Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	733,536	G→T	S207I (AGT→ATT)	graR_1 →	Response regulator protein GraR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	733,536	0	G	T	100.0%	28.0 / NA	15	S207I (AGT→ATT)	graR_1	Response regulator protein GraR
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (13/2);  total (13/2)

CAAAAAAAATCAAATCGTTTCGAGAGATACAATTATCACTGCATTATGGGATGATGAAGCATTTGTTAGTGATAATACGTTAACAGTAAATGTGAATCGTTTACGAAAAAAATTATCTGAAATTAGTATGGATAGTGCAATCGAAACAAAAGTAGGAAAAGGATATATGGCTCATGAATAATTTGAAATGGGTAGCTTATTTTTTGAAATCTCGCATGAACTGGATATTTTGGATATTGTTTTTAAAC  >  USA300TCH1516_ALE/733411‑733658                                                                                                                              |                                                                                                                           cAAAAAAAATCAAATCGTTTCGAGAGATACAATTATCACTGCATTATGGGATGATGAAGCATTTGTTAGTGATAATACGTTAACAGTAAATGTGAATCGTTTACGAAAAAAATTATCTGAAATTATTATGGATAg                                                                                                                   >  2:161369/1‑135 (MQ=255)    aaaaaaTCAAATCGTTTCGAGAGATACAATTATCACTGCATTATGGGATGATGAAGCATTTGTTAGTGATAATACGTTAACAGTAAATGTGAATCGTTTACAAAAAAAATTATCTGAAATTATTCTGGAACGTGc                                                                                                                >  2:9713/1‑135 (MQ=255)    aaaaaaTCAAATCGATTCGAGAGATACAATTATCACTGCATTATGGGATACTGAAGCTTTTGTTAGTGATAATACGTTAACAGTAAATGTGAATCGTTTACGAAAAAAACTATCTGATATTATTATGGATAGTGc                                                                                                                >  2:10307/1‑135 (MQ=255)                cGTTTCGAGAGATACAATTATCACTGCATTATGGGATGATGAAGCATTTGTTAGTGATAATACGTTAACAGTAAATGTGAATCGTTTACGAAAAAAATTATCTGAAATTATTATGGCTAGTGCAATCGACACaaa                                                                                                    >  2:120806/1‑135 (MQ=255)                cGTTTCGAGAGATACAATTATCACTGCATTATGGGATGATGAAGCATTTGTTAGTGATAATACGTTAACAGTAAATGTGAATCGTTTACGAAAAAAATTATCTGAAATTATTATGGATAGTGCAATCGAAACaaa                                                                                                    >  2:68197/1‑135 (MQ=255)                cGTTTCGAGAGATACAATTATCACTGCATTATGGGATGATAAAGCATTTGTTAGTGATAATACGTTAACAGTAAATTTGAATCGTTTACGAAAAAAAGTATCTGAAATTATTATGGATAGTGCAATCGAAACaaa                                                                                                    >  1:210192/1‑135 (MQ=255)                      gagagaTACAATTATCACTGCATTATTGGATGATGAAGCATTTGTTAGTGATAATACGTTAACAGTAAATGTGAATCGTTTACGAAAAAAATTATCTGTATTTTTTATTGTTAGTGCAATCGAAACAAAAGTAgg                                                                                              <  1:209978/135‑1 (MQ=255)                      gagagaTACAATTATCACTGCATTATGGGATGATGAAGCATTTGTTAGTGATAATACGTTAACAGTAAATGTGAATCGTTTACGAAAAAAATTATCTGAAATTATTATGGCTACTGCAATCGAAACAAAAGTAgg                                                                                              >  2:223969/1‑135 (MQ=255)                          gaTACAATTATCACTGCATTATGGGATGATGAAGCATTTGTTAGTGATAATACGTTAACAGTAAATGTGAATCGTTTACGAAAAAAATTATCTGAAATTATTATAGATAGTGCAATCGAAACAAAAGTAGGaaaa                                                                                          >  2:1219/1‑135 (MQ=255)                                                     gatgaAGCATTTGTTAGTGATAATACGTTAACAGTAAATGTGAATCGTTTACGAAAAAAATTATCTGAAATTATTATGGATAGTGCAATCGAAACAAAAGTAGGAAAAGGATATATGGCTCTTGTATACTTTGaa                                                               >  2:205220/1‑135 (MQ=255)                                                                                    cAGTAAATGTGAATCGTTTACGAAAAAAATTATCTGAAATTATTATGGATAGTACAATCGAAACAAAAGTAGGAAAAGGATATATGGCTCATGAATAATTTGAAATGGGTAGCTTATTTTTTGAAATCTCGCATg                                >  1:147530/1‑135 (MQ=255)                                                                                        aaaTGTGAATCGTTTACGAAAAAAATTCTCTAAAATAATAATGGTTCCTGCAATCAAAACAAAAGTAGGAAAAGGATATATGGCTCATGAATAATTTGAAATGGGTAGCTTATTTTTTGAAATCTCGCATGAACt                            <  1:161369/135‑1 (MQ=255)                                                                                            gtgAATCGTTTACGAAAAAAATTATCTGAAATTATTATGAATAGTGCAATCGAAACAAAAGTAGGAAAAGGATATATGGCTCATGAATAATTTGAAATGGGTAGCTTATTTTTTGAAATCTCGCATGAACTGGat                        >  1:159469/1‑135 (MQ=255)                                                                                                    tttACGAAAAAAATTATCTGAAATTATTATGGATAGTGCAATCGAAACAAAAGAAGGAAAAGGATATATGGCTCATGAATAATTTGAAATGGGTACCTTATTTTTTGAAACCTCACATGAAATGTACCTTTTggc                >  2:225089/1‑134 (MQ=255)                                                                                                                  tATCTGAAATTATTATGGATAGTGCAATCGAAACAAAAGCAGGAAAAGGATATATGGCTCATGAATAATTTGAAATCGGAAGCTTATTTTTTGAAATCTCCCATCAACTGGATATCATGGATATTGTTTTTAAAc  >  2:99961/1‑135 (MQ=255)                                                                                                                              |                                                                                                                           CAAAAAAAATCAAATCGTTTCGAGAGATACAATTATCACTGCATTATGGGATGATGAAGCATTTGTTAGTGATAATACGTTAACAGTAAATGTGAATCGTTTACGAAAAAAATTATCTGAAATTAGTATGGATAGTGCAATCGAAACAAAAGTAGGAAAAGGATATATGGCTCATGAATAATTTGAAATGGGTAGCTTATTTTTTGAAATCTCGCATGAACTGGATATTTTGGATATTGTTTTTAAAC  >  USA300TCH1516_ALE/733411‑733658

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: ‑