Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	2,682,977	T→C	intergenic (‑112/+53)	qseG ← / ← qseE	two‑component system QseEF‑associated lipoprotein QseG/two component system sensor histidine kinase QseE/GlrK

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,682,977	0	T	C	100.0%	96.9 / NA	27	intergenic (‑112/+53)	qseG/qseE	two‑component system QseEF‑associated lipoprotein QseG/two component system sensor histidine kinase QseE/GlrK
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (17/10);  total (17/10)

CGTTGAAAAATGTGTCGCATATTCACCAGACTTAAAGCCTATCCCAGTGGGCGTAATTGTTGCAGACAGTCTGGACATGGACAGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACTGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCGTGTTTTTCGACGACGGTAATTCAATGCGGAAACAAACGTCTTGCCCGCTCTCGTCGACCAGATA  >  NZ_CP009273/2682846‑2683101                                                                                                                                    |                                                                                                                             cGTTGAAAAATGTGTCGCATATTCACCAGACTTAAAGCCTATCCCAGTGGGCGTAATTGTTGCAGACAGTCTGGACATGGACAGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCggg                                                                                                                       >  2:91543/1‑139 (MQ=255)  gTTGAAAAATGTGTCGCATATTCACCAGACTTAAAGCCTATCCCAGTGGGCGTAATTGATGCAGACAGGCTGGACATGGACAGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCgggg                                                                                                                      >  1:256890/1‑139 (MQ=255)                          ccAGACTTAAAGCCTATCCCAGTGGGCGTAATTGTTGCAGACAGTCTGGACATGGACAGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCt                                                                                              <  2:395299/139‑1 (MQ=255)                            aGACTTAAAGCCTATCCCAGTGGGCGTAATTGTTGCAGACAGTCTGGACATGGACAGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTga                                                                                            <  1:194150/139‑1 (MQ=255)                                   aaGCCTATCCCAGTGGGCGTAATTGTTGCAGACAGTCTGGACATGGACAGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTgatagga                                                                                       >  2:62177/1‑137 (MQ=255)                                    aGCCTATCCCAGTGGGCGTAATTGTTGCAGACAGTCTGGACATGGACAGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTgataggatag                                                                                    <  1:76235/139‑1 (MQ=255)                                        tATCCCAGTGGGCGTAATTGTTGCAGACAGTCTGGACATGGACAGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTg                                                                                >  2:99336/1‑139 (MQ=255)                                                tGGGCGTAATTGTTGCAGACAGTCTGGACATGGACAGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCat                                                                         >  2:145441/1‑138 (MQ=255)                                                                 gACAGTCTGGACATGGACAGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCGTGTTTTTcgac                                                       <  2:173975/139‑1 (MQ=255)                                                                   cAGTCTGGACATGGACAGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCGTGTTTTTcgacga                                                     <  1:91543/139‑1 (MQ=255)                                                                    aGTCTGGACATGGACAGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCGTGTTTTTCgacgac                                                    >  2:7606/1‑139 (MQ=255)                                                                      tCTGGACATGGACAGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCGTGTTTTTcgacga                                                     <  1:264028/136‑1 (MQ=255)                                                                      tCTGGACATGGACAGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCGTGTTTTTcgacga                                                     >  2:264028/1‑136 (MQ=255)                                                                      tCTGGACATGGACAGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCGTGTTTTTCGACGACgg                                                  >  1:253512/1‑139 (MQ=255)                                                                                gacaGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAg                                                                                                 >  1:267264/1‑82 (MQ=255)                                                                                gacaGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAg                                                                                                 <  2:267264/82‑1 (MQ=255)                                                                                gacaGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCGTGTTTTTCGACGACGGTAATTCAATg                                        >  1:178928/1‑139 (MQ=255)                                                                                     cgcgGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCGTGTTTTTCGACGACGGTAATTCAATGCGGa                                    >  2:204638/1‑138 (MQ=255)                                                                                                   aGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCGTGTTTTTCGACGACGGTAATTCAATGCGGAAACAAACGTCTTGcc                     <  1:145441/139‑1 (MQ=255)                                                                                                             tCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCGTGTTTTTCGACGACGGTAATTCAATGCGGAAACAAACGTCTTGCCCGCTCtcgt            <  1:306321/138‑1 (MQ=255)                                                                                                                 aCGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCGTGTTTTTCGACGACGGTAATTCAATGCGGAAACAAACGTCTTGCCCGCTCTCGTCGAc        >  2:373885/1‑138 (MQ=255)                                                                                                                  cGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCGTGTTTTTCGACGACGGTAATTCAATGCGGAAACAAACGTCTTGCCCGCTCTCGTCGAcc       <  1:373885/138‑1 (MQ=255)                                                                                                                  cGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCGTGTTTTTCGACGACGGTAATTCAATGCGGAAACAAACGTCTTGCCCGCTCTCGTCGAc        >  2:228922/1‑137 (MQ=255)                                                                                                                  cGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCGTGTTTTTCGACGACGGTAATTCAATGCGGAAACAAACGTCTTGCCCGCTCTCGTCGAc        >  2:337185/1‑137 (MQ=255)                                                                                                                  cGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCGTGTTTTTCGACGACGGTAATTCAATGCGGAAACAAACGTCTTGCCCGCTCTCGTCGAc        >  2:432769/1‑137 (MQ=255)                                                                                                                     gAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCGTGTTTTTCGACGACGGTAATTCAATGCGGAAACAAACGTCTTGCCCGCTCTCGTCGACCAGa    >  2:178672/1‑138 (MQ=255)                                                                                                                      aaGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCGTGTTTTTCGACGACGGTAATTCAATGCGGAAACAAACGTCTTGCCCGCTCTCGTCGACCAGATa  >  2:180391/1‑139 (MQ=255)                                                                                                                                    |                                                                                                                             CGTTGAAAAATGTGTCGCATATTCACCAGACTTAAAGCCTATCCCAGTGGGCGTAATTGTTGCAGACAGTCTGGACATGGACAGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACTGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCGTGTTTTTCGACGACGGTAATTCAATGCGGAAACAAACGTCTTGCCCGCTCTCGTCGACCAGATA  >  NZ_CP009273/2682846‑2683101

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑