Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,247,097	(T)6→7	intergenic (‑118/‑306)	bltD_2 ← / → coaW	Spermine/spermidine acetyltransferase/Type II pantothenate kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,247,091	1	.	T	100.0%	37.0 / NA	13	intergenic (‑112/‑312)	bltD_2/coaW	Spermine/spermidine acetyltransferase/Type II pantothenate kinase
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base T (6/7);  total (6/7)

CCCCTATCTTTTTATATATGAAGCATGAATCCCCATATTATTTTACCTATTATTTCACTACGATACCATTATTTGCTCTAAGTTAAATAAATTACTTATTTATA‑TTTTTTAAATTTCAAAATTAATGTACTATTCCTCATTACTTATCATTTTAATCAGAGACTTACAAATACACTGCGTACGAACTACTTTTAATATTGCGTCACTAACTAACA  >  USA300TCH1516_ALE/2246988‑2247202                                                                                                         |                                                                                                                ccccTATCTTTTTATATATGCAGCATGAATAACCACATTAATGGACCTATTATTTCACTACGATACCATTATTTGCTCTAAGTTAAATAAATTACTTATTTATATTTTTTTAAATTTCAAAATTAATGTACTATTCCTCAt                                                                             >  1:122464/1‑141 (MQ=255)  cccTATCTTTTTATATATGAAGCATGAATCCCCATATTATTTTACCTATTATTTCACTACGATACCATTATTTGCTCTAAGTTAAATAAATTACTTATTTATATTTTTTTAATTTTCAAAATTAATTTACTATTCTTCttt                                                                            >  2:216580/1‑141 (MQ=255)    cTATCTTTTTATATATGAAGCATGAATCCCCATATTATTTTACCTATTATTTCACTACGATACCATTATTTGCTCTAAGTTAAATAAATTACTTATTTATATTTTTTTAAATTTCACAATTAATGTACTATTCCTCtttcc                                                                          >  2:28205/1‑139 (MQ=255)              atatatGAAGCATGAATCCCCATATTATTTTACCTATTATTTCACTACGATACCATTATTTGCTCTAAGTTAAATAAATTACTTATTTATATTTTTTTAAATTTCAAAATTAATGTACTATTCCTAATTACTTATCAtttt                                                                >  1:238532/1‑141 (MQ=255)                            gaTCCCCATATTATTTTACCTATTATTTCACTACGATACCATTATTTGCTCTAAGTTAAATAAATTACTTATTTATATTTTTTTAAATTTCAAAATTAATGGACTATTCCTCATTACTTATCATTTTAATCAGAGACTTAc                                                  <  2:96991/140‑1 (MQ=255)                            aaTCCCCATATTATTTTACCTATTATTTCACTACGATACCATTATTTGCTCTAAGTTAAATAAATTACTTATTTATATTTTTTTAAATTTCAAAATTAATGTACTATTCCTCATTACTTATCATTTTAATCAGAGACTTAc                                                  <  2:52480/141‑1 (MQ=255)                                          tttACCTATTATTTCACTACGATACCATTATTTGCTCTAAGTTAAATAAATTACTTATTTATATTTTTTTAAATTTCAAAATTAATGTACTATTCCTCATTACTTATCATTTTAATCAGAGACTTACAAATACACTGCGTa                                    <  1:211396/141‑1 (MQ=255)                                                      ttCACTACGATACCATTATTTGCTCTAAGTTAAATAAATTACTTATTTATATTTTTTTAAATTTCAAAATTAATGTACTATTCCTCATTACTTATCATTTTAATCAGAGACTTACAAATACACTGCGTACGAACTACtttt                        >  1:135642/1‑141 (MQ=255)                                                         aCTACGATACCATTATTTGCTCTAAGTTAAATAAATTACTTATTTATATTTTTTTAAATTTCAAAATTAATGTACTATTCCTCATTACTTATCATTTTAATCAGAGACTTACAAATACACTGCGTACGAACTACTTTTAat                     <  1:90480/141‑1 (MQ=255)                                                                 aCCATTATTTGCTCTAAGTTAAATAAATTACTTATTTATATTTTTTTAAATTTCAAAATTAATGTACTATTCCTCATTACTTATCATTTTAATCAGAGACTTACAAATACACTGCGTACGAACTACTTTTAATATTGCGTc             <  2:252577/141‑1 (MQ=255)                                                                  ccATTATTTGCTCTAAGTTAAATAAATTACTTATTTATATTTTTTTAAATTTCAAAATTAATGTACTATTCCTCATTACTTATCATTTTAATCAGAGACTTACAAATACACTGCGTACGAACTACTTTTAATATTGCGTCa            <  2:122464/141‑1 (MQ=255)                                                                      tattTGCTCTAAGTTAAATAAATTACTTATTTATATTTTTTTAAATTTCAAAATTAATGTACTATTCCTCATTACTTATCATTTTAATCAGAGACTTACAAATACACTGCGTACGAACTACTTTTAATATTGCGTCactaa        <  1:36981/141‑1 (MQ=255)                                                                            ctctAAGTTAAATAAATTACTTATTTATATTTTTTTAAATTTCAAAATTAATGTACTATTCCTCATTACTTATCATTTTAATCAGAGACTTACAAATACACTGCGTACGAACTACTTTTAATATTGCGTCACTAACTAACa  >  1:140943/1‑141 (MQ=255)                                                                                                         |                                                                                                                CCCCTATCTTTTTATATATGAAGCATGAATCCCCATATTATTTTACCTATTATTTCACTACGATACCATTATTTGCTCTAAGTTAAATAAATTACTTATTTATA‑TTTTTTAAATTTCAAAATTAATGTACTATTCCTCATTACTTATCATTTTAATCAGAGACTTACAAATACACTGCGTACGAACTACTTTTAATATTGCGTCACTAACTAACA  >  USA300TCH1516_ALE/2246988‑2247202

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑