Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	39,378	C→A	D586Y (GAT→TAT)	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	A	100.0%	137.6 / NA	47	D586Y (GAT→TAT)	pbp	Beta‑lactam‑inducible penicillin‑binding protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (23/24);  total (23/24)

ATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATCTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTG‑TCTTTTAATAAGTGAGGT  >  USA300TCH1516_ALE/39251‑39496                                                                                                                                |                                                                                                                        atcatGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTa                                                                                                                  <  2:124579/135‑1 (MQ=255)    atGTTTGGATTATCTTTATTATATGATATAAACCACCCAATTTGTCTGTTAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTAtgt                                                                                                               <  1:265612/135‑1 (MQ=255)    atGTTTGGATTATCTTTATCATATGATATAAACCACCCGATTTGTCTGCCTGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTAtgt                                                                                                               <  1:265664/135‑1 (MQ=255)         tGGATTATCTTTATCTTATGATATTAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGCGTTCTGTAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGtttt                                                                                                          <  2:476705/135‑1 (MQ=255)             ttATCTTTATCATATGATATAAACCACCCAATTTGTCTGCACGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTtttattt                                                                                                      >  2:154988/1‑135 (MQ=255)                  tttATCATTTGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGAc                                                                                                 <  2:188019/135‑1 (MQ=255)                  tttATCATATGATATAACCCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGAc                                                                                                 <  2:111603/135‑1 (MQ=255)                  tttATCATATGATATAAACCACCCAATTTGTCTGTCAGGTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGAc                                                                                                 <  1:103839/135‑1 (MQ=255)                        atatGATATAAACCACCCTATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACttgttg                                                                                           <  1:253246/135‑1 (MQ=255)                         tatGATATAAACCACCCCATTTGTCTGCCAGCTCCTCCCTGCTTTGTTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGc                                                                                          <  1:291882/135‑1 (MQ=255)                          atGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCa                                                                                         <  2:513874/135‑1 (MQ=255)                          atGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCa                                                                                         <  2:511995/135‑1 (MQ=255)                                taAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCAt                                                                                   >  2:35400/1‑135 (MQ=255)                                taAACCACCCAATTTGTCTGCAAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCAt                                                                                   >  1:366455/1‑135 (MQ=255)                                 aaaCAACCAAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTACAGTAACGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATCCCATc                                                                                  >  2:139525/1‑135 (MQ=255)                                    ccaccCAATTTGTCTGCCAGTTACTCCTTGTTTCATTTTAAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGt                                                                               >  1:107373/1‑135 (MQ=255)                                    ccaccCAATTTGTATGCCAGATTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTATGACTTGTTGCATACCATCAGt                                                                               >  1:544224/1‑135 (MQ=255)                                       cccAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTaa                                                                            >  1:561833/1‑135 (MQ=255)                                       cccAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATATGTTTTATTTAGGACTTGTTGCCTACCATCAGGTaa                                                                            >  1:245043/1‑135 (MQ=255)                                             ttGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTGTTTGCATGCCATGAGTTCAtgggtt                                                                      >  2:409027/1‑130 (MQ=255)                                               gTCTGCTAGTTTTTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGa                                                                    <  1:56343/135‑1 (MQ=255)                                               gTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATTTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGa                                                                    <  1:246570/135‑1 (MQ=255)                                                   gCCTGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATAtt                                                                >  1:365376/1‑135 (MQ=255)                                                   gCCCGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATAtt                                                                >  1:156906/1‑135 (MQ=255)                                                   gCCCGTTTCTCCTTGTTTCATATAGAGTTCTGCAGTACCGAATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTTTTGCATACCATCAGTTAATAGATTGATAtt                                                                >  1:76573/1‑135 (MQ=255)                                                   gCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATAtt                                                                <  2:34119/135‑1 (MQ=255)                                                   gCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATATACGACTTGTTGCATACCATCAGTTAATAGATTGATAtt                                                                <  2:298184/135‑1 (MQ=255)                                                    ccAGTTTCTCCTTGTTTCATTTTGAGATATGCAGTACCGGATTTGCCAATTAAGTTTGCATGAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATAttt                                                               >  1:189328/1‑135 (MQ=255)                                                          tctcCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTg                                                         <  2:296832/135‑1 (MQ=255)                                                          tctcCCTGTTTCATTTTGAGTTCTGCAGTATCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTg                                                         <  2:118626/135‑1 (MQ=255)                                                          tctcCCTGTATCATTTTCAGTTCTTCATTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTg                                                         <  2:262753/135‑1 (MQ=255)                                                             ccTTGTTTCTTTTTGAGTTATGCAGTAACGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCATTTAATAGATTGATATTTTCTTTTGaa                                                      >  1:588385/1‑135 (MQ=255)                                                                tGTTTCATTTTGAGTTCTGCAATACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAaata                                                   >  1:212509/1‑135 (MQ=255)                                                                         ttGAGTTCTGCAGTACCGGATTTGCCAATAAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTttc                                          >  1:30298/1‑135 (MQ=255)                                                                          tgtgTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTttct                                         >  1:574368/4‑135 (MQ=255)                                                                                  gCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGTTATTTTTTTTGGAAATAATATTTTTCTTCCAAACt                                 <  1:572452/135‑1 (MQ=255)                                                                                  gCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATCTTTTCTTTGGAAATCATATTTTTCTTCCaaaat                                 >  1:70428/1‑133 (MQ=255)                                                                                   cAGTACCGGATTTGCCAATTAAGTTTGCATAATATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACtt                                <  2:57900/135‑1 (MQ=255)                                                                                    aggaCCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACttt                               <  2:515469/132‑1 (MQ=255)                                                                                     gTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACAATCAGTTAATTGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTg                              >  2:251381/1‑135 (MQ=255)                                                                                        ccGGATTTGTCAATTAAGTTTGCATAAGATTTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGttt                           <  2:489872/135‑1 (MQ=255)                                                                                            aTTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCg                       >  1:496492/1‑135 (MQ=255)                                                                                            aTTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTATTATTTACGACTTTGTGGATAACATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTGTTGTTCAAAACTTGGTTATTCg                       >  2:266838/1‑135 (MQ=255)                                                                                                      tAAGTTTGCATATGATCTATAAATATATTCTTTATTTGTTTTATTTACGACTTGTTGCATACCATCTGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTG‑TCTTTtaa            <  2:494222/135‑1 (MQ=255)                                                                                                      tAAGATTGCATAAGATCTATAAATATATTCGGGATGTGTTGTATTTACGACGTGTTGCATACCATCTGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCGAAACTTTGTTTTTCGTG‑TCTTTtaa            >  2:272679/1‑135 (MQ=255)                                                                                                                tAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTT‑GTGTTCTTTTAATTAGTGATGt  >  2:483811/1‑135 (MQ=255)                                                                                                                tAAAATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTG‑TCTTTTAATAAGTGAggc  <  1:150964/135‑2 (MQ=255)                                                                                                                                |                                                                                                                        ATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATCTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTG‑TCTTTTAATAAGTGAGGT  >  USA300TCH1516_ALE/39251‑39496

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: ‑