Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,002,200	T→G	100%	M173R (ATG→AGG)	mecA →	Adapter protein MecA 1

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,002,200	0	T	G	100.0%	53.2 / NA	17	M173R (ATG→AGG)	mecA	Adapter protein MecA 1
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base G (8/9);  total (8/9)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATATGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAGTTTATTTAAAT  >  USA300TCH1516_ALE/1002095‑1002327                                                                                                          |                                                                                                                                aaaaTACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTGTTATTATGCTGTATATTTTg                                                                                              >  2:112769/1‑141 (MQ=255)       cAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATCTGTTATATAGGGTTGATGGTACTTATTCTGATGTGGTATATTTTGATAGTc                                                                                        <  2:283371/141‑1 (MQ=255)        aaGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTCTGCTGTATATTTTGATAGTCa                                                                                       >  2:55769/1‑141 (MQ=255)          gAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATg                                                                                     >  2:111008/1‑141 (MQ=255)               aTCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGAt                                                                                <  2:188426/141‑1 (MQ=255)                tCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATc                                                                               <  1:111008/141‑1 (MQ=255)                   ttGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTGCAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCaag                                                                            >  1:341132/1‑141 (MQ=255)                      ttaaaTTTAACGATTGAGAATATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCaagaag                                                                         <  1:357025/139‑1 (MQ=255)                                               tattaATTATGCGTATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAAtt                                                <  2:257846/141‑1 (MQ=255)                                                       aTGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAAt                                        <  2:251142/141‑1 (MQ=255)                                                          cATATCATAGCAATACAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCCTGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTg                                     <  1:174950/141‑1 (MQ=255)                                                               cATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATAAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTAt                                >  1:171877/1‑141 (MQ=255)                                                                        caaaTAACTACAGAGTTTGAAGATTTGTTATTTAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATCTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAacagac                       <  2:356087/139‑1 (MQ=255)                                                                                  cAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAg             >  1:108781/1‑141 (MQ=255)                                                                                          gAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGACGtttattta     >  2:210190/1‑141 (MQ=255)                                                                                             gATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAGTTTATTTAAAt  <  1:148403/141‑1 (MQ=255)                                                                                             gATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGGCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAGTTTATTTAAAt  >  1:88382/1‑141 (MQ=255)                                                                                                          |                                                                                                                                AAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATATGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAGTTTATTTAAAT  >  USA300TCH1516_ALE/1002095‑1002327

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: ‑