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%	149.7 / NA	41	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 (24/17);  total (24/17)

AGTGGGCGTAATTGTTGCAGACAGTCTGGACATGGACAGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACTGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCGTGTTTTTCGACGACGGTAATTCAATGC  >  NZ_CP009273/2682891‑2683064                                                                                       |                                                                                        aGTGGGCGTAATTGTTGCAGACAGTCTGGACATGGACAGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGccc                                                                                     <  1:5546/91‑1 (MQ=255)  gTGGGCGTAATTGTTGCAGACAGTCTGGACATGGACAGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCg                                                                                    >  1:259766/1‑91 (MQ=255)      gCGTAATTGTTGCAGACAGTCTGGACATGGACAGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGc                                                                                >  2:43336/1‑91 (MQ=255)      gCGTAATTGTTGCAGACAGTCTGGACATGGACAGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGc                                                                                >  2:789215/1‑91 (MQ=255)              gttgCAGACAGTCTGGACATGGACAGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGa                                                                        >  1:240729/1‑91 (MQ=255)              gttgCAGACAGTCTGGACATGGACAGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGa                                                                        <  1:716847/91‑1 (MQ=255)                 gCAGACAGTCTGGACATGGACAGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACaa                                                                     <  2:792650/91‑1 (MQ=255)                        gTCTGGACATGGACAGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACaaataaaat                                                              >  2:457444/1‑91 (MQ=255)                        gTCTGGACATGGACAGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACaaataaaat                                                              >  1:447255/1‑91 (MQ=255)                           tggacatggacaGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGc                                                           <  2:434863/91‑1 (MQ=255)                           tggacatggacaGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGc                                                           <  2:837324/91‑1 (MQ=255)                               catggacaGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTga                                                       <  2:627201/91‑1 (MQ=255)                               catggacaGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTga                                                       <  1:2592/91‑1 (MQ=255)                                 tggacaGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTgata                                                     >  1:427850/1‑91 (MQ=255)                                  ggacaGCGCGGAGAACCCGGCGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTgatag                                                    >  2:210240/1‑91 (MQ=255)                                  ggacaGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGccc                                                                                     <  1:860161/58‑1 (MQ=255)                                  ggacaGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGccc                                                                                     >  2:860161/1‑58 (MQ=255)                                  ggacaGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTgatag                                                    >  2:554436/1‑91 (MQ=255)                                  ggacaGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTgatag                                                    >  1:621764/1‑91 (MQ=255)                                  ggacaGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTgatag                                                    >  1:41970/1‑91 (MQ=255)                                  ggacaGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTgatag                                                    >  2:363937/1‑91 (MQ=255)                                     caGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTgataggat                                                 <  1:713941/91‑1 (MQ=255)                                      aGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTgataggata                                                >  1:442160/1‑91 (MQ=255)                                      aGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTgataggata                                                <  2:219661/91‑1 (MQ=255)                                      aGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTgataggata                                                >  2:146621/1‑91 (MQ=255)                                      aGCCCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGCACTGCCAAATAGAATAACCTgataggata                                                >  2:685554/1‑91 (MQ=18)                                       gcgcGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACaa                                                                     >  2:404770/1‑69 (MQ=255)                                       gcgcGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACaa                                                                     <  1:404770/69‑1 (MQ=255)                                       gcgcGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTgataggatag                                               >  2:434883/1‑91 (MQ=255)                                               aaaCCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAg                                       >  1:49720/1‑91 (MQ=255)                                                    ggAGCGTACATATCGTACGTTAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCatta                                  <  2:431218/91‑1 (MQ=255)                                                           aCATATCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCgtg                           >  1:71071/1‑91 (MQ=255)                                                              tatCGTACGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCGTGttt                        >  2:240256/1‑91 (MQ=255)                                                                    aCGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACaaataaaa                                                               <  1:88054/46‑1 (MQ=255)                                                                    aCGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACaaataaaa                                                               >  2:88054/1‑46 (MQ=255)                                                                    aCGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCGTGTTTTTcgac                  >  1:278494/1‑91 (MQ=255)                                                                     cGTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCGTGTTTTTcgacg                 <  2:41970/91‑1 (MQ=255)                                                                      gTGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCGTGTTTTTcgacga                >  2:630686/1‑91 (MQ=255)                                                                       tGAAGATTTCGAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCGTGTTTTTCgacgac               <  2:316587/91‑1 (MQ=255)                                                                                 gAGCACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCGTGTTTTTCGACGACGGTAATTCaa     <  2:442160/91‑1 (MQ=255)                                                                                    cACCGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCGTGTTTTTCGACGACGGTAATTCAATGc  <  2:581868/91‑1 (MQ=255)                                                                                       |                                                                                        AGTGGGCGTAATTGTTGCAGACAGTCTGGACATGGACAGCGCGGAGAAACCGGAGCGTACATATCGTACGTGAAGATTTCGAGCACTGCCCGGGGCCGAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGCATTATTTCGTGTTTTTCGACGACGGTAATTCAATGC  >  NZ_CP009273/2682891‑2683064

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑