Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,004,062	(A)8→7	intergenic (‑2285/+99)	USA300TCH1516_01884 ← / ← perR	tRNA‑Ile/Peroxide‑responsive repressor PerR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,004,055	0	A	.	100.0%	152.0 / NA	33	intergenic (‑2278/+106)	USA300TCH1516_01884/perR	tRNA‑Ile/Peroxide‑responsive repressor PerR
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (22/11);  total (22/11)

TCACTTTATGGATAGTTATTTAGTAGACCTTCGTTTGAATATTTTTATGTTTATTTATAAAGGATACTAGTTATTAGTTAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCATAAAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTAATTTGTCATACTACCAAAGTTAAATTATTTATCTTGGCATTCTTTACAAACTCCATA  >  USA300TCH1516_ALE/2003914‑2004193                                                                                                                                              |                                                                                                                                           tCACTTTATGTATAGTTATTTAGTAGACCTTCGTTTGAATATTTTTATGTTTATTTATAAAGGATACTAGTTATTAGTTAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCATaaaaaaa                                                                                                                                      <  4:347502/148‑1 (MQ=255)                 tATTTAGTAGACCTTCGTTTGAATATTTTTATGTTTATTTATAAAGGATACTAGTTATTAGTTAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCAt                                                                                                                     >  3:238579/1‑148 (MQ=255)                 tATTTAGTAGACCTTCGTTTGAATATTTTTATGTTTATTTATAAAGGATACTAGTTATTAGTTAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCAt                                                                                                                     >  3:108446/1‑148 (MQ=255)                  aTTTAGTAGACCTTCGTTTGAATATTTTTATGTTTATTTATAAAGGATACTAGTTATTAGTTAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATg                                                                                                                    >  4:54575/1‑148 (MQ=255)                        tagACCTTCGTTTGAATATTTTTATGTTTATTTATAAAGGATACTAGTTATTAGTTAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCAt                                                                                                                     >  2:61676/1‑141 (MQ=255)                         agACCTTCGTTTGAATATTTTTATGTTTATTTATAAAGGATACTAGTTATTAGTTAATACCACTTCCGTAGTTAGAATCTTCTTTTCTTCACTTTAAATATTTNTCAGAATAAGCAT‑CAACAAAGTTAAACAAATTCCacg                                                                                                                    >  2:48688/1‑139 (MQ=255)                             cTTCGTTTGAATATTTTTATGTTTATTTATAAAGGATACTAGTTATTAGTTAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAActt                                                                                                         >  3:22552/1‑148 (MQ=255)                                 gTTTGAATATTTTTATGTTTATTTATAAAGGATACTAGTTATTAGTTAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTa                                                                                                     <  4:238525/148‑1 (MQ=255)                                      aaTATTTTTATGTTTACTTATAAAGGATACTAGTTATTAGTTAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAatat                                                                                                <  4:16808/148‑1 (MQ=255)                                             ttATGTTTATTTATAAAGGATACTAGTTATTAGTTAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAatat                                                                                                <  2:36379/141‑1 (MQ=255)                                             ttATGTTTATTTATAAAGGATACTAGTTATTAGTTAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGctt                                                                                         <  4:225379/148‑1 (MQ=255)                                             ttATGTTTATTTATAAAGGATACTAGTTATTAGTTAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGctt                                                                                         <  4:190042/148‑1 (MQ=255)                                                    tatttatAAAGGATACTAGTTATTAGTTAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTtata                                                                                  >  3:69500/1‑148 (MQ=255)                                                         ataAAGGATACTAGTTATTAGTTAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGcttactta                                                                                    <  1:52963/141‑1 (MQ=255)                                                          taAAGGATACTAGTTATTAGTTAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTtat                                                                                   >  2:35790/1‑141 (MQ=255)                                                                           taGTTAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTa                                                           >  4:321946/1‑148 (MQ=255)                                                                            aGTTAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTaa                                                          <  4:267480/148‑1 (MQ=255)                                                                               tAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTAAttt                                                       >  4:289974/1‑148 (MQ=255)                                                                               tAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTAAttt                                                       >  4:260777/1‑148 (MQ=255)                                                                               tAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTAAttt                                                       >  3:132705/1‑148 (MQ=255)                                                                                   aCCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTAATTTGTCa                                                   >  3:9634/1‑148 (MQ=255)                                                                                    ccACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTAATTTGTCAt                                                  >  3:354165/1‑148 (MQ=255)                                                                                          ccGTAGTTAGAATATTCTTTTCTTCAATTTACATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTAATTTGTCa                                                   >  1:43649/1‑141 (MQ=255)                                                                                          ccGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTAATTTGTCa                                                   >  1:18285/1‑141 (MQ=255)                                                                                                         tcttttcttCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTAATTTGTCATACTACCAAAGTTAAAttattt                             <  3:387803/148‑1 (MQ=255)                                                                                                          cttttcttCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTAATTTGTCATACTACCAAAGTTAAAttatttt                            >  4:203281/1‑147 (MQ=255)                                                                                                          cttttcttCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTGTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTAATTTGTCATACTACCAAAGTTAAAttattta                            >  4:246810/1‑148 (MQ=255)                                                                                                           ttttcttCAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTAATTTGTCATACTACCAAAGTTAAAttatttat                           <  4:22552/148‑1 (MQ=255)                                                                                                                  cAATTTAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTAATTTGTCATACTACCAAAGTTAAATTATTTATCTTGGCa                    >  3:354386/1‑148 (MQ=255)                                                                                                                       tAAATATTTTTCAGAATAAGCNT‑NAAANAAGTTAAACAACCTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTAATTTGTCATACTACCAAAGTTAAACTATTTATCTTgg                      <  1:48688/141‑1 (MQ=255)                                                                                                                       tAAATATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTAATTTGTCATACTACCAAAGTTAAATTATTTATCTTGGCATTCtt               <  3:54575/148‑1 (MQ=255)                                                                                                                         aaTATTTTTCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACATCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTAATTTGTCATACTACCAAAGTTAAATAATTTATCTTGGCa                    >  1:3285/1‑141 (MQ=255)                                                                                                                               tttCAGAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTAATTTGTCATACTACCAAAGTTAACTTATTTATCTTGGCATTCttt              <  1:35790/141‑1 (MQ=255)                                                                                                                                    gAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTAATTTGTCATACTACCAAAGTTAAATTATTTATCTTGGCATTCTTTACAAACTCCATa  >  4:76021/1‑148 (MQ=255)                                                                                                                                    gAATAAGCAT‑AAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTAATTTGTCATACTACCAAAGTTAAATTATTTATCTTGGCATTCTTTACAAACTCCATa  >  4:84022/1‑148 (MQ=255)                                                                                                                                              |                                                                                                                                           TCACTTTATGGATAGTTATTTAGTAGACCTTCGTTTGAATATTTTTATGTTTATTTATAAAGGATACTAGTTATTAGTTAATACCACTTCCGTAGTTAGAATATTCTTTTCTTCAATTTAAATATTTTTCAGAATAAGCATAAAAAAAAGTTAAACAACTTTCATGTCGTTTAACTTCTTAAATATTACGCTTACTTATATGAAGTAAGCTAACGCTTTTTTAATTTGTCATACTACCAAAGTTAAATTATTTATCTTGGCATTCTTTACAAACTCCATA  >  USA300TCH1516_ALE/2003914‑2004193

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