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%	84.7 / NA	25	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 (15/10);  total (15/10)

TACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATAC  >  NZ_CP009273/1972605‑1972771                                                                                        |                                                                                 tACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCT‑AATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑Ggggggg                                                                              >  1:316141/1‑90 (MQ=255)        aGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGc                                                                        <  1:675041/90‑1 (MQ=255)             tGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGAttt                                                                   >  2:665267/1‑90 (MQ=255)                 tCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCaa                                                               >  1:15593/1‑90 (MQ=255)                   tttACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCaata                                                             >  1:506166/1‑90 (MQ=255)                         cTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGA‑TTTCAATAATGCGTg                                                      >  1:617486/1‑90 (MQ=255)                          ttATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGTGGCGTTTTTCATTAATGCgga                                                      >  1:478468/1‑88 (MQ=255)                           tATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGGCTGCGATTTTCAATAATGCggg                                                      >  2:448586/1‑88 (MQ=255)                                    tttttCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATca                                            <  2:566480/90‑1 (MQ=255)                                     ttttCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATcac                                           >  1:277678/1‑90 (MQ=255)                                      tttCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATcaca                                          >  2:738880/1‑90 (MQ=255)                                         ccTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACaa                                       <  2:416036/90‑1 (MQ=255)                                            aaaTCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAac                                    <  2:118660/90‑1 (MQ=255)                                                 gACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCa                               >  2:643553/1‑90 (MQ=255)                                                   cGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAAt                             <  1:55170/90‑1 (MQ=255)                                                   agCAACCGGACTCCTCCCCACCCGCAACTTCAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAAt                             <  2:478468/89‑1 (MQ=255)                                                    gCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAAtt                            <  1:738880/90‑1 (MQ=255)                                                                  cACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtg              >  1:611794‑M1/1‑82 (MQ=255)                                                                    cTACACGCATATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTa                           <  2:153727/75‑1 (MQ=255)                                                                    cTACACGCACATACAAC‑GGGTGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTa                           >  1:153727/1‑75 (MQ=255)                                                                    cTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcg            >  2:740212‑M1/1‑80 (MQ=255)                                                                           cacaTACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagt     >  2:83676‑M1/1‑73 (MQ=255)                                                                             caTACAAC‑GGGGGGGGGCTGCGA‑TTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccc  <  2:617486‑M1/90‑21 (MQ=255)                                                                              aTACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccc  >  2:114532‑M1/1‑70 (MQ=255)                                                                              aTACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaaca        >  2:197127‑M1/1‑70 (MQ=255)                                                                              aTACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaaca        <  1:197127‑M1/84‑15 (MQ=255)                                                                                        |                                                                                 TACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATAC  >  NZ_CP009273/1972605‑1972771

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑