaaTATCGATAAAAAGCTTACAATACTTTATGTTTTTATGATATATTTTTACTGTATTAAGTAAGTGGAAGATTTGGAAAGAGTTTTGATAACTGGTGGGGCTGGTTTTATTGGGTCGCATTTAGTAGATGATTTac                         <  1:82635/140‑1 (MQ=255)
                                                                                                                     atCGATAAAAAGCTTACAATACTTTATGTTTTTATGATATATTTTTAATGTATAAATGAGGTGGAAGATTTGGAAAGAGTTTTGATAACTGGTGGGGCTGGTTTTATTGGGTCGCATTTAGTAGATGATTTACAACAAGAt                 <  2:60024/141‑1 (MQ=255)
                                                                                                                     atCGATAAAAAGCTTACAATACTTTATGTTTTTATGATATATTTTTAATGTATAAATGAGGTGGAAGATTTGGAAAGAGTTTTGATAACTGGTGGGGCTGGTTTTATTGGGTCGCATTTAGTAGATGATTTACAACAAGAt                 >  1:149460/1‑141 (MQ=255)
                                                                                                                        gagagaaaGGTTACAATACTTTATGTGTATATGATCTCTTCTCGATGTATAAATGAGACGGAAGATTCGGAAAGAGTTCTGATGATGGGTGGGGCTGGTATTGTTGGGCCGCATTTAGTAGATGATTTACAGCAAGAatat              >  2:49024/6‑141 (MQ=255)
                                                                                                                            aaaaGCTTACAATACTTTATGTTTTTACGATATATTTTTAATGTATAAATGAGGTGGAAGATTTGGAAAGAGTTTTGATAACTGGTGGGGCTGGTTTTATTGGGTCGCATTTAGTAGATGATTTACAACAAGATTatgatg          <  1:298749/141‑1 (MQ=255)
                                                                                                                                   tACAATACTTTATGTTTTTATGATATATTTTTAATGTATAAATGAGGTGGAAGATTTGGAAAGAGTTTTGATAACTGGTGGGGCTGGTTTTATTGGGTCGCATTTAGTAGATGATTTACAACAAGATTATGATGTTTATGt   <  1:237273/141‑1 (MQ=255)
                                                                                                                                    aCAATACGTTATGTTTTTATGATATATTGTTAATGTATAAATGAGGTGGAAGATTTGGAAAGAGTTTTGATAACTGGTGGGGCTGGTTTTATTGGGTCGCATTTAGTAGATGATTTACAACAAGATTATGATGTTTATGtt  <  1:349661/141‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                       
GCATTATTAGTATTAACACACCCAAGATATTATAAAACATCACAAAAACACCACTATCTAATTTATCTCAATAAAAATTCACAAAGTTATCTCATTTTATTTTTATAAATAAAAAATATCGATAAAAAGCTTACAATACTTTATGTTTTTATGATATATTTTTAATGTATAAATGAGGTGGAAGATTTGGAAAGAGTTTTGATAACTGGTGGGGCTGGTTTTATTGGGTCGCATTTAGTAGATGATTTACAACAAGATTATGATGTTTATGTT  >  USA300TCH1516_ALE/148001‑148273

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: ‑