Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	554,427	A→G	intergenic (+217/‑3)	fimA → / → fimC	type 1 fimbrial major subunit FimA/type 1 fimbria chaperone FimC

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	554,427	0	A	G	100.0%	138.9 / NA	42	intergenic (+217/‑3)	fimA/fimC	type 1 fimbrial major subunit FimA/type 1 fimbria chaperone FimC
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (20/22);  total (20/22)

TGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAACTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCGC  >  NZ_CP009273/554349‑554512                                                                               |                                                                                      tgatgTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACt                                                                            <  2:244839/90‑1 (MQ=255)      tgttgtAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAAt                                                                       <  2:846912/90‑1 (MQ=255)      tgttgtAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAAt                                                                       >  1:1265656/1‑90 (MQ=255)      tgttgtAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAAt                                                                       >  1:1529664/1‑90 (MQ=255)      tgttgtAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAAt                                                                       >  1:217101/1‑90 (MQ=255)       gttgtAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAGTACACAAGGCGTATTAGCTATGATGACTAAAATa                                                                      <  2:264371/90‑1 (MQ=255)       gttgtAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATa                                                                      <  1:58637/90‑1 (MQ=255)          gtAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTatgatg                                                                               >  1:53803/1‑78 (MQ=255)          gtAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTatgatg                                                                               <  2:53803/78‑1 (MQ=255)               aaaCCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGAc                                                                             >  2:871763/1‑75 (MQ=255)               aaaCCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGAc                                                                             <  1:871763/75‑1 (MQ=255)                aaCCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAGAATAAAGTTATTg                                                             >  1:1372335/1‑90 (MQ=255)                    aaaGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGc                                                         <  1:551145/90‑1 (MQ=255)                    aaaGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGc                                                         <  1:609723/90‑1 (MQ=255)                          aTCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATta                                                   <  2:1509209/90‑1 (MQ=255)                               ttCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTAtattt                                              <  2:730381/90‑1 (MQ=255)                               ttCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTAtattt                                              <  1:1198731/90‑1 (MQ=255)                               ttCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTAtattt                                              <  2:1419041/90‑1 (MQ=255)                                 cTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATg                                                          >  2:37633/1‑76 (MQ=255)                                 cTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATg                                                          <  1:37633/76‑1 (MQ=255)                                          ccTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCAt                                   >  2:1429314/1‑90 (MQ=255)                                           cTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCAtt                                  >  1:1339210/1‑90 (MQ=255)                                                 tttGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGcc                            <  1:670820/90‑1 (MQ=255)                                                   tGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAg                          >  1:1185409/1‑90 (MQ=255)                                                         cAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCa                    >  1:565404/1‑90 (MQ=255)                                                            gAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCAtgc                 <  1:906443/90‑1 (MQ=255)                                                            gAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCAtgc                 <  1:1050093/90‑1 (MQ=255)                                                               tACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCAtgctgc              <  1:944292/90‑1 (MQ=255)                                                                     aGGCGTATTAGTTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCa                           >  2:253032/1‑71 (MQ=255)                                                                     aGGCGTATTAGTTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCa                           <  1:253032/71‑1 (MQ=255)                                                                     aGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAgg        >  1:146917/1‑90 (MQ=255)                                                                     aGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAgg        >  1:1504774/1‑90 (MQ=255)                                                                     aGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAgg        >  2:447799/1‑90 (MQ=255)                                                                      ggCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAggg       >  2:1087073/1‑90 (MQ=255)                                                                        cGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGAt     <  1:722914/90‑1 (MQ=255)                                                                        cGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGAt     <  2:344383/90‑1 (MQ=255)                                                                         gTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATc    <  2:146917/90‑1 (MQ=255)                                                                          tATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCg   >  1:419476/1‑90 (MQ=255)                                                                          tATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCg   >  1:655786/1‑90 (MQ=255)                                                                           aTTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGa      >  2:1079336/1‑86 (MQ=255)                                                                           aTTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGa      <  1:1079336/86‑1 (MQ=255)                                                                           aTTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCGc  >  1:365259/1‑90 (MQ=255)                                                                               |                                                                                      TGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAACTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCGC  >  NZ_CP009273/554349‑554512

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑