Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	55,712	A→G	Y466Y (TAT→TAC)	lptD ←	lipopolysaccharide assembly protein LptD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	55,712	0	A	G	100.0%	113.2 / NA	33	Y466Y (TAT→TAC)	lptD	lipopolysaccharide assembly protein LptD
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (14/19);  total (14/19)

ATTTTGCCGTCAACTTTGAATTGCGGCATTACGCGGTTAACGGATTCGTCCAGCTTGGTCGTGTTTCTGGAGTTATACCAGTCAAGATTGGTTTGCTGATAATGGGTTGCCAGCAACTTCGCTTCGGTATTGATGCTGCCCCAGTTATTAGA  >  NC_000913/55638‑55789                                                                           |                                                                              aTTTTGCCGTCAACTTTGAATTGCGGCATTACGCGGTTAACGGATTCGTCCAGCTTGGTCGTGTTTCTGGAGTTGTACCAg                                                                         >  1:13599/1‑81 (MQ=255)    ttGCCGTCAACTTTGAATTGCGGCATTACGCGGTTAACGGATTCGTCCAGCTTGGTCGTGTTTCTGGAGTTGTACCAGTc                                                                       <  1:13543/80‑1 (MQ=255)          tCAACTTTGAATTGCGGCATTACGCGGTTAACGGATTCGTCCAGCTTGGTCGTGTTTCTGGAGTTGTACCAGTCAAGATTg                                                                >  2:13600/1‑81 (MQ=255)            aaCTTTGAATTGCGGCATTACGCGGTTAACGGATTCGTCCAGCTTGGTCGTGTTTCTGGAGTTGTACCAGTCAAGATTGGt                                                              <  2:13544/81‑1 (MQ=255)                 tGAATTGCGGCATTACGCGGTTAACGGATTCGTCCAGCTTGGTCGTGTTTCTGGAGTTGTACCAGTCAAGATTGGTTTGCt                                                         >  1:13605/1‑81 (MQ=255)                  gAATTGCGGCATTACGCGGTTAACGGATTCGTCCAGCTTGGTCGTGTTTCTGGAGTTGTACCAGTCAAGATTGGTTTGCt                                                         <  1:13545/80‑1 (MQ=255)                  gAATTGCGGCATTACGCGGTTAACGGATTCGTCCAGCTTGGTCGTGTTTCTGGAGTTGTACCAGTCAAGATTGGTTTGCt                                                         <  1:13546/80‑1 (MQ=255)                        cGGCATTACGCGGTTAACGGATTCGTCCAGCTTGGTCGTGTTTCTGGAGTTGTACCAGTCAAGATTGGTTTGCTGATAAt                                                   <  1:13547/80‑1 (MQ=255)                              tACGCGGTTAACGGATTCGTCCAGCTTGGTCGTGTTTCTGGAGTTGTACCAGTCAAGATTGGTTTGCTGATAATGGGTTGc                                            >  1:13606/1‑81 (MQ=255)                                cgcgGTTAACGGATTCGTCCAGCTTGGTCGTGTTTCTGGAGTTGTACCAGTCAAGATTGGTTTGCTGATAATGGGTTGcc                                           <  2:13548/80‑1 (MQ=255)                                 gcgGTTAACGGATTCGTCCAGCTTGGTCGTGTTTCTGGAGTTGTACCAGTCAAGATTGGTTTGCTGATAATGGGTTGCCAg                                         >  2:13589/1‑81 (MQ=255)                                 gcgGTTAACGGATTCGTCCAGCTTGGTCGTGTTTCTGGAGTTGTACCAGTCAAGATTGGTTTGCTGATAATGGGTTGCCAg                                         <  2:13549/81‑1 (MQ=255)                                     ttAACGGATTCGTCCAGCTTGGTCGTGTTTCTGGAGTTGTACCAGTCAAGATTGGTTTGCTGATAATGGGTTGCCAGCAAc                                     <  2:13550/81‑1 (MQ=255)                                      tAACGGATTCGTCCAGCTTGGTCGTGTTTCTGGAGTTGTACCAGTCAAGATTGGTTTGCTGATAATGGGTTGCCAGCAAct                                    >  1:13604/1‑81 (MQ=255)                                      tAACGGATTCGTCCAGCTTGGTCGTGTTTCTGGAGTTGCACCAGTCAAGATTGGTTTGCTGATAATGGGTTGCCAGCAAct                                    >  1:13615/1‑81 (MQ=255)                                              tCGTCCAGCTTGGTCGTGTTTCTGGAGTTGTACCAGTCAAGATTGGTTTGCTGATAATGGGTTGCCAGCAActtcgcttcg                            >  1:13609/1‑81 (MQ=255)                                                  ccAGCTTGGTCGTGTTTCTGGAGTTGTACCAGTCAAGATTGGTTTGCTGATAATGGGTTGCCAGCAACTTCGCTTCGGTAt                        >  2:13608/1‑81 (MQ=255)                                                  ccAGCTCGGTCGTGTTTCTGGAGTTGTACCAGTCAAGATTGGTTTGCTGATAATGGGTTGCCAGCAACTTCGCTTCGGTAt                        >  2:13607/1‑81 (MQ=255)                                                   cAGCTTGGTCGTGTTTCTGGAGTTGTACCAGTCAAGATTGGTTTGCTGATAATGGGTTGCCAGCAACTTCGCTTCGGTAt                        <  1:13552/80‑1 (MQ=255)                                                   cAGCTTGGTCGTGTTTCTGGAGTTGTACCAGTCAAGATTGGTTTGCTGATAATGGGTTGCCAGCAACTTCGCTTCGGTAt                        <  2:13551/80‑1 (MQ=255)                                                        tGGTCGTGTTTCTGGAGTTGTACCAGTCAAGATTGGTTTGCTGATAATGGGTTGCCAGCAACTTCGCTTCGGTATTGAtgc                  >  1:13592/1‑81 (MQ=255)                                                         ggTCGTGTTTCTGGAGTTGTACCAGTCAAGATTGGTTTGCTGATAATGGGTTGCCAGCAACTTCGCTTCGGTATTGAtgc                  <  2:13553/80‑1 (MQ=255)                                                         ggTCGTGTTTCTGGAGTTGTACCAGTCAAGATTGGTTTGCTGATAATGGGTTGCCAGCAACTTCGCTTCGGTATTGAtg                   <  2:13554/79‑1 (MQ=255)                                                          gTCGTGTTTCTGGAGTTGTACCAGTCAAGATTGGTTTGCTGATAATGGGTTGCCAGCAACTTCGCTTCGGTATTGAtgctg                <  2:13556/81‑1 (MQ=255)                                                          gTCGTGTTTCTGGAGTTGTACCAGTCAAGATTGGTTTGCTGATAATGGGTTGCCAGCAACTTCGCTTCGGTATTGAtgct                 <  2:13555/80‑1 (MQ=255)                                                             gtgtTTCTGGAGTTGTACCAGTCAAGATTGGTTTGCTGATAATGGGTTGCCAGCAACTTCGCTTCGGTATTGATGCTGccc             >  1:13597/1‑81 (MQ=255)                                                             gtgtTTCTGGAGTTGTACCAGTCAAGATTGGTTTGCTGATAATGGGTTGCCAGCAACTTCGCTTCGGTATTGATGCTGccc             >  1:13596/1‑81 (MQ=255)                                                             gtgtTTCTGGAGTTGTACCAGTCAAGATTGGTTTGCTGATAATGGGTTGCCAGCAACTTCGCTTCGGTATTGATGCTGcc              <  2:13557/80‑1 (MQ=255)                                                              tgtTTCTGGAGTTGTACCAGTCAAGATTGGTTTGCTGATAATGGGTTGCCAGCAACTTCGCTTCGGTATTGATGCTGcccc            <  2:13558/81‑1 (MQ=255)                                                                   cTGGAGTTGTACCAGTCAAGATTGGTTTGCTGATAATGGGTTGCCAGCAACTTCGCTTCGGTATTGATGCTGCCCCAGtt        <  1:13559/80‑1 (MQ=255)                                                                      gAGTTGTACCAGTCAAGATTGGTTTGCTGATAATGGGTTGCCAGCAACTTCGCTTCGGTATTGATGCTGCCCCAGttatt     <  1:13560/80‑1 (MQ=255)                                                                        gTTGTACCAGTCAAGATTGGTTTGCTGATAATGGGTTGCCAGCAACTTCGCTTCGGTATTGATGCTGCCCCAGttatta    >  2:13613/1‑79 (MQ=255)                                                                        gTTGTACCAGTCAAGATTGGTTTGCTGATAATGGGTTGCCAGCAACTTCGCTTCGGTATTGATGCTGCCCCAGTTATTaga  <  2:13561/81‑1 (MQ=255)                                                                           |                                                                              ATTTTGCCGTCAACTTTGAATTGCGGCATTACGCGGTTAACGGATTCGTCCAGCTTGGTCGTGTTTCTGGAGTTATACCAGTCAAGATTGGTTTGCTGATAATGGGTTGCCAGCAACTTCGCTTCGGTATTGATGCTGCCCCAGTTATTAGA  >  NC_000913/55638‑55789

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑