Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,829,452	T→G	intergenic (‑163/‑130)	yicJ ← / → BW25113_RS18990	glycoside‑pentoside‑hexuronide family transporter/tRNA‑Sec

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,829,452	0	T	G	100.0%	98.8 / NA	27	intergenic (‑163/‑130)	yicJ/BW25113_RS18990	glycoside‑pentoside‑hexuronide family transporter/tRNA‑Sec
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base G (10/17);  total (10/17)

CTGAGACCGATAACGCATTTTGTAAACCATCCCTGTGAGAGCGAATATTCCGATATCTGGTTATTAATTTATGATTCTTGTTTTATGTGATCGTGGTAGCGTTAATTCCGCTCATATATCATTGTAAAATATGGGTTTTATATGAACTATAATGCTTTCGTGATAATACGCTGCGTGTATTAGGCGGAAAAAACTGATCTGGGGGATGTAGAAACTCAAGGAAGTAGCTATAATGCGCCCCGCCTCCATGTAGCAATCGAGGCGCGGA  >  NZ_CP009273/3829317‑3829584                                                                                                                                        |                                                                                                                                     cTGAGACCGATAACGCATTTTGTAAACCATCCCTGTGAGAGCGAATATTCCGATATCTGGTTATTAATTTATGATTCTTGTTTTATGTGATCGTGGTAGCGTTAATTCCGCTCATATATCATTGTAAAATATGGGgtt                                                                                                                                    >  2:433264/1‑138 (MQ=255)    agaCCGATAACGCATTTTGTAAACCATCCCTGTGAGAGCGAATATTCCGATATCTGGTTATTAATTTATGATTCTTGTTTTATGTGATCGTGGTAGCGTTAATTCCGCTCATATATCATTGTAAAATATGGGGTTtata                                                                                                                                <  2:154783/139‑1 (MQ=255)      aCCGATAACGCATTTTGTAAACCATCCCTGTGAGAGCGAATATTCCGATATCTGGTTATTAATTTATGATTCTTGTTTTATGTGATCGTGGTAGCGTTAATTCCGCTCATATATCATTGTAAAATATGGGGTTTATATg                                                                                                                              <  1:238183/139‑1 (MQ=255)                     tGTAAACCATCCCTGTGAGAGCGAATATTCCGATATCTGGTTATTAATTTATGATTCTTGTTTTATGTGATCGTGGTAGCGTTAATTCCGCTCATATATCATTGTAAAATATGGGGTTTATATGAACTATAATGCTTTc                                                                                                               >  1:190032/1‑139 (MQ=255)                       tAAACCATCCCTGTGAGAGCGAATATTCCGATATCTGGTTATTAATTTATGATTCTTGTTTTATGTGATCGTGGTAGCGTTAATTCCGCTCATATATCATTGTAAAATATGGGGTTTATATGAACTATAATGCTTTCg                                                                                                              <  1:481331/138‑1 (MQ=255)                               cccTGTGAGAGCGAATATTCCGATATCTGGTTATTAATTTATGATTCTTGTTTTATGTGATCGTGGTAGCGTTAATTCCGCTCATATATCATTGTAAAATATGGGGTTTATATg                                                                                                                              <  1:229593/114‑1 (MQ=255)                               cccTGTGAGAGCGAATATTCCGATATCTGGTTATTAATTTATGATTCTTGTTTTATGTGATCGTGGTAGCGTTAATTCCGCTCATATATCATTGTAAAATATGGGGTTTATATg                                                                                                                              >  2:229593/1‑114 (MQ=255)                                ccTGTGAGAGCGAATATTCCGATATCTGGTTATTAATTTATGATTCTTGTTTTATGTGATCGTGGTAGCGTTAATTCCGCTCATATATCATTGTAAAATATGGGGTTTATATGAACTATAATGCTTTCGTGATAATACg                                                                                                    <  1:433264/139‑1 (MQ=255)                                ccTGTGAGAGCGAATATTCCGATATCTGGTTATTAATTTATGATTCTTGTTTTATGTGATCGTGGTAGCGTTAATTCCGCTCATATATCATTGTAAAATATGGGGTTTATATGAACTATAATGCTTTCGTGATAATACg                                                                                                    <  2:102233/139‑1 (MQ=255)                                    tgAGAGCGAATATTCCGATATCTGGTTATTAATTTATGATTCTTGTTTTATGTGATCGTGGTAGCGTTAATTCCGCTCATATATCATTGTAAAATATGGGGTTTATATGAACTATAATGCTTTCGTGATAATACGCt                                                                                                  <  1:3711/137‑1 (MQ=255)                                    tgAGAGCGAATATTCCGATATCTGGTTATTAATTTATGATTCTTGTTTTATGTGATCGTGGTAGCGTTAATTCCGCTCATATATCATTGTAAAATATGGGGTTTATATGAACTATAATGCTTTCGTGATAATACGCTGc                                                                                                <  1:466021/139‑1 (MQ=255)                                                ttCCGATATCTGGTTATTAATTTATGATTCTTGTTTTATGTGATCGTGGTAGCGTTAATTCCGCTCATATATCATTGTAAAATATGGGGTTTATATGAACTATAATGCTTTCGTGATAATACGCTGCGTGTATTAGGCg                                                                                    >  2:479634/1‑139 (MQ=255)                                                            gTTATTAATTTATGATTCTTGTTTTATGTGATCGTGGTAGCGTTAATTCCGCTCATATATCATTGTAAAATATGGGGTTTATATGAACTATAATGCTTTCGTGATAATACGCTGCGTGTATTAGGCGGAAAAAACt                                                                           <  2:11900/136‑1 (MQ=255)                                                                    tttATGATTCTTGTTTTATGTGATCGTGGTAGCGTTAATTCCGCTCATATATCATTGTAAAATATGGGGTTTATATGAACTATAATGCTTTCGTGATAATACGCTGCGTGTATTAGGCGGAAAAAACTGATCTGGGGGa                                                                <  2:486250/139‑1 (MQ=255)                                                                          aTTCTTGTTTTATGTGATCGTGGTAGCGTTAATTCCGCTCATATATCATTGTAAAATATGGGGTTTATATGAACTATAATGCTTTCGTGATAATACGCTGCGTGTATTAGGCGGAAAAAACTGATCTGGGGGATGTAGa                                                          <  1:71884/139‑1 (MQ=255)                                                                          aTTCTTGTTTTATGTGATCGTGGTAGCGTTAATTCCGCTCATATATCATTGTAAAATATGGGGTTTATATGAACTATAATGCTTTCGTGATAATACGCTGCGTGTATTAGGCGGAAAAAACTGATCTGGGGGATGTAGa                                                          <  1:451067/139‑1 (MQ=255)                                                                                     aTGTGATCGTGGTAGCGTTAATTCCGCTCATATATCATTGTAAAATATGGGGTTTATATGAACTATAATGCTTTCGTGATAATACGCTGCGTGTATTAGGCGGAAAAAACTGATCTGGGGGATGTAGAAACTCAAGGa                                                <  1:383361/138‑1 (MQ=255)                                                                                      tgtgATCGTGGTAGCGTTAATTCCGCTCATATATCATTGTAAAATATGGGGTTTATATGAACTATAATGCTTTCGTGATAATACGCTGCGTGTATTAGGCGGAAAAAACTGATCTGGGGGATGTAGAAACTCAAGGAAg                                              <  1:454681/139‑1 (MQ=255)                                                                                                gTAGCGTTAATTCCGCTCATATATCATTGTAAAATATGGGGTTTATATGAACTATAATGCTTTCGTGATAATACGCTGCGTGTATTAGGCGGAAAAAACTGATCTGGGGGATGTAGAAACTCAAGGAAGTAGCTATAAt                                    >  2:366833/1‑139 (MQ=255)                                                                                                     gTTAATTCCGCTCATATATCATTGTAAAATATGGGGTTTATATGAACTATAATGCTTTCGTGATAATACGCTGCGTGTATTAGGCGGAAAAAACTGATCTGGGGGATGTAGAAACTCAAGGTAGTAGCTATAATGCGcc                               >  2:349795/1‑139 (MQ=255)                                                                                                         aTTCCGCTCATATATCATTGTAAAATATGGGGTTTATATGAACTATAATGCTTTCGTGATAATACGCTGCGTGTATTAGGCGGAAAAAACTGATCTGGGGGATGTAGAAACTCAAGGAAGTAGCTATAATGCGCCCCGc                           <  2:190032/139‑1 (MQ=255)                                                                                                               cTCATATATCATTGTAAAATATGGGGTTTATATGAACTATAATGCTTTCGTGATAATACGCTGCGTGTATTAGGCGGAAAAAACTGATCTGGGGGATGTAGAAACTCAAGGAAGTAGCTATAATGCGCCCCGCCTCCAt                     >  1:90589/1‑139 (MQ=255)                                                                                                               cTCATATATCATTGTAAAATATGGGGTTTATATGAACTATAATGCTTTCGTGATAATACGCTGCGTGTATTAGGCGGAAAAAACTGATCTGGGGGATGTAGAAACTCAAGGAAGTAGCTATAATGCGCCCCGCCTCCAt                     >  1:16061/1‑139 (MQ=255)                                                                                                                            gTAAAATATGGGGTTTATATGAACTATAATGCTTTCGTGATAATACGCTGCGTGTATTAGGCGGAAAAAACTGATCTGGGGGATGTAGAAACTCAAGGAAGTAGCTATAATGCGCCCCGCCTCCATGTAGCAATCGAgg        >  2:187803/1‑139 (MQ=255)                                                                                                                            gTAAAATATGGGGTTTATATGAACTATAATGCTTTCGTGATAATACGCTGCGTGTATTAGGCGGAAAAAACTGATCTGGGGGATGTAGAAACTCAAGGAAGTAGCTATAATGCGCCCCGCCTCCATGTAGCAATCGAgg        >  2:401789/1‑139 (MQ=255)                                                                                                                            gTAAAATATGGGGTTTATATGAACTATAATGCTTTCGTGATAATACGCTGCGTGTATTAGGCGGAAAAAACTGATCTGGGGGATGTAGAAACTCAAGGAAGTAGCTATAATGCGCCCCGCCTCCATGTAGCAATCGAgg        >  1:419140/1‑139 (MQ=255)                                                                                                                            gTAAAATATGGGGTTTATATGAACTATAATGCTTTCGTGATAATACGCTGCGTGTATTAGGCGGAAAAAACTGATCTGGGGGATGTAGAAACTCAAGGAAGTAGCTATAATGCGCCCCGCCTCCATGTAGCAATCGAg         <  2:419140/138‑1 (MQ=255)                                                                                                                                  tatGGGGTTTATATGAACTATAATGCTTTCGTGATAATACGCTGCGTGTATTAGGCGGAAAAAACTGATCTGGGGGATGTAGAAACTCAAGGAAGTAGCTATAATGCGCCCCGCCTCCATGTAGCAATCGAGGCGCGGa  <  1:479634/139‑1 (MQ=255)                                                                                                                                     ggggTTTATATGAACTATAATGCTTTCGTGATAATACGCTGCGTGTATTAGGCGGAAAAAACTGATCTGGGGGATGTAGAAACTCAAGGAAGTAGCTATAATGCGCCCCGCCTCCATGTAGCAATCGAGGCGCgg   >  1:59622/1‑135 (MQ=255)                                                                                                                                     ggggTTTATATGAACTATAATGCTTTCGTGATAATACGCTGCGTGTATTAGGCGGAAAAAACTGATCTGGGGGATGTAGAAACTCAAGGAAGTAGCTATAATGCGCCCCGCCTCCATGTAGCAATCGAGGCGCgg   >  2:157743/1‑135 (MQ=255)                                                                                                                                        |                                                                                                                                     CTGAGACCGATAACGCATTTTGTAAACCATCCCTGTGAGAGCGAATATTCCGATATCTGGTTATTAATTTATGATTCTTGTTTTATGTGATCGTGGTAGCGTTAATTCCGCTCATATATCATTGTAAAATATGGGTTTTATATGAACTATAATGCTTTCGTGATAATACGCTGCGTGTATTAGGCGGAAAAAACTGATCTGGGGGATGTAGAAACTCAAGGAAGTAGCTATAATGCGCCCCGCCTCCATGTAGCAATCGAGGCGCGGA  >  NZ_CP009273/3829317‑3829584

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑