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%	62.8 / NA	19	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 (11/8);  total (11/8)

ATATTCACCAGACTTAAAGCCTATCCCAGTGGGCGTAATTGTTGCAGACAGTCTGGACATGGACAGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACTGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCGTGTTTTTCGACGACGGTAATTCAATGCGGAAACAAACGTCTTGCCCGCTCTCGTCGACCAGATACAGTTCCCC  >  NZ_CP009273/2682864‑2683110                                                                                                                  |                                                                                                                                      atatTCACCAGACTTAAAGCCTATCCCAGTGGGCGTAATTGTTGCAGACAGTCTGGACATGGACAGCGCGGAGAAACCGGAGCGTACATATCGTACGTGGAGATTTCGAGCACCGCCCGGGGCCGAACTGACaaataaa                                                                                                              <  2:201016/139‑1 (MQ=255)         cAGACTTAAAGCCTATCCCAGTGGGCGTAATTGTTGCAGACAGTCTGGACATGGACAGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTg                                                                                                      <  1:287450/139‑1 (MQ=255)                      tATCCCAGTGGGCGTAATTGTTGCAGACAGTCTGGACATGGACAGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTg                                                                                         >  1:330183/1‑139 (MQ=255)                        tCCCAGTGGGCGTAATTGTTGCAGACAGTCTGGACATGGACAGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGt                                                                                        <  1:376257/138‑1 (MQ=255)                        tCCCAGTGGGCGTAATTGTTGCAGACAGTCTGGACATGGACAGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGt                                                                                        >  2:436574/1‑138 (MQ=255)                                  cGTAATTGTTGCAGACAGTCTGGACATGGACAGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTAttt                                                                             >  2:199862/1‑139 (MQ=255)                                               gACAGTCTGGACATGGACAGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCGTGTTTTTcgac                                                                >  1:445300/1‑139 (MQ=255)                                                      tggacatggacaGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCGTGTTTTTCGACGACGGt                                                          >  2:444678/1‑138 (MQ=255)                                                              gacaGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTgatagga                                                                                                <  1:57458/92‑1 (MQ=255)                                                              gacaGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTgatagga                                                                                                >  2:57458/1‑92 (MQ=255)                                                              gacaGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCGTGTTTTTCGACGACGGTAATTCAATg                                                 >  2:95844/1‑139 (MQ=255)                                                                     cgGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCGTGTTTTTCGACGACGGTAATTCAATGCGGaaa                                           >  1:481384/1‑138 (MQ=255)                                                                                gAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCGTGTTTTTCGACGACGGTAATTCAATGCGGAAACAAACGTCTTGc                               >  1:441614/1‑139 (MQ=255)                                                                                    gTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCGTGTTTTTCGACGACGGTAATTCAATGCGGAAACAAACGTCTTGCCCGc                           <  1:199862/139‑1 (MQ=255)                                                                                           tCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCGTGTTTTTCGACGACGGTAATTCAATGCGGAAACAAACGTCTTGCCCGCTCtcgt                     <  1:436574/138‑1 (MQ=255)                                                                                               aCGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCGTGTTTTTCGACGACGGTAATTCAATGCGGAAACAAACGTCTTGCCCGCTCTCGTCGAc                 >  1:58289/1‑138 (MQ=255)                                                                                               aCGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCGTGTTTTTCGACGACGGTAATTCAATGCGGAAACAAACGTCTTGCCCGCTCTCGTCGAc                 >  1:548486/1‑138 (MQ=255)                                                                                                  tGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCGTGTTTTTCGACGACGGTAATTCAATGCGGAAACAAACGTCTTGCCCGCTCTCGTCGACCAGa             <  2:548486/139‑1 (MQ=255)                                                                                                             aGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCGTGTTTTTCGACGACGGTAATTCAATGCGGAAACAAACGTCTTGCCCGCTCTCGTCGACCAGATACAGTTcccc  <  2:441614/139‑1 (MQ=255)                                                                                                                  |                                                                                                                                      ATATTCACCAGACTTAAAGCCTATCCCAGTGGGCGTAATTGTTGCAGACAGTCTGGACATGGACAGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACTGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCGTGTTTTTCGACGACGGTAATTCAATGCGGAAACAAACGTCTTGCCCGCTCTCGTCGACCAGATACAGTTCCCC  >  NZ_CP009273/2682864‑2683110

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑