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%	77.5 / NA	24	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 (8/16);  total (8/16)

TTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTG  >  NZ_CP009273/1972604‑1972776                                                                                        |                                                                                      ttACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGgggg                                                                                     <  1:242872/90‑1 (MQ=255)     aaaTAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGgggggggg                                                                                 >  1:212525/1‑90 (MQ=255)         aGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGc                                                                             <  1:464325/90‑1 (MQ=255)               gggTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGAtttt                                                                       <  1:266692/90‑1 (MQ=255)                     ttACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCaataa                                                                 <  2:37298/90‑1 (MQ=255)                          cTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGt                                                            <  2:292823/90‑1 (MQ=255)                           ttATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTg                                                           >  2:337437/1‑90 (MQ=255)                           ttATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTg                                                           >  2:280277/1‑90 (MQ=255)                           ttATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTg                                                           >  2:150122/1‑90 (MQ=255)                            tATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGa                                                          >  2:3591/1‑90 (MQ=255)                                       tttCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATcaca                                               >  1:18567/1‑90 (MQ=255)                                               aTCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAacac                                       <  1:3591/90‑1 (MQ=255)                                                    cGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAAt                                  <  1:280277/90‑1 (MQ=255)                                                     gCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAAtt                                 <  2:333535/90‑1 (MQ=255)                                                     gCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAAtt                                 <  2:212525/90‑1 (MQ=255)                                                             aCTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAAtt                                 <  1:152977/82‑1 (MQ=255)                                                             aCTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAAtt                                 >  2:152977/1‑82 (MQ=255)                                                               tCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaa                       <  1:134433‑M1/90‑5 (MQ=255)                                                                   cACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtg                   <  1:213453‑M1/90‑9 (MQ=255)                                                                        cacGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaac              <  1:182908‑M1/90‑14 (MQ=255)                                                                            cacaTACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagt          <  1:228985‑M1/90‑18 (MQ=255)                                                                               aTACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGc                                                       >  1:451284/1‑42 (MQ=255)                                                                               aTACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGc                                                       <  2:451284/42‑1 (MQ=255)                                                                               aTACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccc       <  1:340273‑M1/90‑21 (MQ=255)                                                                               aTACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccc       <  2:401055‑M1/90‑21 (MQ=255)                                                                                    aCGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgata  >  1:97441‑M1/1‑65 (MQ=255)                                                                                        |                                                                                      TTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTG  >  NZ_CP009273/1972604‑1972776

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑