Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,184,613	A→T	I207N (ATC→AAC)	phoQ ←	two‑component system sensor histidine kinase PhoQ

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,184,613	0	A	T	100.0%	33.7 / NA	10	I207N (ATC→AAC)	phoQ	two‑component system sensor histidine kinase PhoQ
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (5/5);  total (5/5)

TCTTTTGCCAGGGCTTCGATGGGGCGTAAACTCCACCAGGCGGCGACCCACAGCAGCGGGATCACTAACAGCAGATTGGCTGAGAGCACATAGATAAACCAGCTCCAGACCATATAGGAACTTTTTAGCTCCACCGGAATGGTAT  >  NZ_CP009273/1184553‑1184697                                                             |                                                                                     tcttTTGCCAGGGCTTCGATGGGGCGTAAACTCCACCAGGCGGCGACCCACAGCAGCGGGTTCACTAACAGCAGATTGGCCGAGAGcaca                                                         <  1:201427/90‑1 (MQ=255)           gggCTTCGATGGGGCGTAAACTCCACCAGGCGGCGACCCACAGCAGCGGGTTCACTAACAGCAGATTGGCTGAGAGCACATAGATAAAcc                                               >  1:197635/1‑90 (MQ=255)           gggCTTCGATGGGGCGTAAACTCCACCAGGCGGCGACCCACAGCAGCGGGTTCACTAACAGCAGATTGGCTGAGAGCACATAGATAAAcc                                               >  1:88838/1‑90 (MQ=255)           gggCTTCGATGGGGCGTAAACTCCACCAGGCGGCGACCCACAGCAGCGGGTTCACTAACAGCAGATTGGCTGAGAGCACATAGATAAAcc                                               <  2:88838/90‑1 (MQ=255)                tCGATGGGGCGTAAACTCCACCAGGCGGCGACCCACAGCAGCGGGTTCACTAACAGCAGATTGGCTGAGAGCACATAGATAAACCAGCTc                                          <  2:457003/90‑1 (MQ=255)                   aTGGGGCGTAAACTCCACCAGGCGGCGACCCACAGCAGCGGGTTCACTAACAGCAGATTGGCTGAGAGCACATAGATAAACCAGCTCCAg                                       <  2:203903/90‑1 (MQ=255)                        gCGTAAACTCCACCAGGCGGCGACCCACAGCAGCGGGTTCACTAACAGCAGATTGGCTGAGAGCACATAGATAAACCAGCTCCAGACCat                                  >  2:141461/1‑90 (MQ=255)                                 ccaccaGGCGGCGACCCACAGCAGCGGGTTCACTAACAGCAGATTGGCTGAGAGCACATAGATAAACCAGCTCCAGACCATATAGGAACt                         >  1:195305/1‑90 (MQ=255)                                      aGGCGGCGACCCACAGCAGCGGGTTCACTAACAGCAGATTGGCTGAGAGCACATAGATAAACCAGCTCCAGACCATATAGGAACTTTTTa                    >  2:111953/1‑90 (MQ=255)                                                        gcGGGTTCACTAACAGCAGATTGGCTGAGAGCACATAGATAAACCAGCTCCAGACCATATAGGAACTTTTTAGCTCCACCGGAATGGTAt  <  1:141461/90‑1 (MQ=255)                                                             |                                                                                     TCTTTTGCCAGGGCTTCGATGGGGCGTAAACTCCACCAGGCGGCGACCCACAGCAGCGGGATCACTAACAGCAGATTGGCTGAGAGCACATAGATAAACCAGCTCCAGACCATATAGGAACTTTTTAGCTCCACCGGAATGGTAT  >  NZ_CP009273/1184553‑1184697

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑