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%	110.8 / NA	40	Y240D (TAC→GAC)	lptD	LPS assembly protein LptD
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base C (24/16);  total (24/16)

GCCACGACGATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTAGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGCTATAA  >  NZ_CP009273/56306‑56477                                                                                       |                                                                                      gctacgacgATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGtt                                                                                    <  2:421184/87‑1 (MQ=255)    acgacgATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTtggt                                                                                 <  1:606572/90‑1 (MQ=255)      gacgaTGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTtggtgg                                                                               <  1:421197/90‑1 (MQ=255)        cgaTGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTtggtggtg                                                                             <  2:34445/90‑1 (MQ=255)          aTGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACACCAAATCGTtggggggggg                                                                           >  1:349302/1‑89 (MQ=255)                 taATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGGGGTGGTGTACTTg                                                                    >  2:318631/1‑90 (MQ=255)                 taATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAATCGTTGGTGGTGGGGTACttt                                                                    >  2:49516/1‑89 (MQ=255)                   aTGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAGTCGTTGGGGGGGGGGTACTTggg                                                                  >  2:53089/1‑89 (MQ=255)                     gcggcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAGTCGTTGGTGGGGGTGTACTTGGCGt                                                                >  2:269952/1‑90 (MQ=255)                      cggcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGtt                                                               >  2:280833/1‑90 (MQ=255)                        gcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAAATCAAAGTCGTTGGGGGTGGTGTACTTGGCGGTCg                                                             >  2:299031/1‑90 (MQ=255)                        gcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAGTCGTTGGTGGGGGTGGACTTGGCGTTCg                                                             >  2:196970/1‑90 (MQ=255)                        gcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAATCGTTGGTGGGGGGGTACTTGGGGTTCg                                                             >  1:207079/1‑90 (MQ=255)                        gcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAATCGTTGGTGGGGGGGGACTTGGGGTGCg                                                             >  1:765970/1‑90 (MQ=255)                        gcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAAATCAAAGTCGTTGGGGGTGGGGGACTTGGCGTTCg                                                             >  1:70520/1‑90 (MQ=255)                        gcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAAATCAAAAACGTTGGGGGGGGGGGAATTGGCGGTCg                                                             >  1:484711/1‑90 (MQ=255)                         cgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAAATCAAAATCGGTGGGGGGGGTGGACTTTGGGTTCgg                                                            >  2:343478/1‑90 (MQ=255)                           tGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGa                                                          <  1:280833/90‑1 (MQ=255)                           tGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGa                                                          <  1:343478/90‑1 (MQ=255)                                  ggCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAATCGTTGGTGGGGGGGTACTTGGGGGTCGGGATCAAGaa                                                   >  2:474207/1‑90 (MQ=255)                                         atatTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGGGTACTTGGCGTTCGGGATCAAGAAACCagag                                            >  2:363750/1‑90 (MQ=255)                                                gcgcGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGGCGTTGGTGGGGGGGTACTTGGCGTTCGGGGTCAAGAAACCAGAGCGACggt                                     >  2:720982/1‑88 (MQ=255)                                                 cgcgATGTTCCAGTAATATGGCAGGGAGAAATCAAAATCGTTGGGGGGGGGGGACTTTGCGTTTGGGGTCAAGAAAACAAAGCGGCGttt                                    >  1:378861/1‑90 (MQ=255)                                                  gcgATGTTCCAGTAATATGGCAGGGAGAACTCAAAGTCGGTGGTGGTGGTGTACTTGGGGGTCGGGATCAAGAAACCAGAGCGACGTTTg                                   >  2:388259/1‑90 (MQ=255)                                                       gTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTcacc                              <  2:207079/90‑1 (MQ=255)                                                               aaTATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCa                      <  1:218115/90‑1 (MQ=255)                                                               aaTATGGCAGGTAGAACTCAAAATCGTTGGTGGGGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCCCCGGCa                      >  2:190511/1‑90 (MQ=255)                                                                 tatGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAAc                    <  2:484711/90‑1 (MQ=255)                                                                  atGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACt                   <  1:671660/90‑1 (MQ=255)                                                                      cAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGGTCAAGAAAACAAAGCGACGTTTGTCACCCACCGGCAACTGGaa               >  2:328897/1‑90 (MQ=255)                                                                       aGGGAGAACTCAAAGGCGTTGGTGGGGGGGTACTTGGCGTTTGGGGTCAAGAAACCAAAGCGGCGTTTGTCACCCACCGGCAACTGCaaa              >  1:33153/1‑90 (MQ=255)                                                                          tAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAg           <  1:616442/90‑1 (MQ=255)                                                                            gAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCaa                     <  2:145212/78‑1 (MQ=255)                                                                            gAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCaa                     >  1:145212/1‑78 (MQ=255)                                                                            gAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAggg         <  2:33153/90‑1 (MQ=255)                                                                              aCTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGc       >  2:140261/1‑90 (MQ=255)                                                                              aCTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGc       <  1:603818/90‑1 (MQ=255)                                                                              aCTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGc       <  2:301524/90‑1 (MQ=255)                                                                                  aaaGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGCtata   <  2:595315/90‑1 (MQ=255)                                                                                   aaGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGCTATaa  >  1:426731/1‑90 (MQ=255)                                                                                       |                                                                                      GCCACGACGATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTAGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGCTATAA  >  NZ_CP009273/56306‑56477

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑