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	96.4%	71.8 / NA	28	A155G (GCA→GGA)	ypdF	Aminopeptidase YpdF
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base C (13/14);  minor base T (0/1);  total (13/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

ATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTGCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTT  >  USA300TCH1516_ALE/1646056‑1646311                                                                                                                                      |                                                                                                                           aTCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTTATGCCTCCTTTTa                                                                                                                      >  1:313960/1‑140 (MQ=255)   cACTTGCAACACCATGTGGTAATGCACCTCTATGACCATATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTaca                                                                                                                    <  2:99403/140‑1 (MQ=255)          aaCACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTTCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACCACAGTTa                                                                                                             >  2:305993/1‑140 (MQ=255)          aaCACCATGTAGTAATGCACCTCTATGACCTGATGCTACAATCGTATCGAATGATGGTCCATCTTCTCCTAATTCTAGCATTTTGCTTTCTATTATTGCCTTTAATTCTTTTTCCAAAATACCTCCTTTTACAACAGTTa                                                                                                             <  2:119598/140‑1 (MQ=255)            cacCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTaaa                                                                                                           <  1:233258/140‑1 (MQ=255)                         tGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACATTTAAAATATATTTCTATg                                                                                              >  2:169078/1‑140 (MQ=255)                               tctATGACCAGATGCTACAATCGTATCTAATGATGGTGCAACTGCACCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTtcat                                                                                        <  1:60551/140‑1 (MQ=255)                                          aTGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAAAAATATTa                                                                             >  2:14818/1‑140 (MQ=255)                                           tGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAg                                                                            <  1:127179/140‑1 (MQ=255)                                                cAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCTTCCTTTTACAACAGTTGAAATATATTCATATGTTTGATAATCAACATTAccttct                                                                       >  2:306680/1‑140 (MQ=255)                                                             tgatgGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAg                                                          <  1:269385/140‑1 (MQ=255)                                                                       tCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTTATGTCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTc                                                <  1:188723/140‑1 (MQ=255)                                                                            tCCTAATTCTAGCATTTTGCTTTCTAATATTTTCTTTCGGCCAACAACAAGCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCAt                                           <  1:60870/140‑1 (MQ=255)                                                                             ccTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATc                                          >  2:237147/1‑140 (MQ=255)                                                                              cTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTAATATGTTTTATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTATTCAGCAttt                                         >  2:327160/1‑138 (MQ=255)                                                                                aaTTCTAGCATTTTGCTTTCTAATATTGCCTTTTCTTTTCCTGCACTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCttt                                       <  1:309237/140‑1 (MQ=255)                                                                                  ttCTATCATTTTTCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGa                                     <  1:78344/140‑1 (MQ=255)                                                                                    cTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTTATATGTTTCATCAACAATATTAGCTGCTTTTTTAATTAAATAAATTTTATCAGCATCTTTTAca                                   >  1:210347/1‑139 (MQ=255)                                                                                    cTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTATAGCAATTTCGTCAGCATCTTTGACg                                   <  2:21822/140‑1 (MQ=255)                                                                                    cTAGCATGTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCGTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACg                                   <  2:22472/140‑1 (MQ=255)                                                                                                   cTAATATTGCCTTTAATTTTTTTTCAGTCATGCCTTCTTTTACAACAGTTAAAAGATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCt                    <  1:132326/140‑1 (MQ=255)                                                                                                     attatTTCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACTGTTAAAATATATTCATATGTTTCATCAACTATATTAGCTGCTTTTTGAATTAATGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTAc                  <  2:82757/138‑1 (MQ=255)                                                                                                         ttGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTATAATTTTATCTACAGTa              >  1:54125/1‑140 (MQ=255)                                                                                                          tGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTAt             >  1:267755/1‑140 (MQ=255)                                                                                                                  aTTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTTTCCATCATCGACGTCTCTAATTTTATCTACAGTATTAGAAATg     >  1:309167/1‑140 (MQ=255)                                                                                                                   ttCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGc    >  1:23955/1‑140 (MQ=255)                                                                                                                    tCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCt   <  1:320120/140‑1 (MQ=255)                                                                                                                     cTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTACAAATCCtt  >  2:228539/1‑140 (MQ=255)                                                                                                                                      |                                                                                                                           ATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTGCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTT  >  USA300TCH1516_ALE/1646056‑1646311

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: ‑