Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,454,626	A→T	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_ALE	2,454,626	0	A	T	100.0%	119.2 / NA	34	L48L (CTA→CTT)	lyrA	Lysostaphin resistance protein A
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (14/20);  total (14/20)

TGAAGAACAATAAAATTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTAGCACCATTAATTGCTGCAATC‑ATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTAATTATTCTAATTATT  >  USA300TCH1516_ALE/2454484‑2454770                                                                                                                                               |                                                                                                                                                  tGAAGAACAATAAAATTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCAcc                                                                                                                                              >  1:634307/1‑148 (MQ=255)  gaagaaCAATAAAATTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCa                                                                                                                                             <  1:287592/148‑1 (MQ=255)   aagaaCAATAAAATTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGTACCAt                                                                                                                                            >  1:170219/1‑148 (MQ=255)   aagaaCAATAAAATTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCAt                                                                                                                                            <  1:309604/148‑1 (MQ=255)   aagaaCAATAAAATTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCACTATGCTCAGATATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCAt                                                                                                                                            <  1:148508/148‑1 (MQ=255)          aTAAAATTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATtgc                                                                                                                                     <  1:584116/148‑1 (MQ=255)           tAAAATTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATtgct                                                                                                                                    <  1:226551/148‑1 (MQ=255)              aaTTTCTGGTTTTCAATGGGCAATGACGATTTTAGGAGCGTTTTTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATGTGAAGTTACAGATCTTGCACCATTAATTGCTGCa                                                                                                                                 >  1:151162/1‑148 (MQ=255)                     ggTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATC‑Attt                                                                                                                         >  1:443297/1‑148 (MQ=255)                     ggTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTATCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTAGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATC‑Attt                                                                                                                         >  1:408449/1‑148 (MQ=255)                     ggTTTTCAATGGGCAATGACGATTTTCGGCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATACTTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATC‑Attt                                                                                                                         <  1:277026/148‑1 (MQ=255)                               gggCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATC‑ATTTGTATACTCGt                                                                                                               <  1:590064/148‑1 (MQ=255)                                           ttttCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATC‑ATTTGTATACTCGTTTTCAAATATaa                                                                                                   <  1:91056/148‑1 (MQ=255)                                                 tcttctTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATC‑ATTTGTATACTCGTTTTCAAATATAAAAAGGt                                                                                             <  1:448407/148‑1 (MQ=255)                                                  cttcttTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATC‑ATTTGTATACTCGTTTTCAAATATAAAAAGGTc                                                                                            >  1:393230/1‑148 (MQ=255)                                                   ttcttTGGCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATC‑ATTTGTATACTCGTTTTCAAATATAAAAAGGTcc                                                                                           <  1:391327/148‑1 (MQ=255)                                                              tACAATGGCGTTATCCATTATGCTCAGAGGTTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGACCTTGCACCATTAATTGCTGCAAGC‑ATTTGGATACTCGTTTTCAAATATAAAAAGGTCCAACTTgagggt                                                                                >  1:337318/1‑143 (MQ=255)                                                                     tcGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTCACAGATCTTGCACCATTAATTGCTGCAATC‑ATTTGTATACTCGTTTTCAAATATAAATAGGTCCAACTTGCAGGTTTAAAAt                                                                         <  1:313760/147‑1 (MQ=255)                                                                           tCCATTAAGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATAGGTG‑ATTCTTTTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCaa                                                                   >  1:461364/1‑148 (MQ=255)                                                                                tATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATC‑ATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGc                                                              <  1:532724/148‑1 (MQ=255)                                                                                     tCAGACATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATC‑ATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTTCAGGTTTAAAATTCTCAATCAGCCTGaa                                                         <  1:37592/148‑1 (MQ=255)                                                                                                  gTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATC‑ATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGt                                            <  1:479820/148‑1 (MQ=255)                                                                                                   tCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATC‑ATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTc                                           <  1:262678/148‑1 (MQ=255)                                                                                                       taATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATC‑ATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTAtt                                       >  1:395920/1‑148 (MQ=255)                                                                                                           tGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATC‑ATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTa                                   >  1:486661/1‑148 (MQ=255)                                                                                                             gtgtCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATC‑ATTTGTATACTCGTTTTCAAATATAAAAAGGTCTAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGc                                 <  1:419316/148‑1 (MQ=255)                                                                                                               gtCAAACAATTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATC‑ATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCtt                               <  1:209620/148‑1 (MQ=255)                                                                                                                     cacTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATC‑ATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAAttt                         >  1:191112/1‑148 (MQ=255)                                                                                                                      acTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATC‑ATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAAtttt                        <  1:25894/148‑1 (MQ=255)                                                                                                                             atTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATC‑ATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTa                 <  1:289915/148‑1 (MQ=255)                                                                                                                             atTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATC‑ATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTa                 <  1:79633/148‑1 (MQ=255)                                                                                                                                  aaGTTACAGATCTTGCACCATTAATTGCTGCAATC‑ATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTAattat            >  1:264750/1‑148 (MQ=255)                                                                                                                                        cAGATCTTGCACCATTAATTGCTGCAATC‑ATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTAATTATTCTAat      >  1:245747/1‑148 (MQ=255)                                                                                                                                            tCTTGCACCATTAATTGCTGCAATC‑ATTTGTATACTCGTTTTCAAATCTACAAAGGAACAAATTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTAATTATTCTAatgttt  >  1:533332/1‑144 (MQ=255)                                                                                                                                               |                                                                                                                                                  TGAAGAACAATAAAATTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTAGCACCATTAATTGCTGCAATC‑ATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTAATTATTCTAATTATT  >  USA300TCH1516_ALE/2454484‑2454770

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑