Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,231,411	A→G	100%	D19G (GAT→GGT)	stp →	Serine/threonine phosphatase stp

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,231,411	0	A	G	100.0%	10.8 / NA	5	D19G (GAT→GGT)	stp	Serine/threonine phosphatase stp
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (3/2);  total (3/2)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GTGGTCAATTAAGAGCAAAGGAACGACAAGTAGAAACGAGGTAAAGACAAATGCTAGAGGCACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAAT  >  USA300TCH1516_ALE/1231306‑1231547                                                                                                          |                                                                                                                                         gtgGTCAATTAAGAGCAAAGGAACGACAAGTAGAAACGAGGTAAAGACAAATGCTAGAGGCACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGGTGCGGGTGGTATTTTTTATAATCAAACTAATcaac                                                                                                       >  1:22056/1‑141 (MQ=255)                         gACAAGTAGAAACGAGGTAAAGACAAATGCTAGAGGCACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGGTGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTa                                                                               <  1:11915/141‑1 (MQ=255)                                                                                      acaTAGAGATAAGAATGAAGGTGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCg                  >  1:23646/1‑141 (MQ=255)                                                                                              aTAAGAATGAAGGTGCGGGTGGTATTTTTTATAATCAGACTAATCAACCACTGTTAGTTCTGTGTGATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAg          <  2:17333/141‑1 (MQ=255)                                                                                                      gAAGGTGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAAt  >  2:59877/1‑141 (MQ=255)                                                                                                          |                                                                                                                                         GTGGTCAATTAAGAGCAAAGGAACGACAAGTAGAAACGAGGTAAAGACAAATGCTAGAGGCACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAAT  >  USA300TCH1516_ALE/1231306‑1231547

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑