Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,188,709	(T)5→4	coding (521/1107 nt)	mnmA ←	tRNA 2‑thiouridine(34) synthase MnmA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,188,705	0	T	.	100.0%	70.2 / NA	17	coding (525/1107 nt)	mnmA	tRNA 2‑thiouridine(34) synthase MnmA
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (8/9);  total (8/9)

GCCCGGTTGCGCCGGGAGATAACGGCCCAGGAACTCGCGGAATTTACGTTCGCCAATGAAGCAAATGCCGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAGCAGGCGGCTCTTGC  >  NZ_CP009273/1188573‑1188820                                                                                                                                     |                                                                                                                    gCCCGGTTGCGCCGGGAGATAACGGCCCAGGAACTCGCGGAATTTACGTTCGCCAATGAAGCAAATGCCGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGGttttc                                                                                                                 >  2:685175/1‑136 (MQ=255)       ttGCGCCGGGAGATAACGGCCCAGGAACTCGCGGAATTTACGTTCGCCAATGAAGCAAATGCCGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGc                                                                                                        >  1:749525/1‑139 (MQ=255)               ggAGATAACGGCCCAGGAACTCGCGGAATTTACGTTCGCCAATGAAGCAAATGCCGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCggg                                                                                                <  1:685175/139‑1 (MQ=255)                  gaTAACGGCCCAGGAACTCGCGGAATTTACGTTCGCCAATGAAGCAAATGCCGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCGGGAAc                                                                                             <  1:57850/139‑1 (MQ=255)                  gaTAACGGCCCAGGAACTCGCGGAATTTACGTTCGCCAATGAAGCAAATGCCGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCGGGAAc                                                                                             <  1:609988/139‑1 (MQ=255)                            cAGGAACTCGCGGAATTTACGTTCGCCAATGAAGCAAATGCCGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAGGCTTTgcg                                                                                   >  1:607976/1‑139 (MQ=255)                                                     ccAATGAAGCAAATGCCGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAAt                                                                               <  2:544509/118‑1 (MQ=255)                                                     ccAATGAAGCAAATGCCGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAAt                                                                               >  1:544509/1‑118 (MQ=255)                                                                    ccGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTg                                           <  2:749525/139‑1 (MQ=255)                                                                    ccGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGG‑TTTTCCAATTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTg                                           <  2:376919/139‑1 (MQ=255)                                                                                 ttttCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTg                                 <  1:507142/136‑1 (MQ=255)                                                                                 ttttCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTg                                 <  1:422412/136‑1 (MQ=255)                                                                                  tttCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGt                             >  1:1340/1‑139 (MQ=255)                                                                                       tcGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGa                        >  1:178998/1‑139 (MQ=255)                                                                                                    accaAGATCTTCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAGCAggc           >  2:734431/1‑139 (MQ=255)                                                                                                              tCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAGCAGGCGGCTCTTGc  >  2:294875/1‑138 (MQ=255)                                                                                                                               cTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTg                                 <  2:333061/90‑1 (MQ=255)                                                                                                                               cTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTg                                 >  1:333061/1‑90 (MQ=255)                                                                                                                                     |                                                                                                                    GCCCGGTTGCGCCGGGAGATAACGGCCCAGGAACTCGCGGAATTTACGTTCGCCAATGAAGCAAATGCCGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAGCAGGCGGCTCTTGC  >  NZ_CP009273/1188573‑1188820

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑