Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	749,249	C→T	S59S (AGC→AGT)	setC →	Sugar efflux transporter C

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	749,249	0	C	T	100.0%	131.7 / NA	40	S59S (AGC→AGT)	setC	Sugar efflux transporter C
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (18/22);  total (18/22)

ATTATAAACTCTTTGTTGCTAATATGTTTCTACTAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGCCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGTTTTTCAATATACTTTTTTGTAGATACAATCTGGTTATTCATATT  >  USA300TCH1516_ALE/749107‑749392                                                                                                                                               |                                                                                                                                                aTTATAAACTCTTTGTTGCTAATATGTTGCTACTAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGtt                                                                                                                                            <  4:340637/148‑1 (MQ=255)  ttATAAACTCTTTGTTGCTAATATGTTTCTACTAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTTTTTTTTTTTATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGttt                                                                                                                                           >  4:412542/1‑148 (MQ=255)  ttATAAACTCTTTGTTGCTAATATGTTTCTACTAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGttt                                                                                                                                           <  3:112790/148‑1 (MQ=255)  ttATAAACTCTTTGTTGCTAATATGTTTCTACTAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGttt                                                                                                                                           <  3:139993/148‑1 (MQ=255)    ataAACTCGTGGTTGCTAATATGTTTCTACGAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACGAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTAc                                                                                                                                         <  4:233387/148‑1 (MQ=255)           ctTTGTTGCTAATATGTTTCTACTAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAAt                                                                                                                                  >  3:164586/1‑148 (MQ=255)           ctTTGTTGCTAATATGTTTCTACTAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAAt                                                                                                                                  >  4:14778/1‑148 (MQ=255)           ctTTGTTGCTAATATGTTTCTACTAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAAt                                                                                                                                  >  4:108554/1‑148 (MQ=255)             ttgttgCTAATATGTTTCTACTAGGTCTGGGTATTGCCGTTACGGTCCCACATCTTGTTCATTTTGCCCCTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTc                                                                                                                                <  3:104124/148‑1 (MQ=255)                 tgCTAATATGTTTCTACTAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTaaa                                                                                                                                   <  1:62045/141‑1 (MQ=255)                 tgCTAATATGTTTCTACTAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAatt                                                                                                                            <  3:57550/148‑1 (MQ=255)                  gCTAATATGTTTCTACTAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTAAGTTTACAGGAAAt                                                                                                                                  >  2:35010/1‑141 (MQ=255)                         tGTTTCTACTAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGTATTTTAATTTTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTCCAGTAAATTCAATTATTGCTAg                                                                                                                    >  4:138288/1‑148 (MQ=255)                         tGTTTCTACTAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAg                                                                                                                    >  4:39248/1‑148 (MQ=255)                                       aTGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGc                                                                                                      <  3:24145/148‑1 (MQ=255)                                       aTGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGc                                                                                                      >  3:328461/1‑148 (MQ=255)                                       aTGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGc                                                                                                      <  3:332829/148‑1 (MQ=255)                                       aTGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGc                                                                                                      <  3:24139/148‑1 (MQ=255)                                       aTGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATCACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGc                                                                                                      >  3:53903/1‑148 (MQ=255)                                                            ccATATCTTGTTCTTTTTGCAACTAAAGATCTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAatta                                                                                 <  3:173252/148‑1 (MQ=255)                                                                    tGTTCTTTTTGCAATTAAAGATTTAGGTATGACAACAAAGCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTTGGATTTGCATCACTTTAATAGAAAAattat                                                                                <  2:40258/141‑1 (MQ=255)                                                                    tGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAattattattatt                                                                         <  4:147028/148‑1 (MQ=255)                                                                     gTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATtc                                                                        >  4:398832/1‑148 (MQ=255)                                                                      ttCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATtct                                                                       >  3:278130/1‑148 (MQ=255)                                                                      ttCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATtct                                                                       >  3:276069/1‑148 (MQ=255)                                                                               cAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCg                                                                     >  2:9730/1‑141 (MQ=255)                                                                                 aCTAAAGATTTAGGTAGGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTaa                                                            >  3:365959/1‑148 (MQ=255)                                                                                  cTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAAt                                                           <  3:167294/148‑1 (MQ=255)                                                                                                  gACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGtttt                                           <  3:245706/148‑1 (MQ=255)                                                                                                  gACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGtttt                                           <  4:353640/148‑1 (MQ=255)                                                                                                             aGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGCTTTTCGGATACGCATCACTTTAATAGAAATATTATTATTATTCTCGCATTATTAGTGGGTGCGCTTGGTTTTTCAATATACtt                                <  4:194979/148‑1 (MQ=255)                                                                                                              gTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGTTTTTCAATATACttt                               >  3:370671/1‑148 (MQ=255)                                                                                                               tATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGTTTTTCAATATACtttt                              <  3:412542/148‑1 (MQ=255)                                                                                                                      tACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGTTTTTCAATATACTTTTTTGTAGa                       >  3:374764/1‑148 (MQ=255)                                                                                                                               cATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGTTTTTCAATATACTTTTTTGTAGATACAATCTg              <  3:414175/148‑1 (MQ=255)                                                                                                                                aTCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGTTTTTCAATATACTTTTTTGTAGATACAATCTgg             >  3:128670/1‑148 (MQ=255)                                                                                                                                 tCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGTTTTTCAATATACTTTTTTGTAGATACAATCTGGt            >  3:249253/1‑148 (MQ=255)                                                                                                                                 tCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGTTTTTCAATATACTTTTTTGTAGATACAATCTGGt            <  3:398832/148‑1 (MQ=255)                                                                                                                                        cGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGTTTTTCAATATACTTTTTTGTAGATACAATCTGGTTATTCat     <  4:32812/148‑1 (MQ=255)                                                                                                                                           ttAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGTTTTTCAATATACTTTTTTGTAGATACAATCTGGTTATTCATAtt  <  4:325470/148‑1 (MQ=255)                                                                                                                                               |                                                                                                                                                ATTATAAACTCTTTGTTGCTAATATGTTTCTACTAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGCCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGTTTTTCAATATACTTTTTTGTAGATACAATCTGGTTATTCATATT  >  USA300TCH1516_ALE/749107‑749392

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑