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%	54.4 / NA	21	Y240D (TAC→GAC)	lptD	LPS assembly protein LptD
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base C (12/9);  total (12/9)

ACGACGATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTAGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGCTATAA  >  NZ_CP009273/56309‑56477                                                                                    |                                                                                      acgacgATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTtggt                                                                                 <  1:1384/90‑1 (MQ=255)  cgacgaTGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGGGAACTCCAAATCGTtgggg                                                                                >  1:582606/1‑88 (MQ=255)   gacgaTGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAGTCGTtggtgg                                                                               >  2:197454/1‑90 (MQ=255)   gacgaTGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAGGCGTtggggg                                                                               >  2:465342/1‑90 (MQ=255)      gaTGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTtggtggtgg                                                                            <  2:299716/90‑1 (MQ=255)                  gcggcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGt                                                                >  2:196876/1‑90 (MQ=255)                    ggcgTGTTGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGGGAACTCAAAAGCGTTGGGGGTGGGGGACTTTGCggtt                                                              >  1:478874/1‑87 (MQ=255)                     gcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAGTCGTTGGGGGGGGGGTACTTGGCGTTCg                                                             >  2:567382/1‑90 (MQ=255)                     gcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAAATCAAAGGCGTTGGGGGGGGTGTACTTGGCGTTCg                                                             >  2:409048/1‑90 (MQ=255)                               ggCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAGTCGTTGGTGGTGGGGTACTTGGCGTTCGGGGTCAAGaa                                                   >  2:464314/1‑90 (MQ=255)                                          ttGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGAc                                        <  2:480482/90‑1 (MQ=255)                                            ggCGCGATGTTCCAGTAATATGGCAGGTAAAACTCAAAATCGTTGGGGGGGGGGTACTTTGCTTTCGGGATCAAAAAAACAGAACGACGt                                      >  2:265226/1‑90 (MQ=255)                                                       ccAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTcacccac                           <  2:213933/90‑1 (MQ=255)                                                            aaTATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCa                      <  1:464314/90‑1 (MQ=255)                                                              tatGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAAc                    <  1:482223/90‑1 (MQ=255)                                                                    aGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCaaa              >  2:15566/1‑90 (MQ=255)                                                                       tAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAg           <  1:15566/90‑1 (MQ=255)                                                                         gAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAggg         >  1:166681/1‑90 (MQ=255)                                                                           aCTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGc       <  1:204485/90‑1 (MQ=255)                                                                               aaaGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGCtata   <  2:214166/90‑1 (MQ=255)                                                                                aaGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGCTATaa  >  1:566032/1‑90 (MQ=255)                                                                                    |                                                                                      ACGACGATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTAGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGCTATAA  >  NZ_CP009273/56309‑56477

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑