Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,232,465	G→C	100%	A124P (GCG→CCG)	prkC →	Serine/threonine‑protein kinase PrkC

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,232,465	0	G	C	100.0%	57.1 / NA	20	A124P (GCG→CCG)	prkC	Serine/threonine‑protein kinase PrkC
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base C (8/12);  total (8/12)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AAGAAGATGACTGTTACTACTTAGTAATGGAATATATCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATGCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAGCTTTAAGTGAGACGTCTTTAACTCA  >  USA300TCH1516_ALE/1232328‑1232589                                                                                                                                          |                                                                                                                             aagaagATGACTGTTACTACTTAGTAATGGAATATATCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGAGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATccg                                                                                                                            >  2:273147/1‑140 (MQ=255)        tgtgtGTTACTACTTAGTAATGGAATATATCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGata                                                                                                                     <  2:261573/136‑1 (MQ=255)             gTTACTACTTAGTAATGGAATATATCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAAAATCCGCATGATATGCGt                                                                                                                >  1:310593/1‑140 (MQ=255)                  tgctTAGTAATGGAATAGTTAGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGt                                                                                                           <  1:162237/138‑1 (MQ=255)                               aaTATATCGAAGGTCCTACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATAtt                                                                                              <  2:64213/140‑1 (MQ=255)                                      cGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCAAGAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCcac                                                                                       >  1:313093/1‑140 (MQ=255)                                            tCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAata                                                                                 >  2:57908/1‑140 (MQ=255)                                             ccGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAatat                                                                                <  2:255259/140‑1 (MQ=255)                                              cGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAatata                                                                               >  1:220275/1‑140 (MQ=255)                                                          aGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCACGATATTTTTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGTCAGc                                                                   >  1:139042/1‑140 (MQ=255)                                                                ttGAAAGTCATGGGCAATAGAGTCTGAACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATaaa                                                             <  2:66254/140‑1 (MQ=255)                                                                           gggCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAat                                                  >  1:201949/1‑140 (MQ=255)                                                                            ggacaatAAGTGTAAACACAGCAAATAATTTAACGAAACAAACATTGGATGGCATTAAACAACCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAata                                                 <  1:306442/134‑1 (MQ=255)                                                                                 ttAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGCTGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGa                                            >  2:158066/1‑140 (MQ=255)                                                                                  tAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGAt                                           <  2:223803/140‑1 (MQ=255)                                                                                  tAAGTGTTGACAAAGCGATTAATTTTCCGAATCAAATACTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCTTCAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGAt                                           <  2:90296/140‑1 (MQ=255)                                                                                     gtgtTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATACTTGAtatt                                        >  1:85942/1‑140 (MQ=255)                                                                                                          ttACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAGCTTTAAGt                   <  2:143595/140‑1 (MQ=255)                                                                                                                  cAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAAGTGCTAAAGCTTTAAGTGAGACGTc           <  1:57908/140‑1 (MQ=255)                                                                                                                           gATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTTAAACCTTAAGGGAGACGTATTTAACTCa  <  1:235414/140‑1 (MQ=255)                                                                                                                           gATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAGCTTTAAGTGAGACGTCTTTAACTCa  <  1:318089/140‑1 (MQ=255)                                                                                                                                          |                                                                                                                             AAGAAGATGACTGTTACTACTTAGTAATGGAATATATCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATGCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAGCTTTAAGTGAGACGTCTTTAACTCA  >  USA300TCH1516_ALE/1232328‑1232589

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: ‑