Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,646,189	G→C	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	96.5%	78.4 / NA	29	A155G (GCA→GGA)	ypdF	Aminopeptidase YpdF
Reads supporting (aligned to +/- strand):  ref base G (0/1);  new base C (12/16);  total (12/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTGC‑TTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATGATATACGG  >  USA300TCH1516_ALE/1646055‑1646326                                                                                                                                       |                                                                                                                                           tATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCC‑TTTTa                                                                                                                                     >  2:246681/1‑141 (MQ=255)  aTCACTTGCAACACCATGTGGTAATGCCCCTCTATGACCAGATGCTACAATCGTATCGACTGATGGTCCATCTGCTCCTACTTCTAGCATTTTGCTTTCTAATATTGCCTCTAATTCTTGTTCATTCGTGcctcc‑tgatac                                                                                                                                    >  2:351474/1‑136 (MQ=255)    cACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGGCATGCCTCC‑TTTTgcaa                                                                                                                                  >  1:290272/1‑141 (MQ=255)    cACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTCTAATTCTTTTTCAGTCATGCCTCC‑TTTTacaa                                                                                                                                  <  2:390100/141‑1 (MQ=255)                   gtgGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCC‑TTTTACAACAGTTAAAATATAtt                                                                                                                   >  2:131274/1‑141 (MQ=255)                        aaTGCACCTCTATGACCAGATGCTACAATCGTATCGAATGCTGGGCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTTCCTTTAATTCTTTTTCAGTCATGCCTCC‑TTTTACAACAGTTAAAATATATTCatat                                                                                                              >  2:128090/1‑141 (MQ=255)                                         aGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCC‑TTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATAtt                                                                                             >  2:415794/1‑141 (MQ=255)                                         aGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCC‑TTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATAtt                                                                                             >  2:225114/1‑141 (MQ=255)                                              cTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCATTCATGCCTCC‑TTTTACAACATTTAAAATATATTCATATGTTTCATCAACAATATTAgctg                                                                                        >  2:221883/1‑141 (MQ=255)                                                    tCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCC‑TTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCttttt                                                                                  <  2:150904/141‑1 (MQ=255)                                                           gAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCC‑TTTTACTTCATTTAAAATATATTCATATGTTTATTCATTATTATTATCTGCTTTTTCAAttta                                                                           >  2:174427/1‑139 (MQ=255)                                                             atgatgGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCC‑TTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAg                                                                         <  1:131274/141‑1 (MQ=255)                                                             atgatgGTCCATCTGCTCCCAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCC‑TTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAg                                                                         <  1:246681/141‑1 (MQ=255)                                                                   gTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCC‑TTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAAttt                                                                   <  1:328351/141‑1 (MQ=255)                                                                          tGCTCCTAAGTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCC‑TTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGc                                                            <  2:40818/141‑1 (MQ=255)                                                                               cTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCC‑TTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCtt                                                       <  2:133778/141‑1 (MQ=255)                                                                                       aGCAGTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCC‑TTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGtct                                               <  1:10752/141‑1 (MQ=255)                                                                                         cATTTTGCTTTTTAATATTGCTTTTAATTCTTTTTCAGTTATGTCTCC‑TTTTACAACAGTTAAGATATATGCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTctct                                             <  2:267305/141‑1 (MQ=255)                                                                                           ttttGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCC‑TTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTaa                                           >  1:302595/1‑141 (MQ=255)                                                                                             ttGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCC‑TTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAAtt                                         <  1:338142/141‑1 (MQ=255)                                                                                              tGCTTTCTAATTGTGCCTTTAATTCTTTTTCAGTCATGCCTCC‑TTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAAttt                                        <  1:388718/141‑1 (MQ=255)                                                                                                          ttGCCTTTCTATCTGGTTCAGTCTTGCCTCC‑GTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTAt                            <  1:99638/141‑1 (MQ=255)                                                                                                          ttGCCTTTAATTCTTTTTCATTTATGCTTCC‑TTTTATAACAGTTAAAATATATTCATATGTTTCATCAACAAGATTAGCTGCTTTTTGCATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTAt                            <  2:6785/141‑1 (MQ=255)                                                                                                          ttGCCTTTAATTCATTTTCAGTTTTG‑CTGCGTTTAAGGACTTTTAAAATATATTCATATGTTTTATCAACTATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTAt                            <  2:310603/141‑1 (MQ=255)                                                                                                                 tAATTCTTTTTCAGTCATGCCTCC‑TTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAAt                     <  2:15854/141‑1 (MQ=255)                                                                                                                  aaTTCTTTTTCAGTCATGCCTCC‑TTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTTTCTACAGTATTAGAAATg                    >  1:376864/1‑141 (MQ=255)                                                                                                                    ttCTTTTTCAGTCATGCCTCC‑TTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCt                  <  1:393926/141‑1 (MQ=255)                                                                                                                      cTTTTTCAGTCATGCCTCC‑TTTTACAACAGTTAAACTATATTCATATGTTTCCTCTACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCTTCTTTGACGTCTCTAATTTTATCTACAGTATTCGCAATGAttt                >  2:283434/1‑140 (MQ=255)                                                                                                                       tttttCAGTCATGCCTCC‑TTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCttat               >  1:240777/1‑141 (MQ=255)                                                                                                                            cAGTCATGCCTCC‑TTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATg          <  1:221883/141‑1 (MQ=255)                                                                                                                                cagtcctcc‑tTTTACATCAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATGatat      <  2:243563/137‑1 (MQ=255)                                                                                                                                    cctcc‑tTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAACATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATGATATACgg  <  1:106180/141‑1 (MQ=255)                                                                                                                                    cctcc‑tGTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATGATATACgg  <  1:232973/141‑1 (MQ=255)                                                                                                                                       |                                                                                                                                           TATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTGC‑TTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATGATATACGG  >  USA300TCH1516_ALE/1646055‑1646326

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: ‑