Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,646,189	G→C	100%	A155G (GCA→GGA)	ypdF ←	Aminopeptidase YpdF

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,646,189	0	G	C	100.0%	198.6 / NA	57	A155G (GCA→GGA)	ypdF	Aminopeptidase YpdF
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base C (30/27);  total (30/27)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTGCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATGATATACG  >  USA300TCH1516_ALE/1646054‑1646325                                                                                                                                        |                                                                                                                                         ttATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACACTCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTATTTCTTTTTCTGTCATGCCTCCtttt                                                                                                                                     <  1:420046/141‑1 (MQ=255) ttATCACTTGCAACACCAGGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCtttt                                                                                                                                     <  1:113295/141‑1 (MQ=255)   aTCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTac                                                                                                                                   >  1:175219/1‑141 (MQ=255)     cACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTacaa                                                                                                                                 <  1:638378/141‑1 (MQ=255)       cTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTacaaca                                                                                                                               <  1:697422/141‑1 (MQ=255)            aaCACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCATTCATGCCTCCTTTTACAACAGTTaa                                                                                                                          >  2:646612/1‑141 (MQ=255)                       gTAATGCACCTCTATGACCAGATGCTACAATCTTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCat                                                                                                               <  1:477505/141‑1 (MQ=255)                       gTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAacatatgaat                                                                                                               <  2:42661/141‑5 (MQ=255)                          aTGCACCTCTATGACCAGATGCTACTATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATg                                                                                                            <  2:107637/141‑1 (MQ=255)                           tGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGt                                                                                                           >  2:814981/1‑141 (MQ=255)                                     taaCCAGATGCAACAATCGTATCGAAAGCTAGTCCATCTGGTCCTATTTCAAAAATTTTACTTTCTAATATTGCCTTTATTTCTTTTAAAGTGAGTGCTCTTTTTTCAACAGTTAAAATATATTCATAGGTCtcatcacaa                                                                                                 >  2:744001/3‑138 (MQ=255)                                     tGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTTAAATATATTCATATGTTTCATcaaca                                                                                                 >  1:211853/1‑141 (MQ=255)                                     tGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATcaaca                                                                                                 >  1:566149/1‑141 (MQ=255)                                         cAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCCTTTTGTGCTTTGATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAatat                                                                                             <  1:397750/141‑1 (MQ=255)                                                tACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTCGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAgctgc                                                                                      >  1:597532/1‑141 (MQ=255)                                                tACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAgctgc                                                                                      <  1:783826/141‑1 (MQ=255)                                                 aCAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAgctgct                                                                                     >  1:589672/1‑141 (MQ=255)                                                   aaTCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCttt                                                                                   >  2:446946/1‑141 (MQ=255)                                                     tCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCttttt                                                                                 <  1:223319/141‑1 (MQ=255)                                                     tCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCttttt                                                                                 <  1:223370/141‑1 (MQ=255)                                                                gatgGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAAAATTAGCTGCTTTTTGAATTAAAGCa                                                                      >  1:771544/1‑141 (MQ=255)                                                                  tgGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAAt                                                                    >  2:655758/1‑141 (MQ=255)                                                                  tgGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAAt                                                                    <  1:836524/141‑1 (MQ=255)                                                                      ccATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCg                                                                >  1:26563/1‑141 (MQ=255)                                                                      ccATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCg                                                                <  1:66821/141‑1 (MQ=255)                                                                             cTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAACTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCACTTTCGTCTGCAt                                                         <  1:591862/141‑1 (MQ=255)                                                                              tCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATc                                                        >  1:638798/1‑141 (MQ=255)                                                                                 tAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCttt                                                     <  1:123100/141‑1 (MQ=255)                                                                                   aTTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGa                                                   <  2:683299/141‑1 (MQ=255)                                                                                    ttCTAGCATTTTGCTTTCTAATATTTCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCACTTTCTTCAGCATCTTTGAc                                                  <  1:461809/141‑1 (MQ=255)                                                                                       tAGCATTTTTCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGtc                                               <  2:212551/141‑1 (MQ=255)                                                                                        aGCATTTTGCTTTCTAATATTGCGTATGATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGtct                                              >  1:831288/1‑141 (MQ=255)                                                                                        aGCATTTTGCTTTCTAATATTCACATGGATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGtct                                              >  1:831254/1‑141 (MQ=255)                                                                                         gCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATTTTTCATCAACAAAATTAGCCGCATCGTGAATTAAAGCAATGTCGTCATCATCATTCAGGtctc                                             >  1:173669/1‑141 (MQ=255)                                                                                         gCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGTATTTTTGACGtctc                                             >  1:126099/1‑141 (MQ=255)                                                                                         gCATTTTGCTTTCTAATATTGCCTATAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGtctt                                             >  1:611406/1‑140 (MQ=255)                                                                                            ttttGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCaaa                                          >  1:669280/1‑141 (MQ=255)                                                                                                   ttCTAAGATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATc                                   <  2:52445/141‑1 (MQ=255)                                                                                                            tgtcTTTAATTCTTTTTCAGGCATGCCGCCTTTTAAAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCCTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTAtt                          <  1:307275/138‑1 (MQ=255)                                                                                                             gCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTa                         <  2:143362/141‑1 (MQ=255)                                                                                                                    aTTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGc                  >  1:124003/1‑141 (MQ=255)                                                                                                                    aTTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTGTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGc                  >  2:606380/1‑141 (MQ=255)                                                                                                                     ttCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCt                 <  1:814981/141‑1 (MQ=255)                                                                                                                      tCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCtt                >  1:186235/1‑141 (MQ=255)                                                                                                                        tttttCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTCTTAGAAATGCttat              <  2:701518/141‑1 (MQ=255)                                                                                                                         ttttCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCACCAATCTTATCTGCTTTTTGAATTCAGGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTTTCTACAGTATTAGCAATActtctt             >  2:818915/1‑141 (MQ=255)                                                                                                                         ttttCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCttatt             >  2:772013/1‑141 (MQ=255)                                                                                                                         ttttCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATCAGAAATGCttatt             >  2:603075/1‑141 (MQ=255)                                                                                                                             cAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATg         <  2:438488/141‑1 (MQ=255)                                                                                                                              aGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAAGTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATGa        >  1:433014/1‑141 (MQ=255)                                                                                                                               gTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATGat       <  2:831254/141‑1 (MQ=255)                                                                                                                               gTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATGat       <  2:831288/141‑1 (MQ=255)                                                                                                                                tCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTACTTTTATCTACAGTATTAGAAATGATTATTAATGata      >  2:532912/1‑141 (MQ=255)                                                                                                                                tCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTTGAAATGCTTATTaataatt      >  2:532680/1‑140 (MQ=255)                                                                                                                                tCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATGata      <  1:335447/141‑1 (MQ=255)                                                                                                                                 cATGCCTCCTTTTACAACAGTTAAAATATATTCATAGGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTACTAGAAATGCTTATTAATGatat     >  1:579718/1‑141 (MQ=255)                                                                                                                                    gCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATGATATACg  >  1:11090/1‑141 (MQ=255)                                                                                                                                        |                                                                                                                                         TTATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTGCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATGATATACG  >  USA300TCH1516_ALE/1646054‑1646325

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑