Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,455,692 Δ1 bp 100% coding (1210/1260 nt) lyrA → Lysostaphin resistance protein A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,455,6920G.83.4% 142.2 / 29.2 48coding (1210/1260 nt)lyrALysostaphin resistance protein A
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base . (24/16);  minor base A (4/3);  total (29/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.47e-01
Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch.

GAATCAGCAGAATCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTA  >  USA300TCH1516_ALE/2455554‑2455826
                                                                                                                                           |                                                                                                                                      
gAATCAGCAGAATCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCaaaa                                                                                                                                      >  1:144115/1‑141 (MQ=255)
gAATCAGCAGAATCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCaaaa                                                                                                                                      >  2:16319/1‑141 (MQ=255)
      gcagAATCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATGGAT‑GCAaaaaaatta                                                                                                                                >  2:59863/1‑138 (MQ=255)
              aGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGaaaaa                                                                                                                       <  2:389097/141‑1 (MQ=255)
               gTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGaaaaaa                                                                                                                      >  1:287199/1‑141 (MQ=255)
               gTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGGTGTAATTGAT‑GCA‑AAAAAATTATCGaaaaaa                                                                                                                      >  1:139012/1‑141 (MQ=255)
                      aaGCACCACAAAGTGACAATTAAACAAACGATCCAAATGAAAATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGATGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTgaaga                                                                                                               <  1:67782/141‑1 (MQ=255)
                            cacaAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCGTCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACactg                                                                                                         >  1:315633/1‑138 (MQ=255)
                             acaAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAAAAATCt                                                                                                        >  1:215551/1‑141 (MQ=255)
                             acaAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAAGAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGGTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCt                                                                                                        >  1:115474/1‑141 (MQ=255)
                               aaaGGGACGATTTAACAAACGATTCAAAGGAAGATGAAATAGAGCAATCATTAAAAGAAGCTGCGACGTATAAACAAGACAGACGTACATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAATACTGAAGAACAATCTTc                                                                                                      <  2:187576/141‑1 (MQ=255)
                                  gTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAATAACAATCTTCAGa                                                                                                   >  1:40278/1‑141 (MQ=255)
                                      cGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCACAAG‑‑ATAATTTATAGTCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATaaa                                                                                               >  1:389975/1‑141 (MQ=255)
                                       gATTTAACAAACTATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGCACAGTCTTCGGATaacc                                                                                              <  2:185135/141‑3 (MQ=255)
                                       gATATAACAAACGATTCAAAGGAAGATGAAATAGATCAATCATTAAAAGAACCTGCGACTTATAAACAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATaaaa                                                                                              <  2:296809/141‑1 (MQ=255)
                                         tttAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCATAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAAc                                                                                            >  1:328360/1‑141 (MQ=255)
                                         tttAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAAc                                                                                            >  2:13416/1‑141 (MQ=255)
                                          ttAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACa                                                                                           >  2:55921/1‑141 (MQ=255)
                                                         aaTGAAGAGGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAGAAAATAACAAAacg                                                                            >  2:23555/1‑141 (MQ=255)
                                                               gATGGAATAGAGCAATGATTAAAAGAACCTGCCACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCt                                                                      <  2:220610/141‑1 (MQ=255)
                                                               aaTGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACATAGCGCTTGCt                                                                      <  2:269846/140‑1 (MQ=255)
                                                                aTGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCgctagcta                                                                     >  2:198057/1‑141 (MQ=255)
                                                                aTGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTa                                                                     >  1:385689/1‑141 (MQ=255)
                                                                     aTAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTAcc                                                                >  1:63196/1‑141 (MQ=255)
                                                                       agagCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACctc                                                              <  2:132066/141‑1 (MQ=255)
                                                                        gagCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACctct                                                             <  1:376576/141‑1 (MQ=255)
                                                                                   aaaaGAACCTGCGACTTATAAAGAATACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAgatga                                                  <  2:268367/141‑1 (MQ=255)
                                                                                   aaaaGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAgatga                                                  >  2:301116/1‑141 (MQ=255)
                                                                                    aaaGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTGATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTGGCTAGTACCTCTTAAAAAgatgat                                                 >  2:213537/1‑141 (MQ=255)
                                                                                    aaaGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACCATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAgatgat                                                 >  1:255989/1‑141 (MQ=255)
                                                                                    aaaGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAAACATCAGATAAAAACAAATAATAACAAAGCACTAGCTAGTACCTCTTAAAAAgataat                                                 >  2:15203/1‑141 (MQ=255)
                                                                                     aaGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTCGCTAGTACGTCTTAAAAAGatgatg                                                >  1:362092/1‑141 (MQ=255)
                                                                                       gAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCt                                              >  2:117688/1‑141 (MQ=255)
                                                                                       aaaacTGTGACTTACAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTGCAGACAAAAACAAATAATAACAAAGCTCTTGCTAGTACCTCTTAAAAAGATGATGCt                                              <  1:306117/137‑1 (MQ=255)
                                                                                            tGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCaa                                         <  2:386398/141‑1 (MQ=255)
                                                                                            tGCGACTTATAAAGAAGACAGACGGTCAACAGTCGTAATTGAT‑TCA‑AAAAAATTATCGAAAAAACTGAAGCACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCaa                                         <  1:53345/141‑1 (MQ=255)
                                                                                            tGCGACTTAAAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCaa                                         <  2:153105/141‑1 (MQ=255)
                                                                                             gCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAg                                        >  1:209057/1‑141 (MQ=255)
                                                                                                 cTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAACGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCt                                    >  1:248080/1‑141 (MQ=255)
                                                                                                 cTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCt                                    >  2:215817/1‑141 (MQ=255)
                                                                                                      aaaGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAATTGATGCTAGCAAGCGCTTTTct                               >  1:247040/1‑141 (MQ=255)
                                                                                                           agacagacGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAACGCTTTTctattct                          >  1:16607/1‑141 (MQ=255)
                                                                                                           agacagacGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTCTTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTctatact                          <  1:77216/141‑1 (MQ=255)
                                                                                                                gacGTTCATCAGTTGTAATTGAT‑GCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACtatata                     <  1:329829/141‑1 (MQ=255)
                                                                                                                  cGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCGAGCGCTTTTCTATACTATAtatt                   >  1:357012/1‑141 (MQ=255)
                                                                                                                      catcaGTTGTAATTGAT‑GCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTAttt               >  1:256597/1‑141 (MQ=255)
                                                                                                                      catcaGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACACTCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGGTGCTAGCCAGCGCATTTCTATACTATATATTAttt               >  1:111188/1‑141 (MQ=255)
                                                                                                                       attaGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATTTTCAGATAAAAACAAATAATAACAACGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTAtttt              <  1:86299/138‑1 (MQ=255)
                                                                                                                            atGTAATTGAT‑GCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTaa         <  2:303790/140‑1 (MQ=255)
                                                                                                                                aaTTGAT‑GCA‑AAAAAATTATCGAAAACACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAAtt     <  1:3721/141‑1 (MQ=255)
                                                                                                                                   tGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTATTAAAAAGATGATGCTAGCAAGCGCTTTTATATAAAATATATTATTTTTATAAAATTTTa  >  2:258304/1‑141 (MQ=255)
                                                                                                                                           |                                                                                                                                      
GAATCAGCAGAATCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTA  >  USA300TCH1516_ALE/2455554‑2455826

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: ‑