Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	55,452	G→T	A553D (GCC→GAC)	lptD ←	lipopolysaccharide assembly protein LptD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	55,452	0	G	T	100.0%	136.9 / NA	39	A553D (GCC→GAC)	lptD	lipopolysaccharide assembly protein LptD
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (25/14);  total (25/14)

GTTCAACGGCAGCATCATCATATATGCGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGTCCCGGAACAGGCCAGAGTAGTCAGATTGCA  >  NC_000913/55390‑55512                                                               |                                                             gTTCAACGGCAGCATCATCATATATGCGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGTCa                                                            <  1:599226/65‑1 (MQ=255) gTTCAACGGCAGCATCATCATATATGCGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGTCa                                                            <  1:3707984/65‑1 (MQ=255)  ttCAACGGCAGCATCATCATATATGCGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGTCaa                                                           <  1:1142011/65‑1 (MQ=255)  ttCAACGGCAGCATCATCATATATGCGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGTCaa                                                           <  1:4055796/65‑1 (MQ=255)   tCAACGGCAGCATCATCATATATGCGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGTCAAt                                                          <  1:3226169/65‑1 (MQ=255)   tCAACGGCAGCATCATCATATATGCGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGTCAAt                                                          <  1:2525206/65‑1 (MQ=255)        ggCAGCATCATCATATATGCGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGTCAATACGGt                                                     <  1:3474853/65‑1 (MQ=255)        ggCAGCATCATCATATATGCGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGTCAATACGGt                                                     <  1:282231/65‑1 (MQ=255)        ggCAGCATCATCATATATGCGAGATGCGACACCGGTCGTCACCTGGTTAGCGGAGTCAATACGGt                                                     <  1:1390888/65‑1 (MQ=255)           agcaTCATCATATATGCGAGGTGTGACACCGGTCGTCACCTGGTTAGCGGAGTCAATACGGTCaa                                                  >  1:663696/1‑65 (MQ=255)            gcaTCATCATATATGCGAGATGTGACCCCGGTCGTCACCTGGTTAGCGGAGTCAATACGGTCAAg                                                 <  1:2069421/65‑1 (MQ=255)                  tcatATATGCGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGTCAATACGGTCAAGAccgcc                                           <  1:1824167/65‑1 (MQ=255)                   catATATGCGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGTCAATACGGTCAAGAccgccg                                          >  1:3279669/1‑65 (MQ=255)                    atatatGCGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGTCAATACGGTCAAGACCGCCGt                                         >  1:875462/1‑65 (MQ=255)                    atatatGCGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGTCAATACGGTCAAGACCGCCGt                                         >  1:4016397/1‑65 (MQ=255)                      atatGCGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGTCAATACGGTCAAGACCGCCGTaa                                       <  1:3894521/65‑1 (MQ=255)                       tatGCGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGTCAATACGGTCAAGACCGCCGTAAg                                      >  1:773069/1‑65 (MQ=255)                       tatGCGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGTCAATACGGTCAAGACCGCCGTAAg                                      >  1:1673290/1‑65 (MQ=255)                        atGCGAGATGTGACACCGGTCGTCACCGGGTTAGCGGAGTCAATACGGTCAAGACCGCCGTAAGt                                     <  1:1684167/65‑1 (MQ=255)                           cGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGTCAATACGGTCAAGACCGCCGTAAGTCCg                                  >  1:217705/1‑65 (MQ=255)                           cGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGTCAATACGGTCAAGACCGCCGTAAGTCCg                                  >  1:679518/1‑65 (MQ=255)                            gagaTGTGACACCGGTCGTCACCTGGTTAGCGGCGTCAATACGGTCAAGACCGCCGTAAGTCCgg                                 >  1:4542487/1‑65 (MQ=255)                                tgtgACACCGGCCGTCACCTGGTTAGCGGAGTCAATACGGTCAAGACCGCCGTAAGTCCGGTccc                             >  1:3834779/1‑65 (MQ=255)                                   gACACCGGTCGTCACCTGGTTAGCGGAGTCAATACGGTCAAGACCGCCGTAAGTCCGGTCCCGGa                          <  1:195789/65‑1 (MQ=255)                                    acacCGGTCGTCACCTGGTTAGCGGAGTCAATACGGTCAAGACCGCCGTAAGTCCGGTCCGGGaa                         >  1:1343235/1‑65 (MQ=255)                                      acCGGTCGTCACCTGGTTAGCGGAGTCAATACGGTCAAGACCGCCGTAAGTCCGGTCCCGGAACa                       >  1:3318212/1‑65 (MQ=255)                                      acCGGTCGTCACCTGGTTAGCGGAGTCAATACGGTCAAGACCGCCGTAAGTCCGGTCCCGGAACa                       >  1:4352808/1‑65 (MQ=255)                                      acCGGTCGTCACCTGGTTAGCGGAGTCAATACGGTCAAGACCGCCGTAAGTCCGGTCCCGGAACa                       >  1:1361999/1‑65 (MQ=255)                                      acCGGTCGTCACCTGGTTAGCGGAGTCAATACGGTCAAGACCGCCGTAAGTCCGGTCCCGGAACa                       >  1:2047764/1‑65 (MQ=255)                                      acCGGTCGTCACCTGGTTAGCGGAGTCAATACGGTCAAGACCGCCGTAAGTCCGGTCCCGGAACa                       >  1:3891685/1‑65 (MQ=255)                                      acCGGTCGTCACCTGGTTAGCGGAGTCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACa                       >  1:3092298/1‑65 (MQ=255)                                      acCGGTCGTCACCTGGTTAGCGGAGTCAATACGGTCAAGACCGCCGCAACTCCGGTCCCGGAACa                       >  1:2908113/1‑65 (MQ=255)                                        cgttcgtcACTTGGTTAGCGGAGTCAATACGGTCAAGACCGCCGTAAGTCCGGTCCCGGAACAgg                     <  1:2759885/62‑1 (MQ=255)                                        cGGTCGTCCCTTGGTTAGCGGAGTCAATACGGTCAAGACCGCCGTAAGTCCGGTCCCGGAACAgg                     <  1:2564431/65‑1 (MQ=255)                                        cGGTCGTCACCTGGTTAGCGCAGTCAATACGGTCAAGACCGCCGTAAGTCCGGTCCCGGAACAgg                     <  1:1812200/65‑1 (MQ=255)                                        cGGTCGTCACCTGGGTAGCGGAGTCACTACGGTCAAGCCCGCCGTAAGTCCGGTCCCGGAACAgg                     <  1:349944/65‑1 (MQ=255)                                         ggTCGTCACCTGGTTAGCGGAGTCAATACGCTCAAGACCGCCGTACGTCCGGTCCCGGAACAGGc                    >  1:576200/1‑65 (MQ=255)                                            cgtcACCTGGTTAGCGGAGTCAATACGGTCAAGACCGCCGTAAGTCCGGTCCCGGAACAGGCCag                 >  1:4022923/1‑65 (MQ=255)                                            cgtcACCTGGTTAGCGGAGTCAATACGGTCAAGACCGCCGTAAGTCCGGTCCCGGAACAGGCCag                 <  1:4567110/65‑1 (MQ=255)                                            cgtcACCTGGTTAGCGGAGTCAATACGGTCAAGACCGCCGTAAGTCCGGTCCCGGAACAGGCCag                 <  1:55527/65‑1 (MQ=255)                                            cgtcACCTGGTTAGCGGAGTCAATACGGTCAAGACCGCCGTAAGTCCGGTCCCGGAACAGCCCag                 >  1:1788731/1‑65 (MQ=255)                                                    ggTTAGCGGAGTCAATACGGTCAAGACCGCCGTAAGTCCGGTCCCGGAACAGGCCAGAGTAGTCa         >  1:3344754/1‑65 (MQ=255)                                                      ttAGGGGATCCAATACGGTCAAGCCCGCCGTAAGTCCGGTCCCGGAACAGGCCAGAGTAGTCAGa       <  1:2618276/65‑1 (MQ=255)                                                           ggAGTCGATACGGTCAAGACCGCCGTAAGTCCGGTCCCGGAACAGGCCAGAGTAGTCAGATTgca  >  1:1772168/1‑65 (MQ=255)                                                           ggAGTCAATACGGTCAAGACCGCCGTAAGTCCGGTCCCGGAACAGGCCAGAGTAGTCAGATTgca  >  1:3862361/1‑65 (MQ=255)                                                           ggAGTCAATACGGTCAAGACCGCCGTAAGTCCGGTCCCGGAACAGGCCAGAGTAGTCAGATTgca  <  1:1135298/65‑1 (MQ=255)                                                           ggAGTCAATACGGTCAAGACCGCCGTAAGTCCGGTCCCGGAACAGGCCAGAGGAGTCAGATTgca  >  1:2380935/1‑65 (MQ=255)                                                           ggAGTCAATACGGTCAAGACCGCCGTAAGTCCGGTCCCGGAACAGGCCAGAGGAGTCAGAGTgca  >  1:2817490/1‑65 (MQ=255)                                                               |                                                             GTTCAACGGCAGCATCATCATATATGCGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGTCCCGGAACAGGCCAGAGTAGTCAGATTGCA  >  NC_000913/55390‑55512

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑