Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	2,684,441	(A)5→4	coding (17/1428 nt)	qseE ←	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	2,684,437	0	A	.	100.0%	29.3 / NA	8	coding (21/1428 nt)	qseE	two component system sensor histidine kinase QseE/GlrK
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (7/1);  total (7/1)

GCTTTGCCAGGCTTGCCATGCCAGCACCAACAGGGGCAGCAGAATCAGCAAAAATGCCAGCATTACCAGTTGTCGTAATGAGCGGGGAAAAACGGGCCAGCGTTTCAAGGTGTTACTCTCGTCAGACGCGAATAGCCTGATGCTAACCGAGGGGAAGTTCAGATACAACAAA  >  NZ_CP009273/2684350‑2684521                                                                                        |                                                                                     gCTTTGCCAGGCTTGCCATGCCAGCACCAACAGGGGCAGCAGAATCAGCAAAAATGCCAGCATTACCAGTTGTCGTAATGAGCGGGGaaa                                                                                    >  2:293566/1‑90 (MQ=255)                                               aGCAAAAATGCCAGCATTACCAGTTGTCGTAATGAGCGGGG‑AAAACGGGCCAGCGTTTCAAGGTGTTACTCTCGTCAGACGCGAATAGcc                                     >  2:516631/1‑90 (MQ=255)                                                gCAAAAATGCCAGCATTACCAGTTGTCGTAATGAGCGGGG‑AAAACGGGCCAGCGTTTCAAGGTGTTACTCTCGTCAGACGCGAATAGCCt                                    <  2:375948/90‑1 (MQ=255)                                                                      ttGTCGTAATGAGCGGGG‑AAAACGGGCCAGCGTTTCAAGGTGTTACTCTCGTCAGACGCGAATAGCCTGATGCTAACCGAGGGGAAGTTc              >  1:225848/1‑90 (MQ=255)                                                                      ttGTCGTAATGAGCGGGG‑AAAACGGGCCAGCGTTTCAAGGTGTTACTCTCGTCAGACGCGAATAGCCTGATGCTAACCGAGGGGAAGTTc              >  2:163308/1‑90 (MQ=255)                                                                       tGTCGTAATGAGCGGGG‑AAAACGGGCCAGCGTTTCAAGGTGTTACTCTCGTCAGACGCGAATAGCCTGATGCTAACCGAGGGGAAGTTCa             >  1:389435/1‑90 (MQ=255)                                                                          cGTAATGAGCGGGG‑AAAACGGGCCAGCGTTTCAAGGTGTTACTCTCGTCAGACGCGAATAGCCTGATGCTAACCGAGGGGAAGTTCAGAt          >  2:198822/1‑90 (MQ=255)                                                                                  gCGGGG‑AAAACGGGCCAGCGTTTCAAGGTGTTACTCTCGTCAGACGCGAATAGCCTGATGCTAACCGAGGGGAAGTTCAGATACAACaaa  >  2:217693/1‑90 (MQ=255)                                                                                  gCGGGG‑AAAACGGGCCAGCGTTTCAAGGTGTTACTCTCGTCAGACGCGAATAGCCTGATGCTAACCGAGGGGAAGTTCAGATACAACaaa  >  2:510547/1‑90 (MQ=255)                                                                                        |                                                                                     GCTTTGCCAGGCTTGCCATGCCAGCACCAACAGGGGCAGCAGAATCAGCAAAAATGCCAGCATTACCAGTTGTCGTAATGAGCGGGGAAAAACGGGCCAGCGTTTCAAGGTGTTACTCTCGTCAGACGCGAATAGCCTGATGCTAACCGAGGGGAAGTTCAGATACAACAAA  >  NZ_CP009273/2684350‑2684521

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑