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%	69.3 / NA	25	Y240D (TAC→GAC)	lptD	LPS assembly protein LptD
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base C (14/11);  total (14/11)

ACGACGATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTAGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGCTAT  >  NZ_CP009273/56309‑56475                                                                                    |                                                                                    acgacgATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTtggt                                                                               <  2:206545/90‑1 (MQ=255)  cgacgaTGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTtggtg                                                                              >  1:187321/1‑90 (MQ=255)      gaTGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTtggtggtgg                                                                          <  1:57002/90‑1 (MQ=255)       aTGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAAATCAAAATCGGtggtggtggg                                                                         >  1:287059/1‑89 (MQ=255)                    ggcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAAGCGGTGGTGGGGGTGGACTTGGCGGTc                                                            >  2:472982/1‑90 (MQ=255)                     gcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCg                                                           <  1:389836/90‑1 (MQ=255)                     gcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGGGGTGTACTTGGCGTTCg                                                           >  1:144378/1‑90 (MQ=255)                     gcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAGTCGTTGGTGGTGGGGTACTTGGCGTTCg                                                           >  1:395617/1‑90 (MQ=255)                     gcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAGTCGTTGGGGGTGGGGTACTTGGCGTTCg                                                           >  2:25040/1‑90 (MQ=255)                     gcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAGTCGTTGGGGGGGGGGTACTTTGCGGTCg                                                           >  2:81073/1‑90 (MQ=255)                        tGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGa                                                        <  2:335095/90‑1 (MQ=255)                                  aTCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAGTCGTTGGGGGTGGTGGACTTGGCGGTCGGGGTCAAGaaaac                                              >  2:99918/1‑88 (MQ=255)                                         tttGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGa                                       <  1:279104/90‑1 (MQ=255)                                           tGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACg                                     >  1:190596/1‑90 (MQ=255)                                             gcgcGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGtt                                   <  1:353956/90‑1 (MQ=255)                                             gcgcGATGTTCCAGTAATATGGCAGGGAGAAATCAAAATCGTTGGGGGGGGGGTACTTGGGGTTCGGGGTCAAGAAACCAGAGCGACGtt                                   >  2:396942/1‑90 (MQ=255)                                              cgcgATGTTCCAGTAATATGGCAGGGAGAACTCAAAAGCGTTGGGGGGGGGGGACTTTGCGTTCGGGATCAAAAAAACAGAGCGGCGttt                                  >  2:279104/1‑90 (MQ=255)                                                             atatGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCaa                   <  2:174494/90‑1 (MQ=255)                                                             atatGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCaa                   <  1:59699/90‑1 (MQ=255)                                                             atatGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCaa                   <  2:287059/90‑1 (MQ=255)                                                                    aGGGAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAAACAGAGCGACGTTTGTCACCCACCGGCAACTGCaaa            >  2:62489/1‑90 (MQ=255)                                                                      gTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATa          <  2:74805/90‑1 (MQ=255)                                                                              cAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGCtat  >  1:79625/1‑90 (MQ=255)                                                                                aaGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGc     <  2:334426/85‑1 (MQ=255)                                                                                aaGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGc     >  1:334426/1‑85 (MQ=255)                                                                                    |                                                                                    ACGACGATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTAGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGCTAT  >  NZ_CP009273/56309‑56475

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑