Predicted mutation
evidence seq id position mutation annotation gene description
RA USA300TCH1516_ALE 19,009 C→T S222F (TCC→TTC)  gdpP → Cyclic‑di‑AMP phosphodiesterase GdpP

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE19,0090CT96.9% 107.5 / NA 32S222F (TCC→TTC) gdpPCyclic‑di‑AMP phosphodiesterase GdpP
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base T (14/17);  total (15/17)
Fisher's exact test for biased strand distribution p-value = 4.69e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTTAGATAACTACGATGAGATTACGCAAAATATGAATGATACGCAGCGTTCGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGAAAAAAGTGTTGGTTATCGTGCCCAATTAACATTAAGTATCGGTGTTGGTG  >  USA300TCH1516_ALE/18881‑19143
                                                                                                                                |                                                                                                                                      
tttAGATAACTACGATGAGATTACGCAAAATATGAATGATACGCAGCGTTCGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTTCGATCAATTCGt                                                                                                                            >  1:175354/1‑141 (MQ=255)
                      aCGCAAAATATGAATGATACGCAGCGTTCGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTTCGATCAATTCGTAGCCTATTTAAATCAAAAAata                                                                                                      >  1:36004/1‑141 (MQ=255)
                      aCGCAAAATATGAATGATACGCAGCGTTCGGAAATCAACGCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGGTCCGAGCAAGTGGTAGCCTATGGAAATCaaaaaaga                                                                                                      >  2:12128/1‑139 (MQ=255)
                             atatGAATGATACGCAGCGTTCGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTTCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTg                                                                                               <  1:140273/141‑1 (MQ=255)
                              tatGAATGATACGCAGCGTTCGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTTCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGa                                                                                              >  2:224533/1‑141 (MQ=255)
                                 gaatgaTACGCAGCGTTCGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTTCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACtt                                                                                           >  1:133598/1‑141 (MQ=255)
                                                ttCGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTTCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAAtt                                                                            <  1:124067/141‑1 (MQ=255)
                                                ttCGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTTCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAAtt                                                                            >  1:169258/1‑141 (MQ=255)
                                                ttCGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTTCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAAtt                                                                            >  1:3172/1‑141 (MQ=255)
                                                  cGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTTCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTg                                                                          <  2:263724/141‑1 (MQ=255)
                                                  cGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTTCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTg                                                                          <  2:206531/141‑1 (MQ=255)
                                                  cGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTTCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTg                                                                          <  1:60958/141‑1 (MQ=255)
                                                   ggAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATTTACCAAACAAAAGATACAGTTTCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGa                                                                         <  1:78036/141‑1 (MQ=255)
                                                   ggAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTTCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGa                                                                         <  1:70862/141‑1 (MQ=255)
                                                   ggAAATCAAATCAATGGTAACGCGTGTTATTAGTTGATGGGCAACTGAGTATAATATATTTTTTAAAAGATACAGTTTCGATCCATTCGTAGCCTATTTAAATCAAGAAATATTAGCTGATTTCGATGACTGTAAATTTgt                                                                         <  2:131733/141‑2 (MQ=255)
                                                      aaTCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTTCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGatat                                                                      <  2:175354/141‑1 (MQ=255)
                                                           aCTCAATGGTAACGCGTGTGATTAGTCGATGGTCAACTTAGTAAAATATATTTTTCAAAAGATACAGTTTCGATCAATTCGTAGCCTATTTAAATCAAAATATATTATCTGACTTAGAAGAATCTAAATTTGATATCTTGa                                                                 >  2:101400/1‑141 (MQ=255)
                                                               aaTGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTTCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCa                                                             <  1:285779/141‑1 (MQ=255)
                                                               aaTGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTTCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCa                                                             <  2:205372/141‑1 (MQ=255)
                                                                              cATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTTCGATCAATTCGTAGCAAAAAAAAAAAAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGAAAAAAg                                              <  2:64581/141‑1 (MQ=255)
                                                                                      gATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTTCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGAAAAAAGTGTTGGtt                                      >  2:108605/1‑141 (MQ=255)
                                                                                       aTGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTTCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGAAAAAAGTGTTGGTTa                                     <  1:10238/141‑1 (MQ=255)
                                                                                             aaCTGAGTATAATATATTTTTCAAAAGATACAGTTTCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGAAAAAAGTGTTGGTTATCGTGc                               >  1:40130/1‑141 (MQ=255)
                                                                                              aCTGAGTATAATATATTTTTCAAAAGATACAGTTTCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGAAAAAAGTGTTGGTTATCGTGcc                              <  1:191418/141‑1 (MQ=255)
                                                                                                            atTTTTCAAAAGATACAGTTTCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGACGAATCTCAATTTGATCTACTGAGCAAATTACGTGAAAAAAGTGTTGGTTATCGTGCCCAATTAACATTAAg                >  1:257503/1‑141 (MQ=255)
                                                                                                                     aaGATACAGTTTCGATNAATTCGTAGCCTNTTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGAAAAAAGTGTTGGTTATCGTGCCCAATTAACATTAAGTATCGgtgt       >  1:264906/1‑141 (MQ=255)
                                                                                                                     aaGATACAGTTTAAAACAATACGTAGCCGATTTAAATAAAAAACTATTAGATAACTTAGAAAAATCTGGGTTGGATCTCTTGGGAAAAAAAAAAAAAAAAAGTGTTGGTTATCGTGCCCAATTAACATTAAGTATCGgtgt       <  2:111912/141‑1 (MQ=255)
                                                                                                                         tACAGTTTCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGAAAAAAGTGTTGGTTATCGTGCCCAATTAACATTAAGTATCGGTGTTGGt   <  1:148340/141‑1 (MQ=255)
                                                                                                                         tACAGTTTCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGAAAAAAGTGTTGGTTATCGTGCCCAATTAACATTAAGTATCGGTGTTGGt   <  1:133041/141‑1 (MQ=255)
                                                                                                                          aCAGTTTCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGAAAAAAGTGTTGGTTATCGTGCCCAATTAACATTAAGTATCGGTGTTGGTg  >  2:196404/1‑141 (MQ=255)
                                                                                                                          aCAGTTTCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGAAAAAAGTGTTGGTTATCGTGCCCAATTAACATTAAGTAACGGTGTTGGTg  >  2:245575/1‑141 (MQ=255)
                                                                                                                          aCAGTTTCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGCCAATTACGTGAAAAAAGTGTTGGTTATCGTGCCCAATTAACATTAAGTATCGGTGTTGGTg  >  2:196412/1‑141 (MQ=255)
                                                                                                                                |                                                                                                                                      
TTTAGATAACTACGATGAGATTACGCAAAATATGAATGATACGCAGCGTTCGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGAAAAAAGTGTTGGTTATCGTGCCCAATTAACATTAAGTATCGGTGTTGGTG  >  USA300TCH1516_ALE/18881‑19143

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: ‑