Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	209,716	T→C	I300T (ATC→ACC)	tilS →	tRNA lysidine(34) synthetase TilS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	209,716	0	T	C	91.7%	24.6 / ‑3.3	12	I300T (ATC→ACC)	tilS	tRNA lysidine(34) synthetase TilS
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base C (7/4);  total (7/5)
Fisher's exact test for biased strand distribution p-value = 4.17e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.93e-01

GAGGATCTGGCAGGAAGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAATCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGAAAACATTGTGCCGTGGCAGAC  >  NZ_CP009273/209645‑209791                                                                        |                                                                            gAGGATCTGGCAGGAAGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCa                                                           >  2:224325/1‑90 (MQ=255)        tGGCAGGAAGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTgtgg                                                    >  1:66125/1‑90 (MQ=255)         ggCAGGAAGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAATCCGACGCTATCAGTCGCAACTgtggt                                                   <  1:369042/90‑1 (MQ=255)             ggAAGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGAt                                               >  1:413988/1‑90 (MQ=255)               aaGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTa                                             <  2:66125/90‑1 (MQ=255)                    gcgctggcgcGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGAGGGATTAAATcc                                        >  1:505495/1‑90 (MQ=255)                               ggAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCa                             <  2:158711/90‑1 (MQ=255)                               ggAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCa                             <  2:319980/90‑1 (MQ=255)                                   gATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGc                         >  2:309212/1‑90 (MQ=255)                                      gCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGaa                      <  1:224325/90‑1 (MQ=255)                                               tGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGAAAACATtgtg             >  2:445977/1‑90 (MQ=255)                                                          gggCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGAAAACATTGTGCCGTGGCAGAc  >  2:288718/1‑90 (MQ=255)                                                                        |                                                                            GAGGATCTGGCAGGAAGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAATCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGAAAACATTGTGCCGTGGCAGAC  >  NZ_CP009273/209645‑209791

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑