Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,336,067	G→A	intergenic (+83/‑111)	lapB → / → pyrF	lipopolysaccharide assembly protein LapB/orotidine‑5'‑phosphate decarboxylase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,336,067	0	G	A	100.0%	114.4 / NA	28	intergenic (+83/‑111)	lapB/pyrF	lipopolysaccharide assembly protein LapB/orotidine‑5'‑phosphate decarboxylase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (13/15);  total (13/15)

GCGGTCTTGATGGCCTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCGCGCCACTTCCGGTGCCCATCATCAAGAAGGTCTGGTCATGACGTTAACTGCTTCA  >  NZ_CP009273/1335965‑1336195                                                                                                       |                                                                                                                                 gcgGTCTTGATGGCCTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAAtttttt                                                                                               <  2:292238/138‑1 (MQ=255) gcgGTCTTGATGGCCTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAAtttttt                                                                                               <  1:841152/138‑1 (MQ=255)         gATGGCCTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTcc                                                                                         <  2:387914/136‑1 (MQ=255)         gATGGCCTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCAc                                                                                       <  1:42759/138‑1 (MQ=255)                    aTTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCt                                                                           <  2:677531/139‑1 (MQ=255)                                                  acaTACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCGCGCCACTTCCgg                                             >  1:669142/1‑139 (MQ=255)                                                      aCTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTcc                                                                                         >  1:466273/1‑91 (MQ=255)                                                      aCTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTcc                                                                                         <  2:466273/91‑1 (MQ=255)                                                      aCTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCGCGCCACTTCCGGTGcc                                         >  2:463876/1‑139 (MQ=255)                                                      aCTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCGCGCCACTTCCGGTGcc                                         >  1:819121/1‑139 (MQ=255)                                                       cTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCGCGCCACTTCCGGTGccc                                        <  2:452870/139‑1 (MQ=255)                                                              ttaATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCGCGCCACTTCCGGTGCCCAtcatca                                 <  1:111354/139‑1 (MQ=255)                                                               taATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTcg                                                         <  1:433880/114‑1 (MQ=255)                                                               taATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTcg                                                         >  2:433880/1‑114 (MQ=255)                                                                aaTGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAA‑TTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCGCGCCACTTCCGGTGCCCATCATCaag                               >  2:428701/1‑138 (MQ=255)                                                                 aTGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGtt                                                            >  1:418796/1‑109 (MQ=255)                                                                 aTGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGtt                                                            <  2:418796/109‑1 (MQ=255)                                                                    ttCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCGCGCCACTTCCGGTGcc                                         <  1:397898/125‑1 (MQ=255)                                                                    ttCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCGCGCCACTTCCGGTGcc                                         >  2:397898/1‑125 (MQ=255)                                                                              cTCCGGCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCg                                                                      >  2:217228/1‑86 (MQ=255)                                                                              cTCCGGCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCg                                                                      <  1:217228/86‑1 (MQ=255)                                                                              cTCCGGCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCGCGCCACTTCCGGTGCCCATCATCAAGAAGGTCTGGTCATg                 <  1:724795/139‑1 (MQ=255)                                                                                 cGGCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCGCGCCACTTCCGGTGCCCATCATCAAGAAGGTCTGGTCATGACg              >  1:324198/1‑139 (MQ=255)                                                                                   gCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCGCGCCACTTCCGGTGCCCATCATCAAGAAGGTCTGGTCATGACGt             >  1:56075/1‑138 (MQ=255)                                                                                    cAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCGCGCCACTTCCGGTGCCCATCATCAAGAAGGTCTGGTCATGACGTTa           <  2:857575/139‑1 (MQ=255)                                                                                      acgacgGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCGCGCCACTTCCGGTGCCCATCATCAAGAAGGTCTGGTCATGACGTTAAc         >  1:729391/1‑139 (MQ=255)                                                                                          cgGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCGCGCCACTTCCGGTGCCCATCATCAAGAAGGTCTGGTCATGACGTTAACTGCt     <  1:168222/139‑1 (MQ=255)                                                                                             cgcAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCGCGCCACTTCCGGTGCCCATCATCAAGAAGGTCTGGTCATGACGTTAACTGCTTCa  >  1:637483/1‑139 (MQ=255)                                                                                                       |                                                                                                                                 GCGGTCTTGATGGCCTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCGCGCCACTTCCGGTGCCCATCATCAAGAAGGTCTGGTCATGACGTTAACTGCTTCA  >  NZ_CP009273/1335965‑1336195

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑