Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	39,378	C→T	D586N (GAT→AAT)	pbp ←	Beta‑lactam‑inducible penicillin‑binding protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	39,378	0	C	T	100.0%	144.0 / NA	38	D586N (GAT→AAT)	pbp	Beta‑lactam‑inducible penicillin‑binding protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (16/22);  total (16/22)

AACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAA‑TTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATCTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCTTTTAATAAGTGAGGTGCGTTAATATTGCCATTATT  >  USA300TCH1516_ALE/39235‑39516                                                                                                                                                 |                                                                                                                                           aaCATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAA‑TTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATAttttct                                                                                                                                        <  2:104403/148‑1 (MQ=255) aaCATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAA‑TTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATAttttct                                                                                                                                        <  1:297015/148‑1 (MQ=255)    aTTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAA‑TTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTa                                                                                                                                     >  1:336741/1‑148 (MQ=255)          aGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAA‑TTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGtt                                                                                                                               <  2:4835/148‑1 (MQ=255)          aGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAA‑TTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGtt                                                                                                                               <  1:253842/148‑1 (MQ=255)            ccATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTGTGCAGTACCGGATTTGCCAATTAGGTTTGCATAAGATCTATAAATATTTTCTTTATGTGttt                                                                                                                              >  2:203533/1‑148 (MQ=255)               tcatcatGTTTGGATTATCTTTATCATATGATATAAACCACCCAA‑TTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGTtttatt                                                                                                                          <  2:238595/148‑1 (MQ=255)               tcatcatGTTTGGATTATCTTTATCATATGATATAAACCACCCAA‑TTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGTtttatt                                                                                                                          <  1:358389/148‑1 (MQ=255)                     tGTTTGGATTATCTTTATCATATGATATAAACCACCCAA‑TTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGTTTTATTTACGAc                                                                                                                    <  1:44265/148‑1 (MQ=255)                         tGGATTATCTTTATCATATGATATAAACCACCCAA‑TTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGTTTTATTTACGACttgt                                                                                                                <  1:322737/148‑1 (MQ=255)                                     aTCATATGATATAAACCACCCAA‑TTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCa                                                                                                    <  1:336420/148‑1 (MQ=255)                                       cATATGATATAAACCACCCAA‑TTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGt                                                                                                  <  2:166884/148‑1 (MQ=255)                                         tatGATATAAACCACCCAA‑TTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTa                                                                                                >  1:242085/1‑148 (MQ=255)                                          atGATATAAACCACCCAA‑TTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTaa                                                                                               >  1:246630/1‑148 (MQ=255)                                          atGATATAAACCACCCAA‑TTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTaa                                                                                               >  1:109829/1‑148 (MQ=255)                                          atGATATAAACCACCCAA‑TTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTaa                                                                                               >  1:219982/1‑148 (MQ=255)                                               ataAACCACCCAA‑TTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAGTAGAt                                                                                          >  1:54965/1‑148 (MQ=255)                                               ataAACCACCCAA‑TTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGAt                                                                                          >  2:159309/1‑148 (MQ=255)                                                    ccaccCAA‑TTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGata                                                                                     >  1:240631/1‑148 (MQ=255)                                                    ccaccCAA‑TTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGata                                                                                     >  1:289677/1‑148 (MQ=255)                                                        ccAA‑TTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTNATAtttt                                                                                 >  2:288194/1‑148 (MQ=255)                                                        ccAA‑TTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATAtttt                                                                                 >  2:301639/1‑148 (MQ=255)                                                                           tctcCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATAtttt                                                               <  2:134053/148‑1 (MQ=255)                                                                                    ttCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCaaa                                                      >  1:296694/1‑148 (MQ=255)                                                                                    ttCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCaaa                                                      >  1:216859/1‑148 (MQ=255)                                                                                     tCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAAc                                                     >  1:145124/1‑148 (MQ=255)                                                                                        ttttGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACttt                                                  <  1:68518/148‑1 (MQ=255)                                                                                        ttttGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACttt                                                  <  1:216405/148‑1 (MQ=255)                                                                                                 cTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCgt                                         <  2:353140/148‑1 (MQ=255)                                                                                                 cTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCgt                                         <  2:160866/148‑1 (MQ=255)                                                                                                  tGCAGTACCTGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCgtg                                        <  2:216247/148‑1 (MQ=255)                                                                                                  tGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCgtg                                        <  1:231116/148‑1 (MQ=255)                                                                                                    cAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTc                                      <  1:200221/148‑1 (MQ=255)                                                                                                       tACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCttt                                   <  2:240322/148‑1 (MQ=255)                                                                                                                    aaTTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCTTTTAATAAGTGAGGt                      >  1:115968/1‑148 (MQ=255)                                                                                                                          gTTTGCATAAGATCTATAAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCTTTTAATAAGTGAGGTGCGTTa                <  1:36756/148‑1 (MQ=255)                                                                                                                                        tataAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCTTTTAATCAGTGCGGTGCGTTAATATTGCCattatt  <  2:270927/148‑1 (MQ=255)                                                                                                                                        tataAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCTTTTAATAAGTGAGGTGCGTTAATATTGCCattatt  <  1:73306/148‑1 (MQ=255)                                                                                                                                        tataAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCTTTTAATAAGTGAGGTGCGTTAATATTGCCattatt  <  2:34228/148‑1 (MQ=255)                                                                                                                                        tataAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCTTTTAATAAGTGAGGTGCGTTAATATTGCCattatt  <  1:52649/148‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                           AACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAA‑TTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATCTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCTTTTAATAAGTGAGGTGCGTTAATATTGCCATTATT  >  USA300TCH1516_ALE/39235‑39516

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑