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%	97.8 / NA	32	A155G (GCA→GGA)	ypdF	Aminopeptidase YpdF
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base C (12/20);  total (12/20)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTGCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATT  >  USA300TCH1516_ALE/1646059‑1646314                                                                                                                                   |                                                                                                                              aCTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGCCACGCCTCCTTTTacaac                                                                                                                     >  1:25893/1‑141 (MQ=255)  cTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTacaaca                                                                                                                    >  1:83199/1‑141 (MQ=255)  cTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTacaaca                                                                                                                    <  2:28600/141‑1 (MQ=255)                tgGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTc                                                                                                      >  1:68292/1‑141 (MQ=255)                     aTGCACCACTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATg                                                                                                 <  1:239253/141‑1 (MQ=255)                           ctctATGACCGTATGCTACACTCGTATCCAATGATGCTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCGTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTtcat                                                                                           <  2:32930/141‑1 (MQ=255)                                tGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATcaaca                                                                                      >  1:216065/1‑141 (MQ=255)                                          cTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAgctg                                                                            >  1:150350/1‑141 (MQ=255)                                           tACAATCGTATCGAATGATGGTCCATCTGCAGGCAATTCGAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAgctgc                                                                           <  1:276431/141‑1 (MQ=255)                                               aTCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCtttt                                                                       <  2:263411/141‑1 (MQ=255)                                                tCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCttttt                                                                      <  1:241902/141‑1 (MQ=255)                                                           gatgGTCGATCTGCTCGTAATGCTAGTAGTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTGTTACAAGAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCa                                                           <  2:127558/141‑1 (MQ=255)                                                                     cTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAg                                                 <  1:183295/141‑1 (MQ=255)                                                                        cTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCAt                                              <  1:240234/141‑1 (MQ=255)                                                                            tAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATGAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCttt                                          <  2:222706/141‑1 (MQ=255)                                                                               ttCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGAc                                       <  1:204975/141‑1 (MQ=255)                                                                                  tAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGtc                                    >  1:174466/1‑141 (MQ=255)                                                                                         ttGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAAtt                             <  2:90042/141‑1 (MQ=255)                                                                                                      ttGTCTTTAATTCTGTTTCAGTCATGTCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATTAATAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGTCGTCTCTAATTTTATCTACAGTAt                <  2:113663/141‑1 (MQ=255)                                                                                                       tgacTTTAATTCTTTTTCAGTTATGCCTCTTTTTAAATTAGTTAAAATATATGTATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTAtt               <  2:109972/138‑1 (MQ=255)                                                                                                        gCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGAATCTTTGACGTCTCTAATTTTATCTACAGTATTa              <  1:83319/141‑1 (MQ=255)                                                                                                         ccTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAg             <  1:150906/141‑1 (MQ=255)                                                                                                           tttAATTCTTTTTTAGTCATGCCTCCTTTTACAACTGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGaa           <  2:89376/141‑1 (MQ=255)                                                                                                           tttAATTCTTTTTCAGTCATGCCTCCTTTTACACCAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAACCAATTTCGTCAGCATCTTTGACGTCTCTCATTTTATCTCCACTATTAGaa           >  2:305049/1‑141 (MQ=255)                                                                                                              aaTTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATg        <  1:61722/141‑1 (MQ=255)                                                                                                              aaTTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCGGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATg        >  1:167157/1‑141 (MQ=255)                                                                                                               aTTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGc       >  1:227826/1‑141 (MQ=255)                                                                                                                ttCTTTTTCATTCATGCCTCCTTTTTCAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCt      <  2:227044/141‑1 (MQ=255)                                                                                                                 tCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCtt     >  1:243149/1‑141 (MQ=255)                                                                                                                 tCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCtt     >  1:210534/1‑141 (MQ=255)                                                                                                                   tttttCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCttat   <  1:49385/141‑1 (MQ=255)                                                                                                                    ttttCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTGATATGTTTCATCAACAATATTAGCTACTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATCAGAACTGCttatt  >  2:296977/1‑141 (MQ=255)                                                                                                                                   |                                                                                                                              ACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTGCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATT  >  USA300TCH1516_ALE/1646059‑1646314

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑