Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,336,062	A→G	intergenic (+78/‑116)	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	1,336,062	0	A	G	100.0%	185.5 / NA	49	intergenic (+78/‑116)	lapB/pyrF	lipopolysaccharide assembly protein LapB/orotidine‑5'‑phosphate decarboxylase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (29/20);  total (29/20)

CCTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCGCGCCA  >  NZ_CP009273/1335978‑1336145                                                                                     |                                                                                    ccTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAg                                                                                >  1:83079/1‑90 (MQ=255) ccTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAg                                                                                >  2:1486458/1‑90 (MQ=255) ccTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAg                                                                                >  1:351838/1‑90 (MQ=255) ccTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAg                                                                                >  1:499159/1‑90 (MQ=255) ccTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAg                                                                                >  2:2735346/1‑90 (MQ=255)    gTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCt                                                                             >  1:2613395/1‑90 (MQ=255)        tttttAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCa                                                                         <  1:1171867/90‑1 (MQ=255)              aaaaaaaTCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGgag                                                                   <  2:2613395/90‑1 (MQ=255)                     tCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGc                                                            <  2:2434678/90‑1 (MQ=255)                                        tACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTAttt                                         >  2:2662235/1‑90 (MQ=255)                                         aCTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGAAACTGTTAATTTTTTATTTc                                        >  1:2139964/1‑90 (MQ=255)                                           tAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCa                                      <  1:1744806/90‑1 (MQ=255)                                            aaTTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCAc                                     <  1:865178/90‑1 (MQ=255)                                            aaTTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCAc                                     <  1:1975597/90‑1 (MQ=255)                                             attattAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACg                                    <  1:1141370/90‑1 (MQ=255)                                             attattAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACg                                    <  2:1764180/90‑1 (MQ=255)                                               tattaATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGaa                                                                 >  1:224887/1‑59 (MQ=255)                                               tattaATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGaa                                                                 <  2:224887/59‑1 (MQ=255)                                               tattaATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACggg                                  >  2:477021/1‑90 (MQ=255)                                                attaATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGt                                 >  1:877516/1‑90 (MQ=255)                                                 ttaATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACg                                    <  2:1768184/86‑1 (MQ=255)                                                 ttaATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACg                                    >  1:1768184/1‑86 (MQ=255)                                                      gTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATg                           >  1:2764419/1‑90 (MQ=255)                                                      gTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATg                           >  1:1861263/1‑90 (MQ=255)                                                        tCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCt                         >  1:1124817/1‑90 (MQ=255)                                                        tCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCt                         >  1:826858/1‑90 (MQ=255)                                                         ccATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTc                        <  2:2968992/90‑1 (MQ=255)                                                           aTTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGc                      <  2:1431116/90‑1 (MQ=255)                                                           aTTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGc                      <  2:351838/90‑1 (MQ=255)                                                            ttGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGcc                     >  2:2102413/1‑90 (MQ=255)                                                              gtgCTCCGGCAACGACGGCGCAGGAAAAGCCTTCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGt                   >  1:1955505/1‑90 (MQ=255)                                                              gtgCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTAttt                                         <  2:1046801/68‑1 (MQ=255)                                                              gtgCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTAttt                                         >  1:1046801/1‑68 (MQ=255)                                                              gtgCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGt                   >  2:977967/1‑90 (MQ=255)                                                              gtgCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGt                   >  1:2901838/1‑90 (MQ=255)                                                              gtgCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGt                   >  2:1738447/1‑90 (MQ=255)                                                                gCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTcc                                       >  1:584544/1‑68 (MQ=255)                                                                gCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTcc                                       <  2:584544/68‑1 (MQ=255)                                                                gCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGGATGCTCGCCGttt                 >  1:2612173/1‑90 (MQ=255)                                                                gCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGttt                 >  1:1236964/1‑90 (MQ=255)                                                                   ccGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTAAATTTTTTATTTCCAc                                     <  2:2389322/67‑1 (MQ=255)                                                                   ccGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTAAATTTTTTATTTCCAc                                     >  1:2389322/1‑67 (MQ=255)                                                                     ggCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCAc                                     <  1:2310689/65‑1 (MQ=255)                                                                     ggCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCAc                                     >  2:2310689/1‑65 (MQ=255)                                                                           gacgGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGCAGAATGCTCGCCGTTTACCTGTTTcgc      >  1:2913992/1‑90 (MQ=255)                                                                              ggCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCGCGcc   <  2:1124817/90‑1 (MQ=255)                                                                               gcgcAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTc                        <  2:2855965/68‑1 (MQ=255)                                                                               gcgcAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTc                        >  1:2855965/1‑68 (MQ=255)                                                                               gcgcAGGAAAAGCATGCCAGGGGGGAAAACGCAACTGTTTATTTTTTATTTCCACTGGTACAATGTTCGCCGTTTACCTGTCTCgcgctg  <  1:1774734/90‑3 (MQ=255)                                                                                     |                                                                                    CCTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCGCGCCA  >  NZ_CP009273/1335978‑1336145

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑