Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,136,234	A→G	E249G (GAA→GGA)	flgL →	flagellar hook‑associated protein FlgL

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,136,234	0	A	G	100.0%	90.9 / NA	25	E249G (GAA→GGA)	flgL	flagellar hook‑associated protein FlgL
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (7/18);  total (7/18)

GCGGATAAAGAAACCGCCGCTGCGGCGTTAGATAAAACCAACCGCGGACTGAAAAACTCGCTGAACAATGTGCTGACTGTTCGCGCGGAATTAGGCACGCAGCTGAACGAACTGGAGTCGCTGGATTCATTAGGTAGCGATCGCGCTTTAGGGCAAACGCAGCAGATGAGCGATC  >  NZ_CP009273/1136146‑1136320                                                                                         |                                                                                       gCGGATAAAGAAACCGCCGCTGCGGCGTTAGATAAAACCAACCGCGGACTGAAAAACTCGCTGAACAATGTGCTGACTGTTCGCGCGGGAt                                                                                      >  2:393883/1‑91 (MQ=255)   ggATAAAGAAACCGCCGCTGCGGCGTTAGATAAAACCAACCGCGGACTGAAAAACTCGCTGAACAATGTGCTGACTGTTCGCGCGGGATTa                                                                                    <  1:393883/91‑1 (MQ=255)        aaGAAACCGCCGCTGCGGCGTTAGATAAAACCAACCGCGGACTGAAAAACTCGCTGAACAATGTGCTGACTGTTCGCGCGGGATTAGGCAc                                                                               <  1:569182/91‑1 (MQ=255)        aaGAAACCGCCGCTGCGGCGTTAGATAAAACCAACCGCGGACTGAAAAACTCGCTGAACAATGTGCTGACTGTTCGCGCGGGATTAGGCAc                                                                               >  2:159400/1‑91 (MQ=255)        aaGAAACCGCCGCTGCGGCGTTAGATAAAACCAACCGCGGACTGAAAAACTCGCTGAACAATGTGCTGACTGTTCGCGCGGGATTAGGCAc                                                                               <  2:411421/91‑1 (MQ=255)          ggaaCCGCCGCTGCGGCGTTAGATAAAACCAACCGCGGACTGAAAAACTCGCTGAACAATGTGCTGACTGTTCGCGCGGGATTAGGCACGc                                                                             <  2:611009/89‑1 (MQ=255)               cgccgcTGCGGCGTTAGATAAAACCAACCGCGGACTGAAAAACTCGCTGAACAATGTGCTGACTGTTCGCGCGGGATTAGGCACGCAGCTg                                                                        <  1:865203/91‑1 (MQ=255)                               gATAAAACCAACCGCGGACTGAAAAACTCGCTGAACAATGTGCTGACTGTTCGCGCGGGATTAGGCACGCAGCTGAACGAACTGGAGTCGc                                                        <  1:528667/91‑1 (MQ=255)                               gATAAAACCAACCGCGGACTGAAAAACTCGCTGAACAATGTGCTGACTGTTCGCGCGGGATTAGGCACGCAGCTGAACGAACTGGAGTCGc                                                        <  2:354922/91‑1 (MQ=255)                                 tAAAACCAACCGCGGACTGAAAAACTCGCTGAACAATGTGCTGACTGTTCGCGCTGGATTAGGCACGCAGCTGAACGAACTGGAGTCGCTg                                                      <  1:855656/91‑1 (MQ=255)                                   aaaCCAACCGCGGACTGAAAAACTCGCTGAACAATGTGCTGACTGTTCGCGCGGGATTAGGCACGCAGCTGAACGAACTGGAGTCGCTGGa                                                    >  2:782418/1‑91 (MQ=255)                                   aaaCCAACCGCGGACTGAAAAACTCGCTGAACAATGTGCTGACTGTTCGCGCGGGATTAGGCACGCAGCTGAACGAACTGGAGTCGCTGGa                                                    <  2:64548/91‑1 (MQ=255)                                     accaaccGCGGACTGAAAAACTCGCTGAACAATGTGCTGACTGTTCGCGCGGGATTAGGCACGCAGCTGAACGAACTGGAGTCGCTGGAtt                                                  <  1:280181/91‑1 (MQ=255)                                     accaaccGCGGACTGAAAAACTCGCTGAACAATGTGCTGACTGTTCGCGCGGGATTAGGCACGCAGCTGAACGAACTGGAGTCGCTGGAtt                                                  <  1:604977/91‑1 (MQ=255)                                        aaccGCGGACTGAAAAACTCGCTGAACAATGTGCTGACTGTTCGCGCGGGATTAGGCACGCAGCTGAACGAACTGGAGTCGCTGGGTTCAt                                               >  2:777288/1‑91 (MQ=255)                                        aaccGCGGACTGAAAAACTCGCTGAACAATGTGCTGACTGTTCGCGCGGGATTAGGCACGCAGCTGAACGAACTGGAGTCGCTGGATTCAt                                               <  2:811109/91‑1 (MQ=255)                                        aaccGCGGACTGAAAAACTCGCTGAACAATGTGCTGACTGTTCGCGCGGGATTAGGCACGCAGCTGAACGAACTGGAGTCGCTGGATTCAt                                               >  2:189920/1‑91 (MQ=255)                                         accGCGGACTGAAAAACTCGCTGAACAATGTGCTGACTGTTCGCGCGGGATTAGGCACGCAGCTGAACGAACTGGAGTCGCTGGATTCact                                              <  1:547665/91‑3 (MQ=255)                                              ggACTGAAAAACTCGCTGAACAATGTGCTGACTGTTCGCGCGGGATTAGGCACGCAGCTGAACGAACTGGAGTCGCTGGATTCATTAGGTa                                         >  2:698752/1‑91 (MQ=255)                                                      aaaCTCGCTGAACAATGTGCTGACTGTTCGCGCGGGATTAGGCACGCAGCTGAACGAACTGGAGTCGCTGGATTCATTAGGTAGCGATcgc                                 <  2:425349/91‑1 (MQ=255)                                                                   aaTGTGCTGACTGTTCGCGCGGGATTAGGCACGCAGCTGAACGAACTGGAGTCGCTGGATTCATTAGGTAGCGATCGCGCTTTAGGGCaaa                    >  2:443527/1‑91 (MQ=255)                                                                    aTGTGCTGACTGTTCGCGCGGGATTAGGCACGCAGCTGAACGAACTGGAGTCGCTGGATTCATTAGGTAGCGATCGCGCTTTAGGGCAAAc                   <  1:316880/91‑1 (MQ=255)                                                                      gtgCTGACTGTTCGCGCGGGAGTAGGCACGCAGCTGAACGAACTGGAGTCGCTGGATTCATTAGGTAGCGATCGCGCTTTAGGGCAAACgc                 <  2:179669/91‑1 (MQ=255)                                                                         cTGACTGTTCGCGCGGGATTAGGCACGCAGCTGAACGAACTGGAGTCGCTGGATTCATTAGGTAGCGATCGCGCTTTAGGGCAAACgcagc              <  1:1712/91‑1 (MQ=255)                                                                                     gcgGGATTAGGCACGCAGCTGAACGAACTGGAGTCGCTGGATTCATTAGGTAGCGATCGCGCTTTAGGGCAAACGCAGCAGATGAGCGATc  <  2:73073/91‑1 (MQ=255)                                                                                         |                                                                                       GCGGATAAAGAAACCGCCGCTGCGGCGTTAGATAAAACCAACCGCGGACTGAAAAACTCGCTGAACAATGTGCTGACTGTTCGCGCGGAATTAGGCACGCAGCTGAACGAACTGGAGTCGCTGGATTCATTAGGTAGCGATCGCGCTTTAGGGCAAACGCAGCAGATGAGCGATC  >  NZ_CP009273/1136146‑1136320

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑