Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,272,733	C→T	intergenic (‑339/‑342)	glmS ← / → mtlA	Glutamine‑‑fructose‑6‑phosphate aminotransferase [isomerizing]/PTS system mannitol‑specific EIICB component

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,272,733	0	C	T	100.0%	107.9 / NA	31	intergenic (‑339/‑342)	glmS/mtlA	Glutamine‑‑fructose‑6‑phosphate aminotransferase [isomerizing]/PTS system mannitol‑specific EIICB component
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (15/16);  total (15/16)

CGATCTTATTAACTTTGTCCATTAAGTCACCCTAATGTTTTACTTAATAAGCTAACGAATGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGCACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTCAAATACAAATATTTATTTGCACAGGCGCTTTAACTGTACTGCCGAACTTTCCCCCTTTCCATTAATCATTATTGTACAACGGTGTTGTT  >  USA300TCH1516_ALE/2272602‑2272861                                                                                                                                    |                                                                                                                                 cGATCTTATTAACTTTGTCCATTAAGTCACCCTAATGTTTTACTTAATAAGCTAACGAATGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATaa                                                                                                                         <  1:50927/141‑1 (MQ=255)    tCTTATTAACTTTGTCCATTAAGTCACCCTAATGTTTTACTTAATAAGCTAACGAATGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAGTACATATATTGTACTCTATAAAGGCCACTCa                                                                                                               >  4:4739/1‑148 (MQ=255)    tCTTATTAACTTTGTCCATTAAGTCACCCTAATGTTTTACTTAATAAGCTAACGAATGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCa                                                                                                               <  3:336023/148‑1 (MQ=255)    tCTTATTAACTTTGTCCATTAAGTCACCCTAATGTTTTACTTAATAAGCTAACGAATGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCa                                                                                                               <  3:178669/148‑1 (MQ=255)    tCTTATTAACTTTGTCCATTAAGTCACCCTAATGTTTTACTTAATAAGCTAACGAATGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCa                                                                                                               >  4:362365/1‑148 (MQ=255)    tCTTATTAACTTTCTCCATTAAGTCACCCTAATGTTTTACTTAATAAGCTAACGAATGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCa                                                                                                               <  3:90782/148‑1 (MQ=255)             cTTTGTCCATTAAGTCACCCTAATGTTTTACTTAATAAGCTAACGAATGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAAc                                                                                                      >  3:88455/1‑148 (MQ=255)                  tCCATTAAGTCACCCTAATGTTTTACTTAATAAGCTAACGAATGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTa                                                                                                 >  4:195301/1‑148 (MQ=255)                        aaGTCACCCTAATGTTTTACTTAATAAGCTAACGAATGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTc                                                                                           <  3:77869/148‑1 (MQ=255)                           tCACCCTAATGTTTTACTTAATAAGCTAACGAATGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTcaaa                                                                                        <  3:129707/148‑1 (MQ=255)                              cccTAATGTTTTACTTAATAAGCTAACGAATGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTcaaatac                                                                                     >  3:292592/1‑148 (MQ=255)                                      ttttACTTAATAAGCTAACGAATGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTCAAATACAAAtattt                                                                             <  4:259242/148‑1 (MQ=255)                                      ttttACTTAATAAGCTAACGAATGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTCAAATACAAAtattt                                                                             <  3:228609/148‑1 (MQ=255)                                      ttgtACTTAATAAGCTAGCGAATGGGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTCTCCTCCTCGTCTACAAATTCATATTTTGTACTCTATAAAGGCCACTCCTATATTAACCTTTAATCTTCAAATACAAAtattt                                                                             <  4:386187/145‑1 (MQ=255)                                       tttACTTAATAAGCTAACGAATGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTCAAATACAAAtattta                                                                            >  3:43820/1‑148 (MQ=255)                                                 aaGCTAACGAATGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTCAAATACAAATATTTATTTGCACAgg                                                                  <  3:263879/148‑1 (MQ=255)                                                   gCTAACGAATGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTCAAATACAAATATTTATTTGCACAGgcg                                                                >  4:64785/1‑148 (MQ=255)                                                     tAACGAATGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATCTTGTACTCTATAAAGGCCACTCATCTATTAACCTTTAATCTTCACATACACATAGTCATTTGccc                                                                     >  2:14964/1‑139 (MQ=255)                                                          aaTGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTCAAATACAAATATTTATTTGCACAGgcg                                                                >  2:21147/1‑141 (MQ=255)                                                           aTGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTCAAATACAAATATTTATTTGCACAGgcgc                                                               <  1:5667/141‑1 (MQ=255)                                                           aTGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTCAAATACAAATATTTATTTGCACAGgcgc                                                               <  1:5683/141‑1 (MQ=255)                                                           aTGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTCAAATACAAATATTTATTTGCACAGGCGCTTTAACt                                                        >  3:294393/1‑148 (MQ=255)                                                           aTGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTCAAATACAAATATTTATTTGCACAGGCGCTTTAACt                                                        <  3:10366/148‑1 (MQ=255)                                                               gCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTCAAATACAAATATTTATTTGCACAGGCGCTTTAACTGTAc                                                    <  4:52940/148‑1 (MQ=255)                                                                  acaTCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTCAAATACAAATATTTATTTGCACAGGCGCTTTAACTGTACTGc                                                 >  4:340426/1‑148 (MQ=255)                                                                  acaTCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTCAAATACAAATATTTATTTGCACAGGCGCTTTAACTGTACTGc                                                 >  3:163891/1‑148 (MQ=255)                                                                         ggATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTCAAATACAAATATTTATTTGCACAGGCGCTTTAACTGTACTGc                                                 >  2:3595/1‑141 (MQ=255)                                                                                  ccgccgATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTCAAATACAAATATTTATTTGCACAGGCGCTTTAACTGTACTGCCGAACTTTCCCCCttt                                 <  4:65887/148‑1 (MQ=255)                                                                                            aTTCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTCAAATACAAATATTTATTTGCACAGGCGCTTTAACTGTACTGCCGAACTTTCCCCCTTTCCATTAATCa                       <  3:362365/148‑1 (MQ=255)                                                                                              tCGATCACTATCCTCCTCGTCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTCAAATACAAATATTTATTTGCACAGGCGCTTTAACTGTACTGCCGAACTTTCCCCCTTTCCATCAATCatt                     >  3:190154/1‑148 (MQ=255)                                                                                                                 tCTACAAATACATATATTGTACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTCAAATACAAATATTTATTTGCACAGGCGCTTTAACTGTACTGCCGAACTTTCCCCCTTTCCATTAATCATTATTGTACAACGGTgttgtt  >  4:280231/1‑148 (MQ=255)                                                                                                                                    |                                                                                                                                 CGATCTTATTAACTTTGTCCATTAAGTCACCCTAATGTTTTACTTAATAAGCTAACGAATGAGCCACATCCGGGATAGCATCCGCCGATCTATTCGATCACTATCCTCCTCGTCTACAAATACATATATTGCACTCTATAAAGGCCACTCATATATTAACCTTTAATCTTCAAATACAAATATTTATTTGCACAGGCGCTTTAACTGTACTGCCGAACTTTCCCCCTTTCCATTAATCATTATTGTACAACGGTGTTGTT  >  USA300TCH1516_ALE/2272602‑2272861

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