Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,003,791	(A)8→7	intergenic (‑185/‑81)	fliC ← / → fliD	flagellar filament structural protein/flagellar filament capping protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,003,784	0	A	.	100.0%	132.9 / NA	32	intergenic (‑178/‑88)	fliC/fliD	flagellar filament structural protein/flagellar filament capping protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (11/21);  total (11/21)

ACCCGTCGGCTCAATCGCCGTCAACCCTGTTATCGTCTGTCGTAAAACAACCTTTAGAATTTTTTTCAAAAACAGCCATTTTTTGTTAGTCGCCGAAATACTCTTTTCTCTGCCCCTTATTCCCGCTATTAAAAAAAACAATTAAACGTAAACTTTGCGCAATTCAGACCGATAACCCCGGTATTCGTTTTACGTGTCGAAAGATAAAAGGAAATCGCATGGCAAGTATTTCATCGCTGGGAGTCGGGTCAGGTCTG  >  NC_000913/2003654‑2003910                                                                                                                                   |                                                                                                                               aCCCGTCGGCTCAATCGCCGTCAACCCTGTTATCGTCTGTCGTAAAACAACCTTTAGAATTTTTTTCAAAAACAGCCATTTTTTGTTAGTCGCCGAAATAATCTGTTCTCTGCCCCTAATTCCCGCTATTaaa                                                                                                                              >  2:201634/1‑133 (MQ=255)      tCGGCTCAATCGCCGTCAACCCTGTTATCGTCTGTCGTAAAACAACCTTTAGAATTTTTTTCAAAAACAGCCATTTTTTGTTAGTCGCCGAAATACTCTTTTCTCTGCCCCTTATTCCCGCTATTaaaaaaac                                                                                                                         >  1:574564/1‑132 (MQ=255)        ggCTCAATCGCCGTCAACCCTGTTATCGTCTGTCGTAAAACAACCTTTAGAATTTTTTTCAAAAACAGCCATTTTTTGTTAGTCGCCGAAATACTCTTTTCTCTGCCCCTTATTCCCGCTATTaaaaaaacaa                                                                                                                       >  2:450013/1‑130 (MQ=255)         gCTCAATCGCCGTCAACCCTGTTATCGTCTGTCGTAAAACAACCTTTAGAATTTTTTTCAAAAACAGCCATTTTTTGTTAGTCGCCGAAATACTCTTTTCTCTGCCCCTTATTCCCGCTATTaaaaaaacaat                                                                                                                      <  1:450013/133‑5 (MQ=255)         gCTCAATCGCCGTCAACCCTGTTATCGTCTGTCGTAAAACAACCTTTAGAATTTTTTTCAAAAACAGCCATTTTTTGTTAGTCGCCGAAATACTCTTTTCTCTGCCCCTTATTCCCGCTATTaaaaaaacaat                                                                                                                      <  1:322171/133‑5 (MQ=255)           tCAATCGCCGTCAACCCTGTTATCGTCTGTCGTAAAACAACCTTTAGAATTTTTTTCAAAAACAGCCATTTTTTGTTAGTCGCCGAAATACTCTTTTCTCTGCCCCTTATTCCCGCTATT‑AAAAAAACAATTa                                                                                                                   <  1:103891/133‑1 (MQ=255)             aaTCGCCGTCAACCCTGTTATCGTCTGTCGTAAAACAACCTTTAGAATTTTTTTCAAAAACAGCCATTTTTTGTTAGTCGCCGAAATACTCTTTTCTCTGCCCCTTATTCCCGCTATT‑AAAAAAACAATTaaa                                                                                                                 >  1:101496/1‑133 (MQ=255)               tCGCCGTCAACCCTGTTATCGTCTGTCG‑AAAACAACCTTTAGAATTTTTTTCAAAAACAGCCATTTTTTGTTAGTCGCCGAAATACTCTTTTCTCTGCCCCTTATTCCCGCTATT‑AAAAAAACAATTAAACGt                                                                                                              <  2:71914/133‑1 (MQ=255)                cGCCGTCAACCCTGTTATCGTCTGTCGTAAAACAACCTTTAGAATTTTTTTCAAAAACAGCCATTTTTTGTTAGTCGCCGAAATACTCTTTTCTCTGCCCCTTATTCCCGCTATT‑AAAAAAACAATTAAACGt                                                                                                              <  2:465803/133‑1 (MQ=255)                     tCAACCCTGTTATCGTCTGTCGTAAAACAACCTTTAGAATTTTTTTCAAAAACAGCCATTTTTTGTTAGTCGCCGAAATACTCTTTTCTCTGCCCCTTATTCCCGCTATT‑AAAAAAACAATTAAACGTAAACt                                                                                                         <  2:101496/133‑1 (MQ=255)                     tCAACCCTGTGATCGACTGTCGTACAACAACCCTTAGAATTGTTTTCAAAAACAGCCATTTTTTGTTAGTCGCCGAAATACTCTTTTCTCTGCCCCTTATTCCCGCTATT‑AAAAAAACAATTAAACGTAAACt                                                                                                         <  2:195564/133‑1 (MQ=255)                          ccTGTTATCGTCTGTCGTAAAACAACCTTTAGAATTTTTTTCAAAAACAGCCATTTTTTGTTAGTCGCCGAAATACTCTTTTCTCTGCCCCTTATTCCCGCTATT‑AAAAAAACAATTAAACGTAAACTTTgcg                                                                                                    <  1:373787/133‑1 (MQ=255)                          ccTGTTATCGTCTGTCGTAAAACAACCTTTAGAATTTTTTTCAAAAACAGCCATTTTTTGTTAGTCGCCGAAATACTCTTTTCTCTGCCCCTTATTCCCGCTATT‑AAAAAAACAATTAAACGTAAACTTTgcg                                                                                                    <  2:600341/133‑1 (MQ=255)                          ccTGTTATCGTCTGTCGTAAAACAACCTTTAGAATTTTTTTCAAAAACAGCCATTTTTTGTTAGTCGCCGAAATACTCTTTTCTCTGCCCCTTATTCCCGCTATT‑AAAAAAACAATTAAACGTAAACTTTgcg                                                                                                    <  2:625268/133‑1 (MQ=255)                                   gTCTGTCGTAAAACAACCTTTAGAATTTTTTTCAAAAACAGCCATTTTTTGTTAGTCGCCGAAATACTCTTTTCTCTGCCCCTTATTCCCGCTATT‑AAAAAAACAATTAAACGTAAACTTTGCGCAATTCAGa                                                                                           >  2:481043/1‑133 (MQ=255)                                    tCTGTCGTAAAACAACCTTTAGAATTTTTTTCAAAAACAGCCATTTTTTGTTAGTCGCCGAAATACTCTTTTCTCTGCCCCTTATTCCCGCTATT‑AAAAAAACAATTAAACGTAAACTTTGCGCAATTCAGAc                                                                                          >  1:468569/1‑133 (MQ=255)                                      tGTCGTAAAACAACCTTTAGAATTTTTTTCAAAAACAGCCATTTTTTGTTAGTCGCCGAAATACTCTTTTCTCTGCCCCTTATTCCCGCTATT‑AAAAAAACAATTAAACGTAAACTTTGCGCAATTCAGACCg                                                                                        >  1:622930/1‑133 (MQ=255)                                        tCGTAAAACAACCTTTAGAATTTTTTTCAAAAACAGCCATTTTTTGTTAGTCGCCGAAATACTCTTTTCTCTGCCCCTTATTCCCGCTATT‑AAAAAAACAATTAAACGTAAACTTTGCGCAATTCAGACCGAt                                                                                      >  1:358051/1‑133 (MQ=255)                                        tCGTAAAACAACCTTTAGAATTTTTTTCAAAAACAGCCATTTTTTGTTAGTCGCCGAAATACTCTTTTCTCTGCCCCTTATTCCCGCTATT‑AAAAAAACAATTAAACGTAAACTTTGCGCAATTCAGACCGAt                                                                                      >  1:42660/1‑133 (MQ=255)                                             aaaCAACCTTTAGAATTTTTTTCAAAAACAGCCATTTTTTGTTAGTCGCCGAAATACTCTTTTCTCTGCCCCTTATTCCCGCTATT‑AAAAAAACAATTAAACGTAAACTTTGCGCAATTCAGACCGATAAccc                                                                                 <  1:93289/133‑1 (MQ=255)                                                  acCTTTAGAATTTTTTTCAAAAACAGCCATTTTTTGTTAGTCGCCGAAATACTCTTTTCTCTGCCCCTTATTCCCGCTATT‑AAAAAAACAATTAAACGTAAACTTTGCGCAATTCAGACCGATAAccc                                                                                 >  2:500940/1‑128 (MQ=255)                                                  acCTTTAGAATTTTTTTCAAAAACAGCCATTTTTTGTTAGTCGCCGAAATACTCTTTTCTCTGCCCCTTATTCCCGCTATT‑AAAAAAACAATTAAACGTAAACTTTGCGCAATTCAGACCGATAAccc                                                                                 <  1:500940/128‑1 (MQ=255)                                                  acCTTTAGAATTTTTTTCAAAAACAGCCATTTTTTGTTAGTCGCCGAAATACTCTTTTCTCTGCCCCTTATTCCCGCTATT‑AAAAAAACAATTAAACGTAAACTTTGCGCAATTCAGACCGATAACCCCGGTa                                                                            >  2:393914/1‑133 (MQ=255)                                                        aGAATTTTTTTCAAAAACAGCCATTTTTTGTTAGTCGCCGAAATACTCTTTTCTCTGCCCCTTATTCCCGCTATT‑AAAAAAACAATTAAACCTAAACTTTGCGCAATTCAGACCGATCACCCAGGTATTCGtt                                                                      >  2:261658/1‑133 (MQ=255)                                                             ttttttCAAAAACAGCCATTTTTTGTTAGTCGCCGAAATACTCTTTTCTCTGCCCCTTATTCCCGCTATT‑AAAAAAACAATTAAACGTAAACTTTGCGCAATTCAGACCGATAACCCCGGTATTCGTTTTACg                                                                 <  1:579293/133‑1 (MQ=255)                                                                  tCAAAAACAGCCATTTTTTGTTAGTCGCCGAAATACTCTTTTCTCTGCCCCTTATTCCCGCTATT‑AAAAAAACAATTAAACGTAAACTTTGCGCAATTCAGACCGATAACCCCGGTATTCGTTTTACGTGTCg                                                            <  2:42660/133‑1 (MQ=255)                                                                         cAGCCATTTTTTGTTAGTCGCCGAAATACTCTTTTCTCTGCCCCTTATTCCCGCTATT‑AAAAAAACAATTAAACGTAAACTTTGCGCAATTCAGACCGATAACCCCGGTATTCGTTTTACGTGTCGAAAGATa                                                     <  1:481043/133‑1 (MQ=255)                                                                                        aGTCGCCGAAATACTCTTTTCTCTGCCCCTTATTCCCGCTATT‑AAAAAAACAATTAAACGTAAACTTTGCGCAATTCAGACCGATAACCCCGGTATTCGTTTTACGTGTCGAAAGATAAAAGGAAATCGCATg                                      <  2:317851/133‑1 (MQ=255)                                                                                         gTCGCCGAAATACTCTTTTCTCTGCCCCTTATTCCCGCTATT‑AAAAAAACAATTAAACGTAAACTTTGCGCAATTCAGACCGATAACCCCGGTATTCGTTTTACGTGTCGAAAGATAAAAGGAAATCGCATgg                                     <  1:151592/133‑1 (MQ=255)                                                                                            gCCGAAATACTCTTTTCTCTGCCCCTTATTCCCGCTATT‑AAAAAAACAATTAAACGTAAACTTTGCGCAATTCAGACCGATAACCCCGGTATTCGTTTTACGTGTCGAAAGATAAAAGGAAATCGCATGGCaa                                  <  2:622930/133‑1 (MQ=255)                                                                                                     ctctTTTCTCTGCCCCTTATTCCCGCTATT‑AAAAAAACAATTAAACGTAAACTTTGCGCAATTCAGACCGATAACCCCGGTATTCGTTTTACGTGTCGAAAGATAAAAGGAAATCGCATGGCAAGTATTTCAt                         >  2:8944/1‑133 (MQ=255)                                                                                                          ttCTCTGCTCCTTATCCCTGCTATT‑AAAAACACAATTAAACGTAAACTTTGCGCAATTCAGACCGATAACCCCGGTATTCGTTTTACGTGTCGAAAGATAAAAGGAAATCGCATGGCAAGTATTTCATCGCTg                    <  1:261658/133‑1 (MQ=255)                                                                                                               tGCCCCTTATTCCCGCTATT‑AAAAAAACAATTAAACGTAAACTTTGCGCAATTCAGACCGATAACCCCGGTATTCGTTTTACGTGTCGAAAGATAAAAGGAAATCGCATGGCAAGTATTTCATCGCTGGGAGt               >  2:332979/1‑133 (MQ=255)                                                                                                               tGCCCCTTATTCCCGCTATT‑AAAAAAACAATTAAACGTAAACTTTGCGCAATTCAGACCGATAACCCCGGTATTCGTTTTACGTGTCGAAAGATAAAAGGAAATCGCATGGCAAGTATTTCATCGCTGGGAGt               <  2:508427/133‑1 (MQ=255)                                                                                                                    cTTATTCCCGCTATT‑AAAAAAACAATTAAACGTAAACTTTGCGCAATTCAGACCGATAACCCCGGTATTCGTTTTACGTGTCGAAAGATAAAAGGAAATCGCATGGCAAGTATTTCATCGCTGGGAGTCGGGt          <  1:8944/133‑1 (MQ=255)                                                                                                                    cTTATTCCCGCTATT‑AAAAAAACAATTAAACGTAAACTTTGCGCAATTCAGACCGATAACCCCGGTATTCGTTTTACGTGTCGAAAGATAAAAGGAAATCGCATGGCAAGTATTTCATCGCTGGGAGTCGGGt          <  1:393914/133‑1 (MQ=255)                                                                                                                            cGCTATT‑AAAAAAACAATTAAACGTAAACTGTGCGCAATTCAGACCGATAACCCCGGTATTCGTTTTACGTGTCGAAAGATAAAAGGAAATCGCATGGCAAGTATTTCATCGCTGGGAGTCGGGTCAGGTCTg  <  1:201634/133‑1 (MQ=255)                                                                                                                                   |                                                                                                                               ACCCGTCGGCTCAATCGCCGTCAACCCTGTTATCGTCTGTCGTAAAACAACCTTTAGAATTTTTTTCAAAAACAGCCATTTTTTGTTAGTCGCCGAAATACTCTTTTCTCTGCCCCTTATTCCCGCTATTAAAAAAAACAATTAAACGTAAACTTTGCGCAATTCAGACCGATAACCCCGGTATTCGTTTTACGTGTCGAAAGATAAAAGGAAATCGCATGGCAAGTATTTCATCGCTGGGAGTCGGGTCAGGTCTG  >  NC_000913/2003654‑2003910

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑