Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	690,117	C→T	V99I (GTC→ATC)	miaB ←	tRNA (N6‑isopentenyl adenosine(37)‑C2)‑methylthiotransferase MiaB

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	690,117	0	C	T	92.9%	42.1 / ‑3.3	14	V99I (GTC→ATC)	miaB	tRNA (N6‑isopentenyl adenosine(37)‑C2)‑methylthiotransferase MiaB
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base T (11/2);  total (11/3)
Fisher's exact test for biased strand distribution p-value = 2.14e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.06e-01

GGGCTGCGGTCGCCACGCACGGAGTTGATCATCTCCGGCAGACGGTGCAGCGTTTGCGGCCCAAAAATAATATCGACATAGTGGGCGCGCTGGCGAATGTGCTCGCCTTCTTGCGATGCCACGCAGCCACCGACGCCGATAATC  >  NZ_CP009273/690041‑690184                                                                             |                                                                    gggCTGCGGTCGCCACGCACGGAGTTGATCATCTCCGGCAGACGGTGCAGCGTTTGCGGCCCAAAAATAATATCGATATAGTGGgcgcgc                                                        >  2:51553/1‑90 (MQ=255)   gCTGCGGTCGCCACGCACGGAGTTGATCATCTCCGGCAGACGGTGCAGCGTTTGCGGCCCAAAAATAATATCGATATAGTGGGCGCGCTg                                                      >  2:308191/1‑90 (MQ=255)                cgcacgGAGTTGATCATCTCCGGCAGACGGTGCAGCGTTTGCGGCCCAAAAATAATATCGATATAGTGGGCGCGCTGGCGAATGTGCTCg                                         >  2:328531/1‑90 (MQ=255)                                tctcCGGCAGACGGTGCAGCGTTTGCGGCCCAAAAATAATATCGATATAGTGGGCGCGCTGGCGAATGTGCTCGCCTTCTTGCGATGCCa                         >  1:412010/1‑90 (MQ=255)                                          aCGGTGCAGCGTTTGCGGCCCAAAAATAATATCGATATAGTGGGCGCGCTGGCGAATGTGCTCGCCTTCTTGCGATGCCACGCAGCCAcc               >  1:131802/1‑90 (MQ=255)                                          aCGGTGCAGCGTTTGCGGCCCAAAAATAATATCGATATAGTGGGCGCGCTGGCGAATGTGCTCGCCTTCTTGCGATGCCACGCAGCCAcc               >  2:30165/1‑90 (MQ=255)                                                       tGCGGCCCAAAAATAATATCGATATAGTGGGCGCGCTGGCGAATGTGCTCGCCTTCTTGCGATGCCACGCAGCCACCGACGCCGATAATc  >  1:141836/1‑90 (MQ=255)                                                       tGCGGCCCAAAAATAATATCGATATAGTGGGCGCGCTGGCGAATGTGCTCGCCTTCTTGCGATGCCACGCAGCCACCGACGCCGATAATc  >  1:145943/1‑90 (MQ=255)                                                       tGCGGCCCAAAAATAATATCGATATAGTGGGCGCGCTGGCGAATGTGCTCGCCTTCTTGCGATGCCACGCAGCCACCGACGCCGATAATc  >  1:432685/1‑90 (MQ=255)                                                       tGCGGCCCAAAAATAATATCGATATAGTGGGCGCGCTGGCGAATGTGCTCGCCTTCTTGCGATGCCACGCAGCCACCGACGCCGATAATc  >  2:119741/1‑90 (MQ=255)                                                       tGCGGCCCAAAAATAATATCGATATAGTGGGCGCGCTGGCGAATGTGCTCGCCTTCTTGCGATGCCACGCAGCCACCGACGCCGATAATc  <  2:141836/90‑1 (MQ=255)                                                       tGCGGCCCAAAAATAATATCGACATAGTGGGCGCGCTGGCGAATGTGCTCGCCTTCTTGCGATGCCACGCAGCCACCGACGCCGATAATc  <  1:412171/90‑1 (MQ=255)                                                                     aataTCGATATAGTGGGCGCGCTGGCGAATGTGCTCGCCTTCTTGCGATGCCACGCAg                    <  1:33851/58‑1 (MQ=255)                                                                     aataTCGATATAGTGGGCGCGCTGGCGAATGTGCTCGCCTTCTTGCGATGCCACGCAg                    >  2:33851/1‑58 (MQ=255)                                                                             |                                                                    GGGCTGCGGTCGCCACGCACGGAGTTGATCATCTCCGGCAGACGGTGCAGCGTTTGCGGCCCAAAAATAATATCGACATAGTGGGCGCGCTGGCGAATGTGCTCGCCTTCTTGCGATGCCACGCAGCCACCGACGCCGATAATC  >  NZ_CP009273/690041‑690184

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑