Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,239,827	G→T	L53M (CTG→ATG)	ycgR ←	flagellar brake protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,239,827	0	G	T	88.9%	24.6 / NA	9	L53M (CTG→ATG)	ycgR	flagellar brake protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base T (4/4);  minor base C (0/1);  total (4/5)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGTTTCGGCGGTAATGGTAATGTGCTGTGCCTTTAGCACGGCGATGTTGTCTTCGGCTTGACTGCCGAAATCCAGCACCAGTTTATCCGGGGTTATTGCCAGTAATTTGCTGATCAGCTGCCCGCCATTCCAACTGAGAC  >  NZ_CP009273/1239753‑1239892                                                                           |                                                                  aGTTTCGGCGGTAATGGTAATGTGCTGTGCCTTTAGCACGGCGATGTTGTCTTCGGCTTGACTGCCGAAATCCATCACCAGTTTATCCgg                                                    <  1:385786/90‑1 (MQ=255) aGTTTCGGCGGTAATGGTAATGTGCTGTGCCTTTAGCACGGCGATGTTGTCTTCGGCTTGACTGCCGAAATCCATCACCAGTTTATCCgg                                                    <  2:419778/90‑1 (MQ=255)    ttCGGCGGTAATGGTAATGTGCTGTGCCTTTAGCACGGCGATGTTGTCTTCGGCTTGACTGCCGAAATCCATCACCAGTTTATCCGGGGt                                                 >  2:16448/1‑90 (MQ=255)                 gtaatgTGCTGTGCCTTTAGCACGGCGATGTTGTCTTCGGCTTGACTGCCGAAATCCATCACCAGTTTATCCGGGGTTATTGCCAGTAAt                                    <  1:247446/90‑1 (MQ=255)                                tttAGCACGGCGATGTTGTCTTCGGCTTGACTGCCGAAATCCATCACCAGTTTATCCGGGGTTATTGCCAGTAATTTGCTGATCAGCTGc                     >  2:402587/1‑90 (MQ=255)                                     cACGGCGATGTTGTCTTCGGCTTGACTGCCGAAATCCATCACCAGTTTATCCGGGGTTATTGCCAGTAATTTGCTGATCAGCTGCCCGcc                >  2:366016/1‑90 (MQ=255)                                                   tttCGGCTTGACTGCCGAAACCCACCCCCAGTTTATCCGGGGTTATTGCAAGTATTTTGTTGATCAGCTGCCCGCCATTCCAACTGAGAc  <  2:243098/89‑1 (MQ=255)                                                   cTTCGGCTTGACTGCCGAAATCCATCACCAGTTTATCCGGGGTTATTGCCAGt                                       >  1:211488/1‑53 (MQ=255)                                                   cTTCGGCTTGACTGCCGAAATCCATCACCAGTTTATCCGGGGTTATTGCCAGt                                       <  2:211488/53‑1 (MQ=255)                                                                           |                                                                  AGTTTCGGCGGTAATGGTAATGTGCTGTGCCTTTAGCACGGCGATGTTGTCTTCGGCTTGACTGCCGAAATCCAGCACCAGTTTATCCGGGGTTATTGCCAGTAATTTGCTGATCAGCTGCCCGCCATTCCAACTGAGAC  >  NZ_CP009273/1239753‑1239892

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑