Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 989,442 C→A 10.0% Q141K (CAG→AAG)  oppC → Oligopeptide transport system permease protein OppC

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE989,4420CA10.0% 128.2 / 3.5 40Q141K (CAG→AAG) oppCOligopeptide transport system permease protein OppC
Reads supporting (aligned to +/- strand):  ref base C (20/16);  new base A (2/2);  total (22/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.19e-01

ACATAGAAATCTTCCGGCAAAAATACCTGTATTAGACAAAGTTCCATTTTTACCTTTTGATGGTAAAGATGCAGATGGCAAGGATGCTTATAAAGCAGCAAATGCTAAAGAAAATTATTGGTTTGGTACTGATCAGTTGGGTCGAGATTTATGGACAAGAACATGGAAAGGTGCTCAAATTTCATTGTTTATCGGTGTTGTTGCAGCGATGTTAGATATTTTTATTGGTGTTGTATATGGTGCGATTTCTGGATTCTTCGGTGGACGTGTC  >  USA300TCH1516_ALE/989309‑989579
                                                                                                                                     |                                                                                                                                         
aCATAGAAATCTTCCGGCAAAAATACCTGTATTAGACAAAGTTCCATTTTTACCTTTTGATGGTAAAGATGCAGATGGCAAGGATGCTTATAAAGCAGCAAATGCTAAAGAAAATTATTGGTTTGGTACTGATCAGTTggg                                                                                                                                    <  2:279505/141‑1 (MQ=255)
           ttCCGGCAAAAATACCTGTATTAGACAAAGTTCCATTTTTACCTTTTGATGGTAAAGATGCAGATGGCAAGGATGCTTATAAAGCAGCAAATGCTAAAGAAAATTATTGGTTTGGTACTGATCAGTTGGGTCGAGATTTAt                                                                                                                         >  2:144930/1‑141 (MQ=255)
           ttCCGGCAAAAATACCTGTATTAGACAAAGTTCCATTTTTACCTTTTGATGGTAAAGATGCAGATGGCAAGGATGCTTATAAAGCAGCAAATGCTAAAGAAAATTATTGGTTTGGTACTGATCAGTTGGGTCGAGATTTAt                                                                                                                         >  1:356646/1‑141 (MQ=255)
           ttCCGGCAAAAATACCTGTATTAGACAAAGTTCCATTTTTACCTTATGATGGTAAAGATGCAGATGGCAAGGATGCTTATAAAGCAGCAAATGCTAAAGAAAATTATTGGTTTGGTACTGATCAGTTGGGTCGAGATTTAt                                                                                                                         >  1:116518/1‑141 (MQ=255)
           caccaataaaaaTACCTGTATTAGACAAAGTTCCATTTTTACCTTTTGATGGTAAAGATGCAGATGGCAAGGATGCTTATAAAGCAGCAAATGCTAAAGAAAATTATTGGTTTGGTACTGATAAGTTGGGTCGAGATTTAt                                                                                                                         >  2:61043/8‑141 (MQ=255)
           caccaataaaaaTACCTGTATTAGACAAAGTTCCATTTTTACCTTTTGATGGTAAAGATGCAGATGGCAAGGATGCTTATAAAGCAGCAAATGCTAAAGAAAATTATTGGTTTGGTACTGATAAGTTGGGTCGAGATTTAt                                                                                                                         >  2:120524/8‑141 (MQ=255)
             ccGGCAAAAATACCTGTATTAGACAAAGTTCCATTTTTACCTTTTGATGGTAAAGATGCAGATGGCAAGGATGCTTATAAAGCAGCAAATGCTAAAGAAAATTATTGGTTTGGTACTGATCAGTTGGGTCGAGATTTATgg                                                                                                                       >  2:6940/1‑141 (MQ=255)
             ccGGCAAAAATACCTGTATTAGACAAAGTTCCATTTTTACCTTTTGATGGTAAAGATGCAGATGGCAAGGATGCTTATAAAGCAGCAAATGCTAAAGAAAATTATTGGTTTGGTACTGAACAGTTGGGTCGAGATTCATgg                                                                                                                       >  1:61857/1‑141 (MQ=255)
                                   aCAAAGTTCCATTTTTACCTTTTGATGGTAAAGATGCAGATGGCAAGGATGCTTATAAAGCAGCAAATGCTAAAGAAAATTATTGGTTTGGTACTGATCAGTTGGGTCGAGATTTATGGACAAGAACATGGAAAGGTGCTc                                                                                                 <  2:300311/141‑1 (MQ=255)
                                   aCAAAGTTCCATTTTTACCTTTTGATGGTAAAGATGCAGATGGCAAGGATGCTTATAAAGCAGCAAATGCTAAAGAAAATTATTGGTTTGGTACTGATCAGTTGGGTCGAGATTTATGGACAAGAACATGGAAAGGTGCTc                                                                                                 <  2:391687/141‑1 (MQ=255)
                                   aCAAAGTTCCATGTTTACCTTTTGATGGTAAAGATGCAGATGGCAAGGATGCTTATAAAGCAGCAAATGCTAAAGAAAACTATTGGTTTGGTACTGATCAGTTGGGTCGAGATTTATGTACAAGAACATGGAAAGGTGCTc                                                                                                 <  2:158070/141‑1 (MQ=255)
                                     aaaGTTCCATTTTTACCTTTTGATGGTAAAGATGCAGATGGCAAGGATGCTTATAAAGCAGCAAATGCTAAAGAAAATTATTGGTTTGGTACTGATCAGTTGGGTCGAGATTTATGGACAAGAACATGGAAAGGTGCTCaa                                                                                               <  2:444056/141‑1 (MQ=255)
                                          tCCATTTTTACCTTTTGATGGTAAAGATGCAGATGGCAAGGATGCTTATAAAGCAGCAAATGCTAAAGAAAATTATTGGTTTGCTACTGATCAGTTGGGTCGAGATTTATGGACAAGAACATGGAAAGGTGCTCAAATTTc                                                                                          >  2:372243/1‑141 (MQ=255)
                                           ccATTTTTACCTTTTGATGGTAAAGATGCAGATGGCAAGGATGCTTATAAAGCAGCAAATGCTAAAGAAAATTATTGGTTTGGTACTGATCAGTTGGGTCGAGATTTATGGACAAGAATATGGAAAGGTGCTCAAATTTCa                                                                                         >  1:311075/1‑141 (MQ=255)
                                                   aCCTTTTGATGGTAAAGATGCAGATGGCAAGGATGCTTATAAAGCAGCAAATGCTAAAGAAAATTATTGGTTTGGTACTGATCAGTTGGGTCGAGATTTATGGACAAGAACATGGAAAGGTGCTCAAATTTCATTGTTTAt                                                                                 >  1:414432/1‑141 (MQ=255)
                                                   aCCTTTTGATGGTAAAGATGCAGATGGCAAGGATGCTTATAAAGCAGCAAATGCTAAAGAAAATTATTGGTTTGGTACTGATCAGTTGGGTCGAGATTTATGGACAAGAACATGGAAAGGTGCTCAAATTTCATTGTTTAt                                                                                 >  1:337563/1‑141 (MQ=255)
                                                            tGGTAAAGATGCAGATGGCAAGGATGCTTATAAAGCAGCAAATGCTAAAGAAAATTATTGGTTTGGTACTGATCAGTTGGGTCGAGATTTATGGACAAGAACATGGAAAGGTGCTCAAATTTCATTGTTTATCGGtgttgt                                                                        <  2:229409/141‑1 (MQ=255)
                                                              gTAAAGATGCAGATGGCAAGGATGCTTATAAAGCAGCAAATGCTAAAGAAAATTATTGGTTTGGTACTGATCAGTTGGGTCGAGATTTATGGACAAGAATATGGAAAGGTGCTCAAATTTCATTGTTTATCGGTGttgttg                                                                      <  2:311075/141‑1 (MQ=255)
                                                                           tGGCAAGGATGCTTATAAAGCAGCAAATGCTAAAGAAAATTATTGGTTTGGTACTGATCAGTTGGGTCGAGATTTATGGACAAGAACATGGAAAGGTGCTCAAATTTCATTGTTTATCGGTGTTGTTGCAGCGATGTTAGa                                                         <  2:178313/141‑1 (MQ=255)
                                                                           tGGCAAGGATGCTTATAAAGCAGCAAATGCTAAAGAAAATTATTGGTTTGGTACTGATCAGTTGGGTCGAGATTTATGGACAAGAACATGGAAAGGTGCTCAAATTTCATTGTTTATCGGTGTTGTTGCAGCGATGTTAGa                                                         <  2:203665/141‑1 (MQ=255)
                                                                                     gCTTATAAAGCAGCAAATGCTAAAGAAAATTATTGGTTTGGTACTGATCAGTTGGGTCGAGATTTATGGACAAGAACATGGAAAGGTGCTCAAATTTCATTGTTTATCGGTGTTGTTGCAGCGATGTTAGATATTTTTAtt                                               <  2:392299/141‑1 (MQ=255)
                                                                                     gCTTATAAAGCAGCAAATGCTAAAGAAAATTATTGGTTTGGTACTGATCAGTTGGGTCGAGATTTATGGACAAGAACATGGAAAGGTGCTCAAATTTCATTGTTTATCGGTGTTGTTGCAGCGATGTTAGATATTTTTAtt                                               <  2:60742/141‑1 (MQ=255)
                                                                                        tataAAGCAGCAAATGCTAAAGAAAATTATTGGTTTGGTACTGATCAGTTGGGTCGAGATTTATGGACAAGAACATGGAAAGGTGCTCAAATTTCATTGTTTATCGGTGTTGTTGCAGCGATGTTAGATATTTTTATTGgt                                            >  1:378812/1‑141 (MQ=255)
                                                                                         ataAAGCAGTAAATGCTAAAGCCATTTATTGGTTTGGTACTGATCAGTTGGGTCGAGATTTATGGACAAGAACATGGAAAGGTGCTCAAATTTCCTTGTTTATCGGTGTTGTTGCAGCGATGTTAGATATTTTTGTTGgtg                                           >  2:22325/1‑141 (MQ=255)
                                                                                         ataAAGCAGCAAATGCTAACTTAGTTTATTGGTTTGGTACTGATAAGTTGGGTCGAGATTTATGGACAAGAACATGGAAAGGTGCTCAAATTTCATTGTTTATCGGTGTTGTTGCAGCGATGTTAGATATTTTTATTGgtg                                           <  1:120524/141‑1 (MQ=255)
                                                                                         ataAAGCAGCAAATGCTAAAGAAAATTATTGGTTTGGTACTGATCAGTTGGGTCGAGATTTATGGACAAGAACATGGAAAGGTGCTCAAATTTCATTGTTTATCGGTGTTGTTGCAGCGATGTTAGATATTTTTATTGgtg                                           >  2:212535/1‑141 (MQ=255)
                                                                                         ataAAGCAGCAAATGCTAAAGAAAATTATTGGTTTGGTACTGATCAGTTGGGTCGAGATTTATGGACAAGAACATGGAAAGGTGCTCAAATTTCATTGTTTATCGGTGTTGTTGCAGCGATGTTAGATATTTTTATTGgtg                                           <  1:6940/141‑1 (MQ=255)
                                                                                         ataAAGCAGCAAATGCTAAAGAAAATTATTGGTTTGGTACTGATCAGTTGGGTCGAGATTTATGGACAAGAACATGGAAAGGTGCTCAAATTTCATTGTTTATCGGTGTTGTTGCAGCGATGTTAGATATTTTTATTGgtg                                           >  1:444826/1‑141 (MQ=255)
                                                                                         ataAAGCAGCAAATGCTAAAGAAAATTATTGGTTTGGTACTGATCAGTTGGGTCGAGATTTATGGACAAGAACATGGAAAGGTGCTCAAATTTCATTGTTTATCGGTGTTGTTGCAGCGATGTTAGATATTTTTATTGgtg                                           >  1:305011/1‑141 (MQ=255)
                                                                                         ataAAGCAGCAAATGCTAAAGAAAATTATTGGTTTGGTACTGATCAGTTGGGTCGAGATTTATGGACAAGAACATGGAAAGGTGCTCAAATTTCATTGTTTATCGGTGTTGTTGCAGCGATGTTAGATATTTTTATTGgtg                                           <  2:61857/141‑1 (MQ=255)
                                                                                         ataAAGCAGCAAATGCTAAAGAAAATTATTGGTTTGGTACTGATAAGTTGGGTCGAGATTTATGGACAAGAACATGGAAAGGTGCTCAAATTTCATTGTTTATCGGTGTTGTTGCAGCGATGTTAGATATTTTTATTGgtg                                           <  1:61043/141‑1 (MQ=255)
                                                                                                     aTGCTAAAGAAAATTATTGGTTTGGTACTGATCAGTTGGGTCGAGATTTATGGACAAGAACATGGAAAGGTGCTCAAATTTCATTGTTTATCGGTGTTGTTGCAGCGATGTTAGATATTTTTATTGGTGTTGTATATGGTg                               >  2:26336/1‑141 (MQ=255)
                                                                                                     aTGCTAAAGAAAATTATTGGTTTGGTAATGATCAGTTGGGTCGAGATTTATGGACAAGAACATGGAAAGGTGCTCAAATTTCATTGTTTATCGGTGTTGTTGCAGCGATGTTAGATATTTTTATTGGTGTTGTATATGGTg                               <  2:230620/141‑1 (MQ=255)
                                                                                                        cTAAAGAAAATTATTGGTTTGGTACTGATCAGTTGGGTCGAGATTTATGGACAAGAACATGGAAAGGTGCTCAAATTTCATTGTTTATCGGTGTTGTTGCAGCGATGTTAGATATTTTTATTGGGGTTGTATATGGTGCGa                            >  2:297939/1‑141 (MQ=255)
                                                                                                                      tggtttggtACTGATCAGTTGGGTCGAGATTTATGGACAAGAACATGGAAAGGTGCTCAAATTTCATTGTTTATCGGTGTTGTTGCAGCGATGTTAGATATTTTTATTGGTGTTGTATATGGTGCGATTTCTGGAttcttc              >  1:315016/1‑141 (MQ=255)
                                                                                                                          ttggtACTGATCAGTTGGGTCGAGATTTATGGACAAGAACATGGAAAGGTGCTCAAATTTCATTGTTTATCGGTGTTGTTGCAGCGATGTTAGATATTTTTATTGGTGTTGTATATGGTGCGATTTCTGGATTCTTCGGTg          <  1:58346/141‑1 (MQ=255)
                                                                                                                          ttggtACTGATCAGTTGGGTCGAGATTTATGGACAAGAACATGGAAAGGTGCTCAAATTTCATTGTTTATCGGTGTTGTTGCAGCGATGTTAGATATTTTTATTGGTGTTGTATATGGTGCGATTTCTGGATTCTTCGGTg          <  1:147185/141‑1 (MQ=255)
                                                                                                                                  gATCAGTTGGGTCGAGATTTATGGACAAGAACATGGAAAGGTGCTCAAATTTCATTGTTTATCGGTGTTGTTGCAGCGATGTTAGATATTTTTATTGGTGTTGTATATGGTGCGATTTCTGGATTCTTCGGTGGACGTGTc  >  2:93153/1‑141 (MQ=255)
                                                                                                                                  gATCAGTTGGGTCGAGATTTATGGACAAGAACATGGAAAGGTGCTCAAATTTCATTGTTTATCGGTGTTGTTGCAGCGATGTTAGATATTTTTATTGGTGTTGTATATGGTGCGATTTCTGGATTCTTCGGTGGACGTGTc  >  2:198606/1‑141 (MQ=255)
                                                                                                                                  gATCAGTTGGGTCGAGATTTATGGACAAGAACATGGAAAGGTGCTCAAATTTCATTGTTTATCGGTGTTGTTGCAGCGATGTTAGATATTTTTATTGGTGTTGTATATGGTGCGATTTCTGGATTCTTCGGTGGACGTGTc  >  1:388441/1‑141 (MQ=255)
                                                                                                                                     |                                                                                                                                         
ACATAGAAATCTTCCGGCAAAAATACCTGTATTAGACAAAGTTCCATTTTTACCTTTTGATGGTAAAGATGCAGATGGCAAGGATGCTTATAAAGCAGCAAATGCTAAAGAAAATTATTGGTTTGGTACTGATCAGTTGGGTCGAGATTTATGGACAAGAACATGGAAAGGTGCTCAAATTTCATTGTTTATCGGTGTTGTTGCAGCGATGTTAGATATTTTTATTGGTGTTGTATATGGTGCGATTTCTGGATTCTTCGGTGGACGTGTC  >  USA300TCH1516_ALE/989309‑989579

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑