Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,972,691	A→G	intergenic (‑237/‑543)	flhD ← / → uspC	flagellar transcriptional regulator FlhD/universal stress protein UspC

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,972,691	0	A	G	100.0%	35.4 / NA	12	intergenic (‑237/‑543)	flhD/uspC	flagellar transcriptional regulator FlhD/universal stress protein UspC
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (5/7);  total (5/7)

CTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACT  >  NZ_CP009273/1972629‑1972772                                                                |                                                                                  cTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGt                                                        <  1:266737/90‑1 (MQ=255)  ttATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTg                                                       >  2:153867/1‑90 (MQ=255)      cTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGGCTGCGATTTTCAATAATGCGTGATg                                                    >  2:264403/1‑90 (MQ=255)                     aaTCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAaca                                    <  2:120404/90‑1 (MQ=255)                       tCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAacac                                   <  1:264403/90‑1 (MQ=255)                           cGCAACTGTACTCGTCACGACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAAt                              <  2:265307/90‑1 (MQ=255)                              aaCTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTAc                           <  2:95253/90‑1 (MQ=255)                                      tCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACCCAAAACACTCAATTACTTAAggaa                   <  1:212850‑M1/90‑5 (MQ=255)                                            cTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcg             >  2:70548‑M1/1‑80 (MQ=255)                                                   cacaTACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagt      >  1:379587‑M1/1‑73 (MQ=255)                                                   cacaTACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagt      >  2:70962‑M1/1‑73 (MQ=255)                                                       tACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccct  <  2:74565‑M1/90‑22 (MQ=255)                                                                |                                                                                  CTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACT  >  NZ_CP009273/1972629‑1972772

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑