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%	191.5 / NA	67	Y240D (TAC→GAC)	lptD	LPS assembly protein LptD
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base C (39/28);  total (39/28)

TGCCACGACGATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTAGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGCTATAA  >  NZ_CP009273/56305‑56477                                                                                        |                                                                                      tGCCACGACGATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAagtcgt                                                                                     >  1:26531/1‑90 (MQ=255)  gCCACGACGATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGtt                                                                                    <  1:1014412/90‑1 (MQ=255)  gCCACGACGATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGtt                                                                                    <  2:741566/90‑1 (MQ=255)     acgacgATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTtggt                                                                                 <  2:590729/90‑1 (MQ=255)     acgacgATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTtggt                                                                                 <  2:542517/90‑1 (MQ=255)     acgacgATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTtggt                                                                                 <  1:95047/90‑1 (MQ=255)     acgacgATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTtggt                                                                                 <  1:523197/90‑1 (MQ=255)     acgacgATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTtggt                                                                                 <  2:8783/90‑1 (MQ=255)       gacgaTGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTtggtgg                                                                               >  2:770542/1‑90 (MQ=255)          gaTGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTtggtggtgg                                                                            <  2:727659/90‑1 (MQ=255)                  taATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTg                                                                    >  2:90691/1‑90 (MQ=255)                  taATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGGGGGGGTGTACTTg                                                                    >  2:1130175/1‑90 (MQ=255)                  taATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAAATCAAAGTCGTTGGTGGTGGGGTACTTg                                                                    >  2:602721/1‑90 (MQ=255)                    aTGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGc                                                                  >  2:1207244/1‑90 (MQ=255)                    aTGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAGTCGTTGGTGGTGGGGTACTTGGc                                                                  >  2:706869/1‑90 (MQ=255)                    aTGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAAATCAAAGGCGGTGGGGGGGGGGTACTTggg                                                                  >  1:198805/1‑89 (MQ=255)                      gcggcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAGTCGTTGGGGGGGGGGTACTTTGCgg                                                                >  2:767891/1‑89 (MQ=255)                       cggcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGtt                                                               <  1:131839/90‑1 (MQ=255)                       cggcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAAATCAAAGTCGTTTGTGGGGGGGGACTTTTCGtt                                                               >  2:674988/1‑90 (MQ=255)                       cggcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAGTCGTTGGTGGTGGTGTACTTTGCGtt                                                               >  1:853429/1‑90 (MQ=255)                       cggcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAGTCGTTGGTGGGGGTGTACTTTGCGtt                                                               >  2:1105560/1‑90 (MQ=255)                       cggcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAGTCGTTGGTGGGGGGGTACTTGGCGtt                                                               >  1:96705/1‑90 (MQ=255)                       cggcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAAATCAAAGTCGTTGGTGGGGGGGTACTTGGGGtt                                                               >  1:331728/1‑90 (MQ=255)                         gcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCg                                                             >  2:40737/1‑90 (MQ=255)                         gcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGGGGTGTACTTGGCGGTCg                                                             >  2:700262/1‑90 (MQ=255)                         gcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGGGGTGGTGTACTTGGCGTTCg                                                             >  2:439777/1‑90 (MQ=255)                         gcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAGTCGTTGGTGGGGGTGTACTTGGCGTTCg                                                             >  2:763321/1‑90 (MQ=255)                         gcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAGTCGTTGGTGGGGGTGTACTTGGCGTTCg                                                             >  1:423036/1‑90 (MQ=255)                         gcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAGTCGTTGGTGGGGGGGTACTTGGCGGTCg                                                             >  2:702967/1‑90 (MQ=255)                         gcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAACTCAAAATCGTTGGGGGGGGTGTACTTTGCGTTCg                                                             >  1:1218675/1‑90 (MQ=255)                         gcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAAATCAAAGTCGTTGGGGGGGGGGGACTTGGCGGTCg                                                             >  2:801623/1‑90 (MQ=255)                         gcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAAATCAAAGACGTTGGGGGTGGGGTACTTTGCGtttg                                                             >  1:909503/1‑88 (MQ=255)                         gcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAAATCAAAATCGTTGGTGGGGGGGTACTTTGCGGTCg                                                             >  1:442920/1‑90 (MQ=255)                         gcgTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGGAGAAATCAAAATCGTTGGGGGGGGGGGACTTGGCGTTCg                                                             >  1:345984/1‑90 (MQ=255)                         gcatGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAAATCGAAGTCGTTGGGGGGGGTGGAGTTGGCGGTCg                                                             >  2:569597/4‑90 (MQ=255)                              aTGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATc                                                        <  2:798619/90‑1 (MQ=255)                                 gtggCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAg                                                     <  1:564789/90‑1 (MQ=255)                                     cATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTTGCGTTCGGGATCAAGaaaa                                                 >  2:813756/1‑89 (MQ=255)                                     cATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGGGTACTTGGCGTTCGGGATCAAGAAAc                                                 >  2:149210/1‑90 (MQ=255)                                               tGGCGCGATGTTCCAGTAATATGGCAGGGAGAAATCAAAATCGTTGGTGGGGGGGTACTTGGGGTTCGGGGTCAAGAAACCAGAGCGACg                                       >  1:959668/1‑90 (MQ=255)                                                 gcgcGATGTTCCAGTAATATGGCAGGGAGAACTCAAAGTCGTTGGTGGGGGGGTACTTGGCGTTCGGGATCAAGAAAACAGAGCGACggt                                     >  2:880964/1‑88 (MQ=255)                                                 gcgcGATGTTCCAGTAATATGGCAGGGAGAAATCAAAATCGTTGGGGGGGGGGTACTTGGCGTTCGGGGGCAAAAAACCAGAGCGGCGtt                                     >  1:133489/1‑90 (MQ=255)                                                  cgcgATGTTCCAGTAATATGGCAGGGAGAACTCAAAATCGTTGGGGGGGGGGTACTTGGGGGTCGGGGTCAAAAAAACAGAGCGACGttt                                    >  1:377377/1‑90 (MQ=255)                                                     gATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTc                                 <  1:90691/90‑1 (MQ=255)                                                                aaTATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCa                      <  2:696201/90‑1 (MQ=255)                                                                aaTATGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCa                      <  1:801623/90‑1 (MQ=255)                                                                aaTATGGCAGGGAGAACTCAAAATCGTTGGGGGGGGTGTACTTTGCGTTTGGGGTCAAGAAACCAGAGCGGCGGTTTTCACCCCCCGGCa                      >  1:700264/1‑90 (MQ=255)                                                                 atatGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCaa                     <  1:1121738/90‑1 (MQ=255)                                                                 atatGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCaa                     <  1:1207244/90‑1 (MQ=255)                                                                 atatGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCaa                     <  1:880964/90‑1 (MQ=255)                                                                  tatGGCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAAc                    <  1:854253/90‑1 (MQ=255)                                                                     ggCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGc                 <  2:93765/90‑1 (MQ=255)                                                                     ggCAGGTAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGc                 >  2:982948/1‑90 (MQ=255)                                                                        aGGTAGGACTCAAAGTCGTTGGGGGGGGTGGAGTTGGCGGTCGGGATTAAGGAAACAAGGGGACGTTTGTCACCCACCCGCAGCTGCaaa              >  1:481732/1‑90 (MQ=255)                                                                           tAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAg           <  2:147817/90‑1 (MQ=255)                                                                           tAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAg           <  1:611862/90‑1 (MQ=255)                                                                           tAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAg           <  1:412959/90‑1 (MQ=255)                                                                           tAGAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAg           <  2:904126/90‑1 (MQ=255)                                                                             gAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAggg         <  2:797193/90‑1 (MQ=255)                                                                             gAACTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAggg         <  1:1236618/90‑1 (MQ=255)                                                                               aCTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGc       <  2:331728/90‑1 (MQ=255)                                                                               aCTCAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGc       <  2:1191626/90‑1 (MQ=255)                                                                                  cAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGCtat    >  2:148496/1‑90 (MQ=255)                                                                                  cAAAGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGCtat    >  1:482171/1‑90 (MQ=255)                                                                                    aaGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAAc                    <  2:1017566/72‑1 (MQ=255)                                                                                    aaGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAAc                    >  1:1017566/1‑72 (MQ=255)                                                                                    aaGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGCTATaa  >  1:1040913/1‑90 (MQ=255)                                                                                    aaGTCGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGCTATaa  >  2:979261/1‑90 (MQ=255)                                                                                        |                                                                                      TGCCACGACGATGCATATAATGCGGCGTGATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTAGTTGGTGGTGGTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGCTATAA  >  NZ_CP009273/56305‑56477

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: ‑