Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	56,392	A→C	Y240D (TAC→GAC)	lptD ←	LPS assembly protein LptD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	56,392	0	A	C	100.0%	47.7 / NA	18	Y240D (TAC→GAC)	lptD	LPS assembly protein LptD
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base C (9/9);  total (9/9)

ACGACGATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTAGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGC  >  NZ_CP009273/56309‑56472                                                                                    |                                                                                 acgacgATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTtggt                                                                            <  1:468851/90‑1 (MQ=255)   gacgaTGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTtggtgg                                                                          <  2:55385/90‑1 (MQ=255)      gaTGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTtggtggtgg                                                                       <  1:517790/90‑1 (MQ=255)                aTGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAAATCAAAATCGTTGGTGGGGGGGTACTTTGc                                                             >  1:165490/1‑90 (MQ=255)                   cggcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGtt                                                          <  1:455226/90‑1 (MQ=255)                    ggcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAGTCGTTGGTGGGGGGGTACTTGGCGTTc                                                         >  1:173715/1‑90 (MQ=255)                     gcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAAACGTTGGGGGGGGGGTACTTGGCGGTCg                                                        >  2:473403/1‑90 (MQ=255)                     gcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAGTCGTTGGTGGGGGTGTACTTGGCGTTCg                                                        >  2:76573/1‑90 (MQ=255)                     gcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAATCGTTGGGGGGGGGGTACTTTGCGTTCg                                                        >  1:195248/1‑90 (MQ=255)                                      atatTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGGGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCagag                                       >  2:539381/1‑90 (MQ=255)                                         tttGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGa                                    <  2:103174/90‑1 (MQ=255)                                         tttGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGa                                    <  2:337946/90‑1 (MQ=255)                                            ggCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGGGGTGGACTTGGCGTTCGGGGTCAAGAAAACAGAGCGACGt                                 >  1:81585/1‑90 (MQ=255)                                                             atatGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCaa                <  2:165490/90‑1 (MQ=255)                                                             atatGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCaa                <  1:473403/90‑1 (MQ=255)                                                              tatGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAAc               <  2:168598/90‑1 (MQ=255)                                                                    aGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCaaa         >  1:210509/1‑90 (MQ=255)                                                                           aCTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGc  >  2:338757/1‑90 (MQ=255)                                                                                    |                                                                                 ACGACGATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTAGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGC  >  NZ_CP009273/56309‑56472

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑