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%	87.7 / NA	21	coding (525/1107 nt)	mnmA	tRNA 2‑thiouridine(34) synthase MnmA
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (7/14);  total (7/14)

GATAACGGCCCAGGAACTCGCGGAATTTACGTTCGCCAATGAAGCAAATGCCGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCA  >  NZ_CP009273/1188590‑1188801                                                                                                                    |                                                                                                 gaTAACGGCCCAGGAACTCGCGGAATTTACGTTCGCCAATGAAGCAAATGCCGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCGGGAAc                                                                          <  1:544892/139‑1 (MQ=255)    aaCGGCCCAGGAACTCGCGGAATTTACGTTCGCCAATGAAGCAAATGCCGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAgg                                                                       >  2:508761/1‑139 (MQ=255)         cccAGGAACTCGCGGAATTTACGTTCGCCAATGAAGCAAATGCCGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAGGCTTTg                                                                  >  2:488246/1‑139 (MQ=255)           cAGGAACTCGCGGAATTTACGTTCGCCAATGAAGCAAATGCCGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAGGCTTTgcg                                                                <  1:282515/139‑1 (MQ=255)           cAGGAACTCGCGGAATTTACGTTCGCCAATGAAGCAAATGCCGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAGGCTTTgcg                                                                >  1:559050/1‑139 (MQ=255)               aaCTCGCGGAATTTACGTTCGCCAATGAAGCAAATGCCGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAAt                                                            <  1:347021/139‑1 (MQ=255)                   cgcgGAATTTACGTTCGCCAATGAAGCAAATGCCGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGc                                                        >  2:469093/1‑139 (MQ=255)                            tACGTTCGCCAATGAAGCAAATGCCGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCt                                                <  2:282134/138‑1 (MQ=255)                             aCGTTCGCCAATGAAGCAAATGCCGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTg                                               <  2:559050/138‑1 (MQ=255)                             aCGTTCGCCAATGAAGCAAATGCCGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTg                                               <  2:23528/138‑1 (MQ=255)                                                   ccGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTg                        <  2:144882/139‑1 (MQ=255)                                                   ccGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTg                        <  2:194076/139‑1 (MQ=255)                                                      gTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTc                     >  1:210188/1‑139 (MQ=255)                                                            tCTTTTTTCTGCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTAtt               <  1:74729/139‑1 (MQ=255)                                                                ttttCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTg              <  2:258213/136‑1 (MQ=255)                                                                      tcGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGa                                              >  2:136142/1‑98 (MQ=255)                                                                      tcGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGa                                              <  1:136142/98‑1 (MQ=255)                                                                       cgcgGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGa     <  2:395646/138‑1 (MQ=255)                                                                         cgGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCa  <  1:108760/139‑1 (MQ=255)                                                                                                              cTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATaa                                      <  2:224713/66‑1 (MQ=255)                                                                                                              cTGCGG‑TTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATaa                                      >  1:224713/1‑66 (MQ=255)                                                                                                                    |                                                                                                 GATAACGGCCCAGGAACTCGCGGAATTTACGTTCGCCAATGAAGCAAATGCCGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCA  >  NZ_CP009273/1188590‑1188801

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑