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%	35.9 / NA	11	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 (6/5);  total (6/5)

TACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCA  >  NZ_CP009273/1972605‑1972768                                                                                        |                                                                              tACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑gggggg                                                                            >  2:186754/1‑90 (MQ=255)        aGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGc                                                                     <  1:86524/90‑1 (MQ=255)        aGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGc                                                                     <  2:98956/90‑1 (MQ=255)                        acTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGGCTGCGATTTTCAATAATGc                                                      <  1:186754/90‑1 (MQ=255)                         cTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGt                                                    <  1:256902/90‑1 (MQ=255)                          ttATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTg                                                   >  2:144194/1‑90 (MQ=255)                           tATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGGCTGCGATTTTCAATAATGCGTg                                                   >  1:208693/1‑90 (MQ=255)                                     ttttCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATcac                                        >  1:296376/1‑90 (MQ=255)                                                                 tCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggt            >  1:32427‑M1/1‑83 (MQ=255)                                                                    cTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcg         >  1:299076‑M1/1‑80 (MQ=255)                                                                    cTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcg         >  2:265972‑M1/1‑80 (MQ=255)                                                                           cacaTACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagt  <  2:299076‑M1/90‑18 (MQ=255)                                                                                        |                                                                              TACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCA  >  NZ_CP009273/1972605‑1972768

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑