Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,054,623	G→A	intergenic (‑124/+404)	sspA ← / ← patA_2	Glutamyl endopeptidase/Putative N‑acetyl‑LL‑diaminopimelate aminotransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,054,623	0	G	A	100.0%	29.8 / NA	14	intergenic (‑124/+404)	sspA/patA_2	Glutamyl endopeptidase/Putative N‑acetyl‑LL‑diaminopimelate aminotransferase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (7/7);  total (7/7)

CCTTTCATCTAAAAACCTCCAAAAAATTTATTTACAAGTTAAATATAACACTAAAAATTTTTAAGTCAATAAGAATATATAAATAAATTAAAAAGTTTTTGTAAAGATTAGAGTTTACAAAAACATTAAGGGAATTAAAATTGAATTGTATTATACTTTATTCAATTGAGTTAAATTGATAAGATCGTCAATTGTTTGCATTTATCTAAAAGAATAAATAAGAAAGGAATTGAGAGCGAATGGAAAGTATTTGTTTATAAT  >  USA300TCH1516_ALE/1054492‑1054752                                                                                                                                    |                                                                                                                                  ccTTTCATCTAAAAACCTCCAAAAAATTTATTTACAAGTTAAATATAACACTAAAAATTTTTAAGTCAATAAGAATATATAAATAAATTAAAAAGTTATTATAAAGATGAGAGTTTACAAAAACATTAAGGAAAt                                                                                                                                >  2:206542/1‑135 (MQ=255)         cTAAAAACCTCCAAAAAATTTATTTACAAGTTAAATATAACACTAAAAATTTTTAAGTCAATAAGAATATATAAATAAATTCAAAATTTTTTGTAAAGATTAGAGTTTACAAAAACATTAAGGAAATTAAaatta                                                                                                                        >  2:157048/1‑134 (MQ=255)                     aaaaaaTTTATTTACAAGTTAAATATAACACTATAAATTTTTAAGTCAATAAGAATATATAATTAAATTAAAATTTTTTTTTTTATATTAGAGTTTACAAAAACATTAAGGAAATTAAAATGGAATTGTATtata                                                                                                            <  1:29642/135‑1 (MQ=255)                        aaaTTTATTTACAAGTTAAATATAACACTAAAAATTATAAAGACAATAAGAATATATAAATAAATTAAAAAGTTTTTGTAAAGATTAGAGTTTACAAAAACATTAAGGAAATTAAAATTGAATTGTATTATACtt                                                                                                         >  1:7642/1‑135 (MQ=255)                                  aCAAGTTAAATATAACACTAAAAATTTTTAAGTCAATAAGAATATATAAATAAATTAAAAAGTTTTTGTAAAGATTAGAGTTTACAAAAACATTAAGGAAATTAAAATTGAATTGTATTATACTTTATTCAATTg                                                                                               >  2:106749/1‑135 (MQ=255)                                                                         gAATATATAAATAAATTAAAAAGTTTTTGTAAAGATTAGAGTTTACAAAAACATTAAGGAAATTAAAATTGAATTGTATTATACTTTATTCAATTGAGTTAAATTGATAAGATCGTCAATTGTTTGCATTTATCt                                                        <  1:149345/135‑1 (MQ=255)                                                                                         tAAAAAGTTTTTGTAAAGATTAGAGTTTACAAAAACATTAAGGAAATTAAAATTGAATTGTATTATACTTTATTCAATTGATTTAAATTGATATTATTGTTAATTGTTTGCATTTATCTAAAAGAATAAATAAGa                                        <  1:67037/135‑1 (MQ=255)                                                                                         tAAAAAGTTTTTGTAAAGATTAGAGTTTACAAAAACATTAAGGAAATTAAAATTGAATTGTATTATACTTTATTCAATTGAGTTAAATTGATAAGTTCGTTAATTGTTTGCATTTATCTAAAAGAATAAATAAGa                                        <  1:204425/135‑1 (MQ=255)                                                                                         tAAAAAGTTTTTGTAAAGATTAGAGTTTACAAAAACATTAAGGAAATTAAAATTGAATTGTATTATACTTTATTCAATTGAGTTAAATTGATAAGATTGTTACTTGTTTTATAATAAGGAAAAGAATAAATAAGa                                        <  1:215249/135‑1 (MQ=255)                                                                                             aaGTTTTTGTAAAGATTAGAGTTTACAAAAACATTAAGGAAATTAAAATTGAATTGTATTATACTTTATTCAATTGAGTTAAATTGATAAGATCGTCAATTGTTTGCATTTATCTAAAAGAATAAATAAGAAAgg                                    >  1:156659/1‑135 (MQ=255)                                                                                                          gATTAGAGTTTACAAAAACATTAAGGAAATTAAAATTGAATTGTATTATACTTTATTCAATTGAGTTAAATTGATAAGATCGTCAATTGTTTGCATTTATCTAAAAGAATAAATAAGAAAGGAATTGAGAGCGaa                       >  2:193691/1‑135 (MQ=255)                                                                                                           aTTAGAGTTTACAAAAACATTAAGGAAATTAAAATTGAATTGTATTATACTTTATTCAATTGAGTTAAATTGATAAGATCGTCAATTGTTTGCATTTATCTAAAAGAATAAATAAGAAAGGAATTGAGAGCGAAt                      <  2:161790/135‑1 (MQ=255)                                                                                                           aTTAAAGTTTATAAAAACATTAAGGAAATTAAAATTGAATTGTAGTATACTTTATTCAATTGAGTTAAATTGATAAGATCGTCAATTGTTTGCATTTATCTAAAAGAATAAATAAGAAAGGAATTGAGAGCGAAt                      <  2:217786/135‑1 (MQ=255)                                                                                                                               tAAGGAAATTAAAATTGAATTGTATTATACTTTATTCAATTGAGTTAAATTGATCCGCTGTTTGGTTGTATGAAAAATAGTAGATGAATAAATAAGAAAGAAATTGAGAGCGAATGGAAAGTATTTGTTTataat  >  2:220276/1‑135 (MQ=255)                                                                                                                                    |                                                                                                                                  CCTTTCATCTAAAAACCTCCAAAAAATTTATTTACAAGTTAAATATAACACTAAAAATTTTTAAGTCAATAAGAATATATAAATAAATTAAAAAGTTTTTGTAAAGATTAGAGTTTACAAAAACATTAAGGGAATTAAAATTGAATTGTATTATACTTTATTCAATTGAGTTAAATTGATAAGATCGTCAATTGTTTGCATTTATCTAAAAGAATAAATAAGAAAGGAATTGAGAGCGAATGGAAAGTATTTGTTTATAAT  >  USA300TCH1516_ALE/1054492‑1054752

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: ‑