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%	113.0 / 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 (15/13);  total (15/13)

ATTCGCGGTCTTGATGGCCTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCGCGCCACTTCCGGTGCCCATCATCAAGAAGGTCTGGTCATGACGTTAACTGCTTCA  >  NZ_CP009273/1335961‑1336195                                                                                                           |                                                                                                                                 aTTCGCGGTCTTGATGGCCTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAAttt                                                                                                  >  2:433524/1‑139 (MQ=255) aTTCGCGGTCTTGATGGCCTGTAATTTTTAAAAAAAATCAGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAAttt                                                                                                  >  2:492931/1‑139 (MQ=255)             gATGGCCTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTcc                                                                                         <  2:177366/136‑1 (MQ=255)             gATGGCCTGTAATTTTTAAAAAAAATCCGACTTCAGTTACAACATACCAATTATTAATGTACCATTGTGCTCCGGCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTcc                                                                                         <  1:487782/136‑1 (MQ=255)                        aTTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCt                                                                           <  1:229096/139‑1 (MQ=255)                           tttAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTg                                                                                                         <  1:562666/106‑1 (MQ=255)                           tttAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTg                                                                                                         >  2:562666/1‑106 (MQ=255)                              aaaaaaaaTCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCg                                                                      <  2:575477/138‑1 (MQ=255)                                               aGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCGCGcc                                                     <  2:323271/138‑1 (MQ=255)                                                          aCTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTCCCTGTTTCGCGCCACTTCCGGTGcc                                         >  1:526832/1‑139 (MQ=255)                                                               ttattaATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCgcgc                                                      <  1:416765/121‑1 (MQ=255)                                                               ttattaATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCgcgc                                                      >  2:416765/1‑121 (MQ=255)                                                                 attaATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCGCGCCACTTCCGGTGCCcatcat                                   >  1:262709/1‑138 (MQ=255)                                                                            aTTGTGCTCCGGCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTc                                                                                          >  1:374000/1‑72 (MQ=255)                                                                            aTTGTGCTCCGGCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTc                                                                                          <  2:374000/72‑1 (MQ=255)                                                                             ttGTGCTCCGGCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCgcgc                                                      <  1:577805/107‑1 (MQ=255)                                                                             ttGTGCTCCGGCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCgcgc                                                      >  2:577805/1‑107 (MQ=255)                                                                                tgCTCCGGCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCGCGCCACTTCCGGTGCCCATCATCAAGAAGGTCTGGTc                    <  1:433524/138‑1 (MQ=255)                                                                                  cTCCGTCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCGCGCCACTTCCGGTGCCCATCATCAAGAAGGTCTGGTCAt                  >  1:42181/1‑138 (MQ=255)                                                                                       gCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCa                                                                                        >  1:426375/1‑63 (MQ=255)                                                                                       gCAACGACGGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCa                                                                                        <  2:426375/63‑1 (MQ=255)                                                                                          acgacgGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCGCGCCACTTCCGGTGCCCATCATCAAGAAGGTCTGGTCATGACGTTAAc         >  1:570074/1‑139 (MQ=255)                                                                                            gacgGCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCGCGCCACTTCCGGTGCCCATCATCAAGACGGTCTGGTCATGACGTTAACTg       >  2:134970/1‑139 (MQ=255)                                                                                               ggCGCAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCGCGCCACTTCCGGTGCCCATCATCAAGAAGGTCTGGTCATGACGTTAACTGCtt    <  2:96347/139‑1 (MQ=255)                                                                                                 cgcAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCGCGCCACTTCCGGTGCCCATCATCaag                               >  2:326136/1‑110 (MQ=255)                                                                                                 cgcAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCGCGCCACTTCCGGTGCCCATCATCaag                               <  1:326136/110‑1 (MQ=255)                                                                                                 cgcAGAAAAAACCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCGCGCCACTTCCGGTGCCCATCATCAAGAAGGTCTGGTCATGACGTTAACTGCTTCa  >  1:436071/1‑139 (MQ=255)                                                                                                 cgcAGAAAAAACCTGCCAGGGGAGAAATCACAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCGCGCCACTTCCGGTGCCCATCATCAAGAAGGTCTGGTCATGACGTTAACTGCTTCa  >  2:391952/1‑139 (MQ=255)                                                                                                           |                                                                                                                                 ATTCGCGGTCTTGATGGCCTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCGCGCCACTTCCGGTGCCCATCATCAAGAAGGTCTGGTCATGACGTTAACTGCTTCA  >  NZ_CP009273/1335961‑1336195

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑