Predicted mutation
evidence seq id position mutation annotation gene description
RA USA300TCH1516_ALE 2,455,698 2 bp→AT coding (1216‑1217/1260 nt) lyrA → Lysostaphin resistance protein A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,455,6980CA91.2% 108.6 / 5.8 34coding (1216/1260 nt)lyrALysostaphin resistance protein A
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base A (11/20);  minor base . (2/1);  total (13/21)
Fisher's exact test for biased strand distribution p-value = 5.44e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.50e-01
*USA300TCH1516_ALE2,455,6990AT97.1% 121.0 / ‑5.1 34H406L (CAT→CTT) lyrALysostaphin resistance protein A
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base T (13/20);  total (13/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

ATCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCC  >  USA300TCH1516_ALE/2455565‑2455832
                                                                                                                                     ||                                                                                                                                     
aTCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGAAAAAACTga                                                                                                                        >  1:146300/1‑149 (MQ=255)
     ttAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAAc                                                                                                                   >  1:80316/1‑149 (MQ=255)
              caccacAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAg                                                                                                          <  1:163958/149‑1 (MQ=255)
                   caAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATaaa                                                                                                     <  1:234257/149‑1 (MQ=255)
                   aaaaataaCGATTAAACAAACGATTCAAATGAAGATGAAATAAAGCAATCATTAAAAGAAACTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATAGAAAAAACTGAAGAACAATCTTCAGATaaa                                                                                                     <  2:191126/142‑1 (MQ=255)
                     aggTGGCGATTTAACGATCGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATaaaaa                                                                                                   <  1:237393/147‑1 (MQ=255)
                                  aCAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACaa                                                                                      <  1:95140/149‑1 (MQ=255)
                                  aCAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACaa                                                                                      >  1:210570/1‑149 (MQ=255)
                                     aaCGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAgc                                                                                   <  2:5388/149‑1 (MQ=255)
                                     aaCGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAgc                                                                                   <  2:5382/149‑1 (MQ=255)
                                      aCGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAgcg                                                                                  >  1:14497/1‑149 (MQ=255)
                                       cGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAgcgc                                                                                 >  1:211049/1‑149 (MQ=255)
                                             aaaTGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGC‑CAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTa                                                                           <  2:75855/149‑1 (MQ=255)
                                              aaTGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAg                                                                          >  1:222962/1‑149 (MQ=255)
                                              aaTGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAg                                                                          >  1:151318/1‑149 (MQ=255)
                                                    gATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACctc                                                                    <  1:170348/149‑1 (MQ=255)
                                                    aaTGAAATAAAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACctc                                                                    <  1:165512/148‑1 (MQ=255)
                                                          aTAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTaaaa                                                              <  2:160531/149‑1 (MQ=255)
                                                            agagCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAg                                                            >  2:84418/1‑149 (MQ=255)
                                                               gCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAgatg                                                         <  2:247292/149‑1 (MQ=255)
                                                               gCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAgatg                                                         <  2:274891/149‑1 (MQ=255)
                                                                 aaTCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAgatgat                                                       >  2:131608/1‑149 (MQ=255)
                                                                             aaCCCGCGACTAATAAAGAAGACAGACGTACATCAGTAGTAATTAAAGAA‑AAAAAAAAAAAAAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAgcgc                                           <  2:52730/149‑1 (MQ=255)
                                                                              aCCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCt                                          <  2:213709/149‑1 (MQ=255)
                                                                                  gCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTc                                      <  2:211049/149‑1 (MQ=255)
                                                                                   cGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTct                                     <  2:14497/149‑1 (MQ=255)
                                                                                           aaaGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTctatactata                             <  1:160851/149‑1 (MQ=255)
                                                                                             agaagaCAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACtatata                           >  1:275313/1‑149 (MQ=255)
                                                                                                   cagacGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTAttt                     >  1:13142/1‑149 (MQ=255)
                                                                                                    agacGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTAtttt                    <  2:102001/149‑1 (MQ=255)
                                                                                                    agacGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTAtttt                    <  1:94623/149‑1 (MQ=255)
                                                                                                             tcaGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTAAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAGGCGCTTTTCTATACTATATATTATTTTTCTAAAAtt           <  1:11586/149‑1 (MQ=255)
                                                                                                                    tAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAacac    >  2:11561/1‑149 (MQ=255)
                                                                                                                      aTTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACAccc  >  2:258664/1‑149 (MQ=255)
                                                                                                                                     ||                                                                                                                                     
ATCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCC  >  USA300TCH1516_ALE/2455565‑2455832

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑