Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	39,195	T→C	K647E (AAA→GAA)	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	39,195	0	T	C	100.0%	174.7 / NA	46	K647E (AAA→GAA)	pbp	Beta‑lactam‑inducible penicillin‑binding protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (30/16);  total (30/16)

GAAGTAACAGCACTTATTAATAATTCATAATAAAACAGTGAAGCAACCATCGTTACGGATTGCTTCACTGTTTTGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCA  >  USA300TCH1516_ALE/39052‑39334                                                                                                                                                |                                                                                                                                            gaAGTAACAGCACTTATTAATAATTCATAATAAAACAGTGAAGCAACCATCGTTACGGATTGCTTCACTGTTTAGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCCCATCATACACTTTACCTGAGATTTCGGCa                                                                                                                                         >  4:81876/1‑148 (MQ=255)  aaGTAACAGCACTTATTAATAATTCATAATAAAACAGTGAAGCAACCATCGTTCAGGATTACGTCACTGTTTTGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTCGGCAt                                                                                                                                        <  3:235699/148‑1 (MQ=255)  aaGTAACAGCACTTATTAATAATTCATAATAAAACAGTGAAGCAACCATCGTTACGGATTGCTTCACTGTTTTGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTCGGCAt                                                                                                                                        <  3:42256/148‑1 (MQ=255)         aGCACTTATTAATAATTCATAATAAAACAGTGAAGCAACCATCGTTACGGATTGCTTCACTGTTTTGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGtagct                                                                                                                                 >  3:64103/1‑148 (MQ=255)         aGCACTTATTAATAATTCATAATAAAACAGTGAAGCAACCATCGTTACGGATTGCTTCACTGTTTTGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGtagct                                                                                                                                 >  4:83508/1‑148 (MQ=255)          gCACTTATTAATAATTCATAATAAAACAGTGAAGCAACCATCGTTACGGATTGCTTCACTGTTTTGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACGCTTTACCTGAGATTTCGGCATTGtagcta                                                                                                                                >  3:411608/1‑148 (MQ=255)                attaACAATTCATAATAAAACAGTGAAGCAACCATCGTTACTGATTGCTTCACTGTTTTGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCAtt                                                                                                                          <  4:264079/148‑1 (MQ=255)                  taataaTTCATAATAAAACAGTGAAGCAACCATCGTTACGGATTGCTTCACTGTTTTGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGtagctag                                                                                                                               <  2:38964/141‑1 (MQ=255)                  taataaTTCATAATAAAACAGTGAAGCAACCATCGTTACGGATTGCTTCACTGTTTTGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTcc                                                                                                                        <  4:129934/148‑1 (MQ=255)                  taataaTTCATAATAAAACAGTGAAGCAACCATCGTTACGGATTGCTTCACTGTTTTGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTcc                                                                                                                        <  3:163782/148‑1 (MQ=255)                   aataatTCATAATAAAACAGTGAAGCAACCATCGTTACGGATTGCTTCACTGTTTTGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACGCTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCt                                                                                                                       <  4:345726/148‑1 (MQ=255)                               taaAACAGTGAAGCAACCATCATTACGGATTGCTTCACTTTTTTGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACa                                                                                                           <  4:244751/148‑1 (MQ=255)                                 aaaCAGTGAAGCAACCATCGTTACGGATTGCTTCACTGTTTTGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATc                                                                                                         >  4:160402/1‑148 (MQ=255)                                   aCAGTGAAGCAACCATCGTTACGGATTGCTTCACTGTTTTGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCtt                                                                                                       >  3:96067/1‑148 (MQ=255)                                    cAGTGAAGCAACCATCGTTACGGATTGCTTCACTGTTTTGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCttt                                                                                                      <  3:330301/148‑1 (MQ=255)                                     aGTGAAGCAACCATCGTTACGGATTGCTTCACTGTTTTGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTa                                                                                                     <  4:406811/148‑1 (MQ=255)                                     aGTGAAGCAACCATCGTTACGGATTGCTTCACTGTTTTGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTa                                                                                                     <  4:143311/148‑1 (MQ=255)                                                            ttGTTTCACTGTTTTGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAACCATCATCATGtt                                                                              >  4:291446/1‑148 (MQ=255)                                                                ttCACTGTTTTGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCcatcatcat                                                                                 >  1:27325/1‑141 (MQ=255)                                                                 tCACTGTNTTGTTATTCCTCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGAt                                                                         <  4:312492/148‑1 (MQ=255)                                                                   aCTGTTTTGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTa                                                                       <  3:164316/148‑1 (MQ=255)                                                                            ttATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCa                                                              <  4:105844/148‑1 (MQ=255)                                                                               ttCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCatat                                                           <  4:232965/148‑1 (MQ=255)                                                                                    cTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGatat                                                      >  3:69414/1‑148 (MQ=255)                                                                                                ttttATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAAt                                          >  3:401682/1‑148 (MQ=255)                                                                                                ttttATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAAt                                          >  3:371571/1‑148 (MQ=255)                                                                                                ttttATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAAt                                          >  3:86428/1‑148 (MQ=255)                                                                                                ttttATTACCGTTCTCATATAGCACATCATACACTTTACTTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACNACCCAAt                                          >  4:312976/1‑148 (MQ=255)                                                                                                    attaCCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGAAGCTAGCCATCCCTTTATCTTGTACACCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCAccc                                             >  1:49004/1‑141 (MQ=255)                                                                                                        ccGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGc                                  >  4:135707/1‑148 (MQ=255)                                                                                                        ccGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGc                                  >  3:38942/1‑148 (MQ=255)                                                                                                        ccGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGc                                  >  3:288359/1‑148 (MQ=255)                                                                                                        ccGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATGAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGc                                  >  4:350555/1‑148 (MQ=255)                                                                                                            tctcATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCGAATTTGTCTGCCAGt                              >  3:344842/1‑148 (MQ=255)                                                                                                            tctcATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGt                              >  3:25282/1‑148 (MQ=255)                                                                                                            tctcATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGt                              >  3:214211/1‑148 (MQ=255)                                                                                                             ctcATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGtt                             >  3:73032/1‑148 (MQ=255)                                                                                                             ctcATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGtt                             >  3:72963/1‑148 (MQ=255)                                                                                                             ctcATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGtt                             >  3:200885/1‑148 (MQ=255)                                                                                                             ctcATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGtt                             >  3:260239/1‑148 (MQ=255)                                                                                                                           catACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCAt               <  3:83508/148‑1 (MQ=255)                                                                                                                              acacTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCAtttt            >  3:281194/1‑148 (MQ=255)                                                                                                                                      ccTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCTTTGTTTCATTTTGAGTTCTg    >  3:224752/1‑148 (MQ=255)                                                                                                                                        tGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCa  >  4:52131/1‑148 (MQ=255)                                                                                                                                        cgagaTTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCa  >  4:225730/2‑148 (MQ=255)                                                                                                                                          agaTTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGtt       >  2:60305/1‑141 (MQ=255)                                                                                                                                                |                                                                                                                                            GAAGTAACAGCACTTATTAATAATTCATAATAAAACAGTGAAGCAACCATCGTTACGGATTGCTTCACTGTTTTGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCA  >  USA300TCH1516_ALE/39052‑39334

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑