Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,891,750	G→A	T53M (ACG→ATG)	rot ←	HTH‑type transcriptional regulator rot

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,891,750	0	G	A	100.0%	92.7 / NA	27	T53M (ACG→ATG)	rot	HTH‑type transcriptional regulator rot
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (15/12);  total (15/12)

TTGAAATGAATAATAACTGTTCTTTCATCGTCAACAGGACGCTCTTTGTAAATCCATTCTAATTCAACTAAATTATTATACGTTCTCGTACGCTTATACGGTTTAACTTCAACAAATCTGTCCATTTCTTTAAGCGTCATAGAACCTTTTTGCCATAAAGTTAGTAAAATTAAAATTTCTTCTCTAGACATTTTGTATTCGCTTTCAATCTCGCTGAAAATTGAGTTAATGTCACCCAAAAGTGTTTCTAATTGCAAAATTCCAAATACAGTG  >  USA300TCH1516_ALE/1891615‑1891887                                                                                                                                        |                                                                                                                                          ttGAAATGAATAATAACTGTTCTTTCATCGTCAACAGGACGCTCTTTGTAAATCCATTCTAATTCAACTAAATTATTATACGTTCTCGTACGCTTATACGGTTTAACTTCAACAAATCTGTCCATTTCTTTAAGCATCATa                                                                                                                                      <  2:161182/141‑1 (MQ=255)    aaaTGAATAATAACTGTTCTTTCATCGTCAACAGGACGCTCTTTGTAAATCCATTCTAATTCAACTAAATTATTATACGTTCTCGTACGCTTATACGGTTTAACTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGaa                                                                                                                                   >  1:289198/1‑141 (MQ=255)    aaaTGAATAATAACTGTTCTTTCATCGTCAACAGGACGCTCTTTGTAAATCCATTCTAATTCAACTAAATTATTATACGTTCTCGTACGCTTATACGGTTTAACTTCAACAAATCTGTCCATTTCATTAAGCATCATAGaa                                                                                                                                   >  1:253377/1‑141 (MQ=255)          ataataACTGTTCTTTCATCGTCAACAGGACGCTCTTTGTAAATCCATTCTACTTCAGCTAAATTATTATACGTTCTCGTACGCTTATACGGTTTAACTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGAACCtttt                                                                                                                             <  1:295224/141‑1 (MQ=255)                    ttCTTTCATCGTCAACAGGACGCTCTTTGTAAATCCATTCTAATTCAACTAAATTATTATACGTTCTCGTACGCTTATACGGTTTAACTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGAACCTTTTTGCCATAAAg                                                                                                                   <  1:143225/141‑1 (MQ=255)                                  aCAGGACGCTCTTTGTAAATCCATTCTAATTCAACTAAATTATTATACGTTCTCGTACGCTTATACGGTTTTACTTCAACAAATCTGTCCATTTCTTTAATCATCATAGAACCTTTTTGCCATAAAGTTAGtaaaattaaa                                                                                                     >  1:136322/1‑141 (MQ=255)                                  aCAGGACGCTCTTTGTAAATCCATTCTAATTCAACTAAATTATTATACGTTCTCGTACGCTTATACGGTTTAACTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGAACCTTTTTGCCATAAAGTTAGtaaaattaaa                                                                                                     >  1:118210/1‑141 (MQ=255)                                  aCAGGACGCTCTTTGTAAATCCATTCTAATTCAACTAAATTATTATACGTTCTCGTACGCTTATACGGTTTAACTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGAACCTTTTTGCCATAAAGTTAGtaaaattaaa                                                                                                     >  1:156377/1‑141 (MQ=255)                                  aCAGGACGCTCTTTGTAAATCCATTCTAATTCAACTAAATTATTATACGTTCTCGTACGCTTATACGGTTTAACTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGAACCTTTTTGCCATAAAGTTAGtaaaattaaa                                                                                                     >  1:103049/1‑141 (MQ=255)                                        cGCTCTTTGTAAATCCATTCTAATTCAACTAAATTATTATACGTTCTCGTACGCTTATACGGTTTAACTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGAACCTTTTTGCCATAACGCTATTAAAATTAAAATttct                                                                                               >  1:2512/1‑141 (MQ=255)                                        cGCTCTTTGTAAATCCATTCTAATTCAACTAAATTATTATACGTTCTCGTACGCTTATACGGTTTAACTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGAACCTTTTTGCCATAAAGTTAGTAAAATTAAAATttct                                                                                               >  1:57719/1‑141 (MQ=255)                                              ttGTAAATCCATTCTAATTCAACTAAATTATTATACGTTCTCGTACGCTTATACGGTTTAACTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGAACCTTTTTGCCATAAAGTTAGTAAAATTAAAATTTCTTCTCTa                                                                                         <  1:254279/141‑1 (MQ=255)                                              ttGTAAATCCATTCTAATTCAACTAAATTATTATACGTTCTCGTACGCTTATACGGTTTAACTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGAACCTTTTTGCCATAAAGTTAGTAAAATTAAAATTTCTTCTCTa                                                                                         <  1:305028/141‑1 (MQ=255)                                                         ttCTAATTCAACTAAATTATTATACGTTCTCGTACGCTTATACGGTTTAACTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGAACCTTTTTGCCATAAAGTTAGTAAAATTAAAATTTCTTCTCTAGACATTTTGTa                                                                              <  2:124838/141‑1 (MQ=255)                                                                  aaCTAAATTATTATACGTTCTCGTACGCTTATACGGTTTAACTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGAACCTTTTTGCCATAAAGTTAGTAAAATTAAAATTTCTTCTCTAGACATTTTGTATTCGCTTTc                                                                     <  2:124298/141‑1 (MQ=255)                                                                           attatACGTTCTCGTACGCTTATACGGTTTAACTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGAACCTTTTTGCCATAAAGTTAGTAAAATTAAAATTTCTTCTCTAGACATTTTGTATTCGCTTTCAATCTCGCt                                                            <  2:77788/141‑1 (MQ=255)                                                                           attatACGTTCTCGTACGCTTATACGGTTTAACTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGAACCTTTTTGCCATAAAGTTAGTAAAATTAAAATTTCTTCTCTAGACATTTTGTATTCGCTTTCAATCTCGCt                                                            <  2:98304/141‑1 (MQ=255)                                                                                         tACGCTTATACGGTTTAACTTCACTAAATCTGTCCATTTCTTTAAGCATCATAGAACCTTTTTGCCATAAAGTTAGTAAAATTACAATTTCTTCTCCTGACATTTTGTCTTCGCTTTCAATCTCGCTGAAAATTGAGTTaa                                              <  2:257931/141‑1 (MQ=255)                                                                                         tACGCTTATACGGTTTAACTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGAACCTTTTTGCCATAAAGTTAGTAAAATTAAAATTTCTTCTCTAGACATTTTGTATTCGCTTTCAATCTCGCTGAAAATTGAGTTaa                                              <  2:25023/141‑1 (MQ=255)                                                                                           cGCTTATACGGTTTAACTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGAACCTTTTTGCCATAAAGTTAGTAAAATTAAAATTTCTTCTCTAGACATTTTGTATTCGCTTTCAATCTCGCTGAAAATTGAGTTAATg                                            >  2:255528/1‑141 (MQ=255)                                                                                                      tttAACTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGAACCTTTTTGCCATAAAGTTAGTAAAATTAAAATTTCTTCTCTAGACATTTTGTATTCGCTTTCAATCTCGCTGAAAATTGAGTTAATGTCACCCAAAAg                                 <  2:73217/141‑1 (MQ=255)                                                                                                          aCTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGAACCTTTTTGCCATAAAGTTAGTAAAATTAAAATTTCTTCTCTAGACATTTTGTATTCGCTTTCAATCTCGCTGAAAATTGAGTTAATGTCACCCAAAAGTGtt                             >  1:235148/1‑141 (MQ=255)                                                                                                          aCTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGAACCTTTTTGCCATAAAGTTAGTAAAATTAAAATTTCTTCTCTAGACATTTTGTATTCGCTTTCAATCTCGCTGAAAATTGAGTTAATGTCACCCAAAAGTGtt                             >  1:63741/1‑141 (MQ=255)                                                                                                          aCTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGAACCTTTTTGCCATAAAGTTAGTAAAATTAAAATTTCTTCTCTAGACATTTTGTATTCGCTTTCAATCTCGCTGAAAATTGAGTTAATGTCACCCAAAAGTGtt                             >  1:225685/1‑141 (MQ=255)                                                                                                          aCTTCAACAAATCTGTCCATTTCTTTAAGCATCATAGAACCTTTTTGCCATAAAGTTAGTAAAATTAAAATTTCTTCTCTAGACATTTTGTATTCGCTTTCAATCTCGCTGAAAATTGAGTTAATGTCACCCAAAAGTGtt                             >  2:170482/1‑141 (MQ=255)                                                                                                                           cATTTCTTTAAGCATCATAGAACCTTTTTGCCATAAAGTTAGTAAAATTAAAATTTCTTCTCTAGACATTTTGTATTCGCTTTCAATCTCGCTGAAAATTGAGTTAATGTCACCCAAAAGTGTTTCTAATTGCAAAATTcc            >  2:302711/1‑141 (MQ=255)                                                                                                                                     aGCATCATAGAACCTTTTTGCCATAAAGTTAGTAAAATTAAAATTTCTTCTCTAGACATTTTGTATTCGCTTTCAATCTCGCTGAAAATTGAGTTAATGTCACCCAAAAGTGTTTCTAATTGCAAAATTCCAAATACAgtg  >  1:58456/1‑141 (MQ=255)                                                                                                                                        |                                                                                                                                          TTGAAATGAATAATAACTGTTCTTTCATCGTCAACAGGACGCTCTTTGTAAATCCATTCTAATTCAACTAAATTATTATACGTTCTCGTACGCTTATACGGTTTAACTTCAACAAATCTGTCCATTTCTTTAAGCGTCATAGAACCTTTTTGCCATAAAGTTAGTAAAATTAAAATTTCTTCTCTAGACATTTTGTATTCGCTTTCAATCTCGCTGAAAATTGAGTTAATGTCACCCAAAAGTGTTTCTAATTGCAAAATTCCAAATACAGTG  >  USA300TCH1516_ALE/1891615‑1891887

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: ‑