Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,237,623	(T)7→8	coding (914/915 nt)	ldcA ←	muramoyltetrapeptide carboxypeptidase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,237,616	1	.	T	87.5%	22.1 / ‑3.6	8	intergenic (‑89/+6)	cvrA/ldcA	potassium/proton antiporter/muramoyltetrapeptide carboxypeptidase
Reads supporting (aligned to +/- strand):  ref base . (0/1);  new base T (3/4);  total (3/5)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCTGTCTCTTATATAAACCCTACCATATTAGCGGCAGAGACAGCGTTTTACTTAGCCCTGAAGCGTGA‑TTTTTTTACATTTTAAGAACAGGATGACCGCTAATCGTCAACTGAGTGCCTTCCCGGGTGTTATTCAGAATGGCATGTGCGCCCAACG  >  NZ_CP009273/1237549‑1237704                                                                     |                                                                                         gCTGTCTCTTATATAACCCCTCCCATATTAGCGGCAGAGACAGCGTTTTACTTAGCCCTGAAGCGTGATTTTTTTTACATTTTAAGAACa                                                                     <  2:350062/90‑1 (MQ=255)                aaCCCTACCATATTAGCGGCAGAGACAGTGTTTTACTTAGCCCTGAAGCGTGATTTTTTTTACATTTTAAGAACAGGATGACCGCTAATc                                                      >  1:572739/1‑90 (MQ=255)                   ccTACCATATTAGCGGCAGAGACAGCGTTTTACTTAGCCCTGAAGCGTGATTTTTTTTACATTTTAAGAACAGGATGACCGCTAATCGTc                                                   <  1:39238/90‑1 (MQ=255)                     tACCATATTAGCGGCAGAGACAGCGTTTTACTTAGCCCTGAAGCGTGATTTTTTTTACATTTTAAGAACAGGATGACCGCTAATCGTCaa                                                 >  2:449707/1‑90 (MQ=255)                          tatTAGCGGCAGAGACAGCGTTTTACTTAGCCCTGAAGCGTGATTTTTTTTACATTTTAAGAACAGGATGACCGCTAATCGTCAACTGAg                                            <  2:108980/90‑1 (MQ=255)                            ttAGCGGCAGAGACAGCGTTTTACTTAGCCCTGAAGCGTGATTTTTTTTACATTTTAAGAACAGGATGACCGCTAATCGTCAACTGAGTg                                          <  1:119695/90‑1 (MQ=255)                            ttAGCGGCAGAGACAGCGTTTTACTTAGCCCTGAAGCGTGATTTTTTTTACATTTTAAGAACAGGATGACCGCTAATCGTCAACTGAGTg                                          >  2:413181/1‑90 (MQ=255)                                                                   gA‑TTTTTTTACATTTTAAGAACAGGATGACCGCTAATCGTCAACTGAGTGCCTTCCCGGGTGTTATTCAGAATGGCATGTGCGCCCAACg  <  1:218072/90‑1 (MQ=255)                                                                     |                                                                                         GCTGTCTCTTATATAAACCCTACCATATTAGCGGCAGAGACAGCGTTTTACTTAGCCCTGAAGCGTGA‑TTTTTTTACATTTTAAGAACAGGATGACCGCTAATCGTCAACTGAGTGCCTTCCCGGGTGTTATTCAGAATGGCATGTGCGCCCAACG  >  NZ_CP009273/1237549‑1237704

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑