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%	89.0 / NA	29	A155G (GCA→GGA)	ypdF	Aminopeptidase YpdF
Reads supporting (aligned to +/- strand):  ref base G (0/1);  new base C (13/15);  total (13/16)
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

TTTTATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTGCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTAT  >  USA300TCH1516_ALE/1646052‑1646313                                                                                                                                          |                                                                                                                             ttttATTTCTTTCAAAACCATATGGTAATGCATCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTGATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGcctcct                                                                                                                            <  1:201411/140‑1 (MQ=255) ttttATCACTTGCAACACCATGTGGTAATGCACCTCTATGATCATATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGcctcct                                                                                                                            <  2:61487/140‑1 (MQ=255)        aCTTGCAACACCATGTTGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAAGTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTacaa                                                                                                                     <  1:37905/140‑1 (MQ=255)               acacCATGTGGTAGGGCACCACGATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTaa                                                                                                              <  1:99509/140‑1 (MQ=255)                     tgtgGTAATGCATCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAatata                                                                                                        <  1:75437/140‑1 (MQ=255)                     tgtgGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCCTGCCTCCTTTTACAACAGTTAAAatata                                                                                                        >  2:223672/1‑140 (MQ=255)                       tgGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCACTCCTGCCTCCTTTTACAACATTTAAAATATAtt                                                                                                      >  1:201648/1‑140 (MQ=255)                            aTGCACCTCTCTGACCAGATGCTACAATCGAATCGAATGATGGTCCATCTGCTCCTAACTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACATCTAAAATATCTTCatat                                                                                                 >  2:4587/1‑140 (MQ=255)                            aTGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGATCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCATTTTACAACAGTTACAATATATTAatat                                                                                                 >  2:134971/1‑140 (MQ=255)                                        gACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTCAAATCTATTCATCTTTTTCATcaaca                                                                                     >  2:79629/1‑140 (MQ=255)                                                gCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAgc                                                                             >  2:74309/1‑140 (MQ=255)                                                  tACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTATTTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAgctg                                                                           <  1:142893/140‑1 (MQ=255)                                                  tACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATCCTTTTTCAGTCATGCCTCCTTTTACAACATTTACAATACATTCATATGTTTCATCAACAATATTAgctg                                                                           <  2:147946/140‑1 (MQ=255)                                                  tACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTATAATATTCCCTTTCATTCTTCTTCATTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAgctg                                                                           <  2:202537/140‑1 (MQ=255)                                                      aTCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTCTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATCTATTCATATGTTTCCTCAACAATATTAGCTGCttt                                                                       >  1:54896/1‑140 (MQ=255)                                                          tATCGAATGATGGTCCATCTGCTCCGAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATACGTTTCATCAACAATATTAGCTGCTTTTTGa                                                                   <  2:73726/140‑1 (MQ=255)                                                               aaTGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACATCAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTaa                                                              <  1:102333/140‑1 (MQ=255)                                                                      gTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAAtt                                                       <  2:180191/140‑1 (MQ=255)                                                                                tCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCAt                                             >  2:238037/1‑140 (MQ=255)                                                                                       tgtAGGATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACGACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGAc                                      >  2:262055/3‑140 (MQ=255)                                                                                             aTTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTTATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGACTTAAAGCAATTTCGTCAGCATCTTTGCCGTctct                                >  2:194719/1‑140 (MQ=255)                                                                                                ttGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAAt                             <  1:239930/140‑1 (MQ=255)                                                                                                       cTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACTTCTCTATTTTTctct                      >  2:126073/1‑140 (MQ=255)                                                                                                                 cTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAACAATTTCATCAGCATCTTTGACATCTCTAATTTTATCTACAGTATTAg            >  1:132310/1‑140 (MQ=255)                                                                                                                         atttttCTTTCACGCATGCTTTTACAACACTTAAAATACATTCATATGTTTCATCATCCATATCAGCTCCTTCTTCAATTAAAGCAATTTCGTCAGCATATTTAACGTCTCTAATTTTATCTACACTATTACAAATGCtt    <  2:197303/139‑1 (MQ=255)                                                                                                                          tttttCATTCATGCCTCCTTGTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCtta   <  1:160692/140‑1 (MQ=255)                                                                                                                          tttttCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCtta   <  1:98954/140‑1 (MQ=255)                                                                                                                          tttttCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCtta   <  1:90635/140‑1 (MQ=255)                                                                                                                          tttttCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCtta   <  1:68764/140‑1 (MQ=255)                                                                                                                          tttttCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCtta   <  1:260643/140‑1 (MQ=255)                                                                                                                           ttttCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATAGTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAAAAATGCttct  >  2:8257/1‑138 (MQ=255)                                                                                                                                          |                                                                                                                             TTTTATCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTGCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTAT  >  USA300TCH1516_ALE/1646052‑1646313

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: ‑