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%	155.0 / NA	47	A155G (GCA→GGA)	ypdF	Aminopeptidase YpdF
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base C (26/21);  total (26/21)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ATTTTATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATT‑CTTTTTCAGTCATGCCTGCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTAT  >  USA300TCH1516_ALE/1646051‑1646313                                                                                                                                            |                                                                                                                             atTTTATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATT‑CTTTTTCAGTCATGcctcct                                                                                                                            >  1:196819/1‑141 (MQ=255)  ttttATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCGTTTAATT‑CTTTTTCATTCATGCCTCCtt                                                                                                                           >  1:533493/1‑141 (MQ=255)       tCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATT‑CTTTTTCAGTCATGCCTCCTTTTaca                                                                                                                      >  1:1639/1‑141 (MQ=255)        cACTTGCAACACCATGTGGTAATGCATCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATT‑CTTTTTGAGTCATGCCTCCTTTTacaa                                                                                                                     <  1:464946/141‑1 (MQ=255)        cACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATT‑CTTTTTCAGTCATGCCTCCTTTTccaa                                                                                                                     >  1:566074/1‑141 (MQ=255)        cACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATT‑CTTTTTCAGTCATGCCTCCTTTTacaa                                                                                                                     >  1:752903/1‑141 (MQ=255)               aaCACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATT‑CTTTTTCAGTCATGCCTCCTTTTACAACAGTTaa                                                                                                              >  2:584452/1‑141 (MQ=255)                   ccATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATT‑CTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAata                                                                                                          >  1:219814/1‑141 (MQ=255)                          gTAATGCACCTCTATGACCAGTTGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATT‑CTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCat                                                                                                   <  1:539989/141‑1 (MQ=255)                              tGCACCTCTTGGACCAGGTGCTACAATCGTATCGAATGATGGTCCATCTGCTTCTAATTCTAGCATTTTGTTTTCTCCTCTT‑CCGTCATTTGCTGTTGCAGTCTTGGCTCCTTTTACAACAGTTTTATTATGTTCATATGt                                                                                               <  2:161754/141‑1 (MQ=255)                                cACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCAAACATTTTGCTTTCTAATATTGCCTTTAATT‑CTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGttt                                                                                             >  2:655613/1‑141 (MQ=255)                                   ctctATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCCCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATT‑CTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTtaat                                                                                          >  2:466912/1‑141 (MQ=255)                                     ctATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATT‑CTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTtcatca                                                                                        <  1:558764/141‑1 (MQ=255)                                          aCCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATT‑CTTTTTCAGTTATGCCTCATTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAat                                                                                   >  2:380621/1‑141 (MQ=255)                                                 gCTACAATCGTATCGAATGATGGTCCATCGGCTCCTAATTCTAGCATTTTGCTTTCTCGTAGTGCCTTTAATG‑CTTTTTCAGTCTGGCCTCCTGGCACAGCAGATAAAATATATTCATCTGTTCCATCAACCATATTAtct                                                                            >  2:349750/1‑141 (MQ=255)                                                       atcgtatcgtATTATTGTCCATCTGCGCCTAATTCTACCATTTTGCTTTCTAATATTGCCTTTAATT‑CTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCtttt                                                                      <  1:129688/141‑1 (MQ=255)                                                       aTCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATT‑CTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCtttt                                                                      <  1:456643/141‑1 (MQ=255)                                                            aTCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATT‑CTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAAt                                                                 >  2:207947/1‑141 (MQ=255)                                                              cGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATT‑CTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATGAGCTGCTTTTTGACTTa                                                               >  2:515153/1‑141 (MQ=255)                                                                 atgatgGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATT‑CTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAg                                                            <  2:328723/141‑1 (MQ=255)                                                                 atgatgGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATT‑CTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAg                                                            >  1:242195/1‑141 (MQ=255)                                                                   gatgGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATT‑CTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCa                                                          >  1:585969/1‑141 (MQ=255)                                                                     tgGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATT‑CTTTTTCAGTCATGCCTCCTTTTACAATAGTTAAAATATATTCATATGTTTCATCAACAATATTTGCTGCCTTTTGAATTAAATCAAt                                                        >  2:490871/1‑141 (MQ=255)                                                                           aTCTTCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATT‑CTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTc                                                  <  2:679500/141‑1 (MQ=255)                                                                             cTGCTCCTAATTTTAGCATTTTGCTTTCTAATATTGCCTTTAATT‑CTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAg                                                <  2:575859/141‑1 (MQ=255)                                                                               gCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATT‑CTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCa                                              >  2:241797/1‑141 (MQ=255)                                                                               gCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATT‑CTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCa                                              >  2:239233/1‑141 (MQ=255)                                                                                     acttCTAGCATTTTGCTTTCTAATATTGCCTTTAATT‑CTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTg                                        <  1:392662/139‑1 (MQ=255)                                                                                     aaTTCTAGCATTTTGCTTTCTAATATTGCCTTTAATT‑CTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTg                                        <  2:667100/141‑1 (MQ=255)                                                                                       ttCTTGCATTTTGCTTTCTAATATTGCCTTTAATT‑CTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGAc                                      <  2:517323/141‑1 (MQ=255)                                                                                        tCTAGCATTTTGCTTTCTAATATTGCCTTTAATT‑CTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACg                                     <  2:730080/141‑1 (MQ=255)                                                                                          tAGCATTTTGCTTTCTAATAATGCCTTTAATT‑CTTTTTCAGTCATGCCTCCTGTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTAGAATTAAAGCAATTTCGTTAGCATCTTTGACGtc                                   >  1:467213/1‑141 (MQ=255)                                                                                            gCATTTTGCTTTCTAATATTGCCTTTAATT‑CTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGtctc                                 >  1:481574/1‑141 (MQ=255)                                                                                             cATTTTCGTTTCGCATATTGCCTTTCATT‑GTTTTTCATTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTctct                                <  2:664756/141‑1 (MQ=255)                                                                                                    cTTTCTAATATTGCCTTTAATT‑CTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAAttttt                         >  2:397486/1‑140 (MQ=255)                                                                                                            tatTGCCTTTAATT‑CTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGt                 <  2:32851/141‑1 (MQ=255)                                                                                                            tatTGCCTTTAATT‑CTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGt                 <  1:207947/141‑1 (MQ=255)                                                                                                              ttGCCTTTAGTT‑CTTTTGCAGTCATCCCTCCTTTTACAACAGTTAATTTATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTAt               <  2:6727/141‑1 (MQ=255)                                                                                                                gCCTTTAATT‑CTGTTTCAGTCATGCCTCATTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTGTTGAATGAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTAttt             >  2:507518/1‑140 (MQ=255)                                                                                                                 ccTTTAATT‑CTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCACCAGTATTAg            >  2:30375/1‑141 (MQ=255)                                                                                                                  cTTTAATT‑CTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGa           <  1:700949/141‑1 (MQ=255)                                                                                                                     tAATT‑CTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAAt        >  1:543217/1‑141 (MQ=255)                                                                                                                      aaTT‑CTTTTTCAGTCCTGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCCACAGTATTAGAAATg       <  1:207139/141‑1 (MQ=255)                                                                                                                       aTT‑CTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGAATTAGAAATGc      >  2:597039/1‑141 (MQ=255)                                                                                                                        tt‑CTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCt     <  1:98064/141‑1 (MQ=255)                                                                                                                        tt‑CTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGAAATTTCGTCAGAATCTTTGAAGTCTCTAATTTTATTTACAGTATTAGAAATGCt     >  2:744016/1‑141 (MQ=255)                                                                                                                           cTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCtta   >  2:485072/1‑141 (MQ=255)                                                                                                                            tttttCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAGCAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCttat  <  2:668472/141‑1 (MQ=255)                                                                                                                                            |                                                                                                                             ATTTTATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATT‑CTTTTTCAGTCATGCCTGCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTAT  >  USA300TCH1516_ALE/1646051‑1646313

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑