Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,455,698 2 bp→AT 100% 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_ALE2,455,6980CA93.3% 85.1 / 1.5 30coding (1216/1260 nt)lyrALysostaphin resistance protein A
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base A (13/14);  minor base . (1/1);  total (15/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.61e-01
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.
Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch.
*USA300TCH1516_ALE2,455,6990AT97.8% 77.7 / ‑6.3 30H406L (CAT→CTT) lyrALysostaphin resistance protein A
Reads supporting (aligned to +/- strand):  ref base A (2/0);  major base T (13/13);  minor base G (0/2);  total (15/15)
Fisher's exact test for biased strand distribution p-value = 4.84e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTT  >  USA300TCH1516_ALE/2455569‑2455825
                                                                                                                                 ||                                                                                                                              
gTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCCaaaaaa                                                                                                                     >  2:265718/1‑141 (MQ=255)
      cAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTgaag                                                                                                               <  1:120061/141‑1 (MQ=255)
        aGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCGTCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTgaagaa                                                                                                             <  1:134458/141‑1 (MQ=255)
          caccacAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACa                                                                                                           >  2:138643/1‑141 (MQ=255)
                    tGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGAt                                                                                                 <  2:49282/141‑1 (MQ=255)
                    ggACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAAAAATTAAGAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGAt                                                                                                 <  1:27568/140‑1 (MQ=255)
                      aCGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAAATATCGAAAAAACTGAAGAACAATCTTCAGATaa                                                                                               >  2:195076/1‑141 (MQ=255)
                       ctaTTAAACAACAGATTCAAATGGAGACGAAAGAGAGCAATCATTAAAAGAACCTGAGACTTACAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGGAGAACAATCTTCAGATaaa                                                                                              <  2:119511/139‑1 (MQ=255)
                                        cAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAAGTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAg                                                                             <  1:247716/141‑1 (MQ=255)
                                         aaaTGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAgc                                                                            <  1:119010/141‑1 (MQ=255)
                                               aGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAACAAATAATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTAGc                                                                      >  2:320753/1‑141 (MQ=255)
                                                         gagCAATCATTAATAGAACCTGCGACTTATAAAGAAGACAGACGTGCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAgcatcatc                                                            <  2:270533/141‑8 (MQ=255)
                                                            cAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTaa                                                         >  1:191168/1‑141 (MQ=255)
                                                                   tAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAgatg                                                  >  2:128580/1‑141 (MQ=255)
                                                                    aaaaGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAgatga                                                 <  1:150015/141‑1 (MQ=255)
                                                                       aGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGc                                              >  1:354283/1‑141 (MQ=255)
                                                                       aGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATATTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTAACCCTTAAAAAGATGATGc                                              >  2:368/1‑141 (MQ=255)
                                                                        gAACCTGGGACGTATAGAGAAGACAGACGTTCATCAGTTGTAAGTGATGCAAAAAAAGTATCGAAAAGACTGAAGAACAATGTTCAGATAAAAACAAATAATAGCAGAGCGCTTGCTAGTACCTCTTGAAAAGATGATGCt                                             <  2:352733/141‑1 (MQ=255)
                                                                          aCCTGCGACTTATAAAGAAGACAGACGTCCATTAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAg                                           <  1:8217/141‑1 (MQ=255)
                                                                           ccTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGc                                          >  1:238741/1‑141 (MQ=255)
                                                                           ccTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTCCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGc                                          >  1:125752/1‑141 (MQ=255)
                                                                                  cTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGACGATGCTAGCAAGCGCt                                   <  1:212172/141‑1 (MQ=255)
                                                                                     ataAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCtttt                                >  2:67898/1‑141 (MQ=255)
                                                                                              acagacGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCACTTAAAAAGATGATGCTAGCAAGCGCTTTTctatactac                       >  1:8574/1‑140 (MQ=255)
                                                                                                agacGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACtatat                     >  2:118728/1‑141 (MQ=255)
                                                                                                  acGTTCATCAGTTGTAATTGATGCAAACAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTatatat                   >  1:263157/1‑141 (MQ=255)
                                                                                                         tcaGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTAttttt            <  1:138643/141‑1 (MQ=255)
                                                                                                          caGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTc           >  1:171336/1‑141 (MQ=255)
                                                                                                              tGTAATTGATGAAAAAAAATTATCGAAAAAACTGAATAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTTGCAAGCGCTTTTCTATACTATATATTATTTTTCTaaa       <  2:84742/141‑1 (MQ=255)
                                                                                                                   ttGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAAtttt  <  2:356822/141‑1 (MQ=255)
                                                                                                                                 ||                                                                                                                              
GTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTT  >  USA300TCH1516_ALE/2455569‑2455825

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: