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%	44.0 / NA	11	coding (525/1107 nt)	mnmA	tRNA 2‑thiouridine(34) synthase MnmA
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (3/8);  total (3/8)

AACTCGCGGAATTTACGTTCGCCAATGAAGCAAATGCCGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAGCAGGCGGCTCTTGCCAT  >  NZ_CP009273/1188604‑1188823                                                                                                      |                                                                                                                       aaCTCGCGGAATTTACGTTCGCCAATTAATCAAATGCCGGTAGAGTCGTTTTTCTTCGCGGTGCCCAGCCCAAGATCTTCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAAt                                                                                  <  2:284821/139‑1 (MQ=255) aaCTCGCGGAATTTACGTTCGCCAATGAAGCAAATGCCGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAAt                                                                                  <  2:374313/139‑1 (MQ=255)               aCGTTCGCCAATGAAGCAAATGCCGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTg                                                                     <  2:552204/138‑1 (MQ=255)                cGTTCGCCAATGAAGCAAATGCCGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGa                                                                    <  2:178811/138‑1 (MQ=255)                          tGAAGCAAATGCCGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAg                                                          >  1:98062/1‑138 (MQ=255)                                              tCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTAtt                                     <  1:23499/139‑1 (MQ=255)                                                                 ccagaccaAGATCTTCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGA‑‑‑GGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAGCAgg               <  1:551435/139‑1 (MQ=255)                                                                     cccaAGATCTTCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAGCAggc              >  2:349358/2‑139 (MQ=255)                                                                               tCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGtata                                                             >  1:435584/1‑82 (MQ=255)                                                                               tCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGtata                                                             <  2:435584/82‑1 (MQ=255)                                                                                 aGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAGCAGGCGGCTCTTGCCAt  <  2:98062/139‑1 (MQ=255)                                                                                                      |                                                                                                                       AACTCGCGGAATTTACGTTCGCCAATGAAGCAAATGCCGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAGCAGGCGGCTCTTGCCAT  >  NZ_CP009273/1188604‑1188823

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑