Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,454,626 A→T 100% L48L (CTA→CTT)  lyrA → Lysostaphin resistance protein A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,454,6260AT100.0% 97.3 / NA 33L48L (CTA→CTT) lyrALysostaphin resistance protein A
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (22/11);  total (22/11)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TAAAATTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTAGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTAATT  >  USA300TCH1516_ALE/2454494‑2454758
                                                                                                                                    |                                                                                                                                    
tAAAATTTCTGGTTTTCAATGTGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAAAACTTTATATTTGAAGTTACAGATCTTGCACCAt                                                                                                                               >  1:395844/1‑140 (MQ=255)
tAAAATTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCAt                                                                                                                               >  1:698606/1‑140 (MQ=255)
tAAAATTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACAAt                                                                                                                               >  1:65006/1‑140 (MQ=255)
tAAAATTTCTGGTTTTCAATGAGCAATCACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCAt                                                                                                                               <  1:531467/140‑1 (MQ=255)
 aaaaTTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCAtt                                                                                                                              <  1:68552/140‑1 (MQ=255)
              ttCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATc                                                                                                                 >  1:576084/1‑140 (MQ=255)
                         aTGACGATTTTCGTCTTCTTTGTCATTACAATGGCTTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACt                                                                                                      <  1:267430/140‑1 (MQ=255)
                                 tttCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCa                                                                                              >  1:475727/1‑140 (MQ=255)
                                    cGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTTTAAAACACTTTATATTTGAAGTTACAGATCTTGCAAAATTAATTGCTGCAATCATTTGTATACTCGTTTTCaaaa                                                                                           >  1:34249/1‑139 (MQ=255)
                                    cGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAat                                                                                           >  1:213733/1‑140 (MQ=255)
                                    cGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTAAAACACTTTATATTTGAAGTTACAGATTTTGCACCTTTAAATGCTGCAATCATTTGTATACTCGTTTTCAAat                                                                                           >  1:620699/1‑140 (MQ=255)
                                                cATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGTTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTcc                                                                               >  1:214912/1‑140 (MQ=255)
                                                     cAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACtt                                                                          <  1:237849/140‑1 (MQ=255)
                                                        tGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACCTGCa                                                                       >  1:204516/1‑140 (MQ=255)
                                                               aTCCATTATGCTCAGAGATTTCCAGTCTATAAGTGGTGTCAAACACTTTATATTTGAAGTTATAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTaa                                                                >  1:549021/1‑140 (MQ=255)
                                                                  cATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTACTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGTTCCAACTTGCAGGTTTAAAAt                                                             >  1:227288/1‑140 (MQ=255)
                                                                      aTGCTCAGAGATTTCCAGTCCATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATGTAAAAAGATCCAACTTGCGGGTTTAAAATtctc                                                         >  1:464315/1‑140 (MQ=255)
                                                                       tGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCa                                                        >  1:726831/1‑140 (MQ=255)
                                                                               gaTTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCt                                                <  1:648942/140‑1 (MQ=255)
                                                                               gaTTTCCAGTCTATAATTGGTGTCAAACACTTTATATTCGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCt                                                <  1:517732/140‑1 (MQ=255)
                                                                                aTTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTg                                               >  1:91576/1‑140 (MQ=255)
                                                                                 tttCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCAATAATTTCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTGTCAATCAGCCTGa                                              >  1:460227/1‑140 (MQ=255)
                                                                                   tCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGAACAATTAATTGCTGCAATAATTTGTATACTAGTTTTCAAATATAAAAAGGTACAACTTGCAGGTTTAAAATTCTCAATCAGCCTGaaa                                            >  1:65349/1‑140 (MQ=255)
                                                                                       gtttataATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTaa                                        <  1:97006/137‑1 (MQ=255)
                                                                                                tcgcttCAAACACCTTATATCTCTACTTACAGATCTTTCACCACTAATTGCTCGAATCATTTGTATACGCGGTTTCAAAGATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTc                               <  1:536437/135‑1 (MQ=255)
                                                                                                    gtCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTAtt                           >  1:16267/1‑140 (MQ=255)
                                                                                                    gtCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTATCAAAAAAAAAAAAGTCCAACTAGCAGATTAAAAAAACTCAATCAGCCTGAAAGTAATTGAACGACTAtt                           >  1:21030/1‑140 (MQ=255)
                                                                                                     tCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTg                          <  1:216047/140‑1 (MQ=255)
                                                                                                            cTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAAAATAAAAAGGAACAACTTGAAGGTTTAAAATTCTAAATAAGCCGGAAAGTAATTAAACGTCTATTGCTAGCtt                   >  1:48399/1‑140 (MQ=255)
                                                                                                                  atTTGAAGTTACATATCTTGCACTATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAAttt             <  1:421473/140‑1 (MQ=255)
                                                                                                                  atTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTAGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAAttt             >  1:28458/1‑140 (MQ=255)
                                                                                                                   tttGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAAATTGCAGGTTTAAACTTCTAAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAAtttt            >  1:101211/1‑140 (MQ=255)
                                                                                                                             cAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTAAAATATAAAAAGGTCCAACTGGCAGGTGTTACTTTCTCGATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTAatt  <  1:144493/140‑1 (MQ=255)
                                                                                                                                    |                                                                                                                                    
TAAAATTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTAGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTAATT  >  USA300TCH1516_ALE/2454494‑2454758

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑