Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	55,482	T→C	D543G (GAC→GGC)	lptD ←	lipopolysaccharide assembly protein LptD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	55,482	0	T	C	100.0%	215.4 / NA	59	D543G (GAC→GGC)	lptD	lipopolysaccharide assembly protein LptD
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (25/34);  total (25/34)

GAGACTCCGTGAAATAGTAGATTTGACCAACGGAAATATTAAAACGTTCAACGGCAGCATCATCATATATGCGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGTCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGCTCTGATCGCGATACGGCACGTACAAATACTGCGCGCGCGGTTCCAGCGTTTGGGTATAACCCGGAGCCAGCA  >  NC_000913/55345‑55614                                                                                                                                          |                                                                                                                                     gagaCTCCGTGAAATAGTAGATTTGACCAACGGAAATATTAAAACGTTCAACGGCAGCATCATCATATATGCGAGAGGTGACACCGGTCGTCACCTGGTTAGCGGAGGCAATAGGGTCAAGACCGCCGTAAGTCCGGccc                                                                                                                                    <  2:115191/140‑1 (MQ=255)    aCTCCGTGAAATAGTAGATTTGACCAACGGAAATATTAAAACGTTCAACGGCAGCATCATCATATATGCGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCgg                                                                                                                                 >  1:703391/1‑140 (MQ=255)      tCCGTGAAATAGTAGATTTGCCCAACGGAAATATTAAAACGTTCAACGGCAGCATCATCATATATGCGAGATGTGACCCCGGTCGTCACCTGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGaa                                                                                                                               <  2:82862/140‑1 (MQ=255)      tCCGTGAAATAGTAGATTTGACCAACGGAAATATTAAAACGTTCAACGGCAGCATCATCATATATGCGAGATGTGACACCGGTCGTCCCCTGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGaa                                                                                                                               <  2:745145/140‑1 (MQ=255)      tCCGTGAAATAGTAGATTTGACCAACGGAAATATTAAAACGTTCAACGGCAGCATCATCATATATGCGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGaa                                                                                                                               <  1:90525/140‑1 (MQ=255)      tCCGTAAAATAGTAGATTTGACAAACGGAAATATTAAAACGTTCAACGGCAGCATCATAATATATGCGAGATGTGACCCCGGTCGTCACCTGGTTAGCGGAGGAAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGaa                                                                                                                               <  2:166990/140‑1 (MQ=255)          tGAAATAGTAGATTTGACCAACGGAAATATTAAAACGTTCAACGGCAGCATCATCATATATGCGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAgg                                                                                                                           <  1:482578/140‑1 (MQ=255)                  tagATTTGACCAACGGAAATATTAAAACGTTCAACGGCAGCATCATCATATATGCGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGagta                                                                                                                   >  2:239754/1‑140 (MQ=255)                    gATTTGACCAACGGAAATATTAAACCGTTCAACGGCAGCATCATCATATATGCGAGATGTGACACCGGTCGTCACCTGGTTAGGGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGagtagt                                                                                                                 <  1:694591/140‑1 (MQ=255)                         gACCAACGGAAATATTAAAACGTTCAACGGCAGCATCATCATATATGCGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGAt                                                                                                            <  1:571889/140‑1 (MQ=255)                               cGGAAATATTAAAACGTTCAACGGCAGCATCATCATATATGCGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTgcagc                                                                                                      >  1:550580/1‑140 (MQ=255)                                         aaaaCGTTCAACGGCAGCATCATCATATATGCGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGt                                                                                            <  2:746181/140‑1 (MQ=255)                                         aaaaCGTTCAACGGCAGCATCATCATATATGCGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGt                                                                                            <  2:749925/140‑1 (MQ=255)                                         aaaaCGTTCAACGGCAGCATCATCATATATGCGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGt                                                                                            <  1:570832/140‑1 (MQ=255)                                          aaccGTTCAACGGCGGCATCATAATATATGAGAGATGTGACCCCGGTCGTCACCGGGTTGGCGGAGGAAATCGGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTc                                                                                           <  2:703391/137‑1 (MQ=255)                                          aaaCGTTCAACGGCAGCATCATCATATATGCGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGGCAATCCGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTc                                                                                           <  2:281172/140‑1 (MQ=255)                                          aaaCGTTCAACGGCAGCATCATCATATATGCGAGATGTGACACCGGTCGTCACCTGGTTAGCAGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTc                                                                                           >  1:28495/1‑140 (MQ=255)                                           aaCGTTCAAGGGCAGCATCATCATATATGCGAGATGTGACACCGTTTGTCACCTGGTTAGCGGAGGAAATGGGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCg                                                                                          <  2:550580/140‑1 (MQ=255)                                           aaCGTTCAACGGCAGCATCATCATATATGCGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCg                                                                                          <  2:109097/140‑1 (MQ=255)                                               ttCAACGGCAGCATCATCATATATGCGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGt                                                                                      >  1:544732/1‑140 (MQ=255)                                               ttCAACGGCAGCATCATCATATATGCGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGt                                                                                      >  1:803193/1‑140 (MQ=255)                                                  aaCGGCAGCATCATCATATATGCGAGATGTGACCCCGGTCGTCACCTGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGTtat                                                                                   <  1:130159/140‑1 (MQ=255)                                                            tcatcatATATGCGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGct                                                                         <  1:354778/140‑1 (MQ=255)                                                              atcatATATGCGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGctct                                                                       >  2:682797/1‑140 (MQ=255)                                                                    tatGCGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTTAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGCTCTGATcgc                                                                 >  2:480394/1‑140 (MQ=255)                                                                     atGCGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGCTCTGATcgcg                                                                >  1:695362/1‑140 (MQ=255)                                                                     atGCGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGCTCTGATcgcg                                                                >  2:402798/1‑140 (MQ=255)                                                                       gCGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGCTCTGATCGCGAt                                                              >  2:76152/1‑140 (MQ=255)                                                                       gCGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGCTCTGATCGCGAt                                                              >  1:733018/1‑140 (MQ=255)                                                                       gCGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGCTCTGATCGCGAt                                                              >  1:377119/1‑140 (MQ=255)                                                                            aTGTGACACCGGTCGTCACCTGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGCTCTGATcg                                                                  <  1:511840/131‑1 (MQ=255)                                                                            aTGTGACACCGGTCGTCACCTGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGCTCTGATcg                                                                  >  2:511840/1‑131 (MQ=255)                                                                             tgtgACACCGGTCGTCACCTGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGCTCTGATCGCGATACGGCa                                                        <  1:239754/140‑1 (MQ=255)                                                                             tgtgACACCGGTCGTCACCTGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGCTCTGATCGCGATACGGCa                                                        <  1:369642/140‑1 (MQ=255)                                                                             tgtgACACCGGTCGTCACCTGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGCTCTGATCGCGATACGGCa                                                        <  2:544732/140‑1 (MQ=255)                                                                              gtgACACCGGTCGTCACCTGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGCTCTGATCGCGATACGGCAc                                                       >  2:600833/1‑140 (MQ=255)                                                                               taacacCGGTCGTCACCTGGTTAGCGGAGGCAATAGGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGCTCTGATCGCGATACGGCACg                                                      <  2:71034/138‑1 (MQ=255)                                                                                 acacCGGTCGTCACCTGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGCTCTGATCGCGATACGGCACGTa                                                    >  2:602340/1‑140 (MQ=255)                                                                                       gtcgtcACCTGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGCTCTGATCGCGATACg                                                           >  2:736094/1‑127 (MQ=255)                                                                                       gtcgtcACCTGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGCTCTGATCGCGATACg                                                           <  1:736094/127‑1 (MQ=255)                                                                                       gtcgtcACCTGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGCTCTGATCGCGATACGGCACGTACAAATa                                              <  1:416599/140‑1 (MQ=255)                                                                                          acagccTGTTTAGGGGAGGAAAACCGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGCTCTGATCGCGATACGGCACGTACAAATACTg                                           <  2:207279/136‑1 (MQ=255)                                                                                             aCCTGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGCTCTGATCGCGATACGGCa                                                        >  2:715162/1‑124 (MQ=255)                                                                                             aCCTGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGCTCTGATCGCGATACGGCa                                                        <  1:715162/124‑1 (MQ=255)                                                                                                tGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGCTCTGATCGCGATACGGCACGTACAAATACTgcgcgcg                                     <  1:682797/140‑1 (MQ=255)                                                                                                tGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGCTCTGATCGCGATACGGCACGTACAAATACTgcgcgcg                                     <  1:604822/140‑1 (MQ=255)                                                                                                  gTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGCTCTGATCGCGATACGGCACGTACAAATACTGcgcgcgcg                                   >  2:438759/1‑140 (MQ=255)                                                                                                      gCGGAGGCAATGCGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGCTCTGATCGCGATACGGCACGTACAAATACTGCGCGCGCGGTTc                               <  2:700703/140‑1 (MQ=255)                                                                                                         gAGGCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGCTCTGATCGCGATACGGCACGTACAAATACTGCGCGCGCGGTTctgt                            >  1:207279/1‑137 (MQ=255)                                                                                                            gCAATACGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGCTCTGATCGCGATACGGCACGTACAAATACTGCGCGCGCGGTTCCAGCGt                         >  1:165395/1‑140 (MQ=255)                                                                                                                tACGGTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGCTCTGATCGCGATACGGCACGTACAAATACTGCGCGCGCGGTTCCAGCGTTTgg                     >  1:121732/1‑140 (MQ=255)                                                                                                                    gtaaaGACCGCCGGAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGCTCTGATCGCGATACGGCACGTACAAATACTGCGCGCGCGGTTCCAGCGTTTGGGtat                 <  2:633702/137‑1 (MQ=255)                                                                                                                    gTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGCTCTGATCGCGATACGGCACGTACAAATACTGCGCGCGCGGTTCCAGCGTTTGGGtat                 >  2:498385/1‑140 (MQ=255)                                                                                                                    gTCAAGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGCTCTGATCGCGATACGGCACGTACAAATACTGCGCGCGCGGTTCCAGCGTTTGGGtat                 <  1:76152/140‑1 (MQ=255)                                                                                                                       aaGACCGCCGTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGCTCTGATCGCGATACGGCACGTACAAATACTGCGCGCGCGGTTCCAGCGTTTGGGTATAAc              >  1:619569/1‑140 (MQ=255)                                                                                                                            cgccgTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGCTCTGATCGCGATACGGCACGTACAAATACTGCGCGCGCGGTTCCAGCGTTTGGGTATAACCCGGa         <  2:28495/140‑1 (MQ=255)                                                                                                                            cgccgTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGCTCTGATCGCGATACGGCACGTACAAATACTGCGCGCGCGGTTCCAGCGTTTGGGTATAACCAGGa         <  1:602340/140‑1 (MQ=255)                                                                                                                               cgTAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGCTCTGATCGCGATACGGCACGTACAAATACTGCGCGCGCGGTTCCAGCGTTTGGGTATAACCCGGAGcc      <  1:438759/140‑1 (MQ=255)                                                                                                                                 tAAGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGCTCTGATCGCGATACGGCACGTACAAATACTGCGCGCGCGGTTCCAGCGTTTGGGTATAACCCGGAGCCAg    <  2:377119/140‑1 (MQ=255)                                                                                                                                   aGTCCGGCCCCGGAACAGGCCAGAGTAGTTAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGCTCTGATCGCGATACGGCACGTACAAATACTGCGCGCGCGGTTCCAGCGTTTGGGTATAACCCGGAGCCAGCa  <  1:480394/140‑1 (MQ=255)                                                                                                                                   aGTCCGGCCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGCTCTGATCGCGATACGGCACGTACAAATACTGCGCGCGCGGTTCCAGCGTTTGGGTATAACCCGGAGCCAGCa  >  2:176196/1‑140 (MQ=255)                                                                                                                                          |                                                                                                                                     GAGACTCCGTGAAATAGTAGATTTGACCAACGGAAATATTAAAACGTTCAACGGCAGCATCATCATATATGCGAGATGTGACACCGGTCGTCACCTGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGTCCCGGAACAGGCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGCTCTGATCGCGATACGGCACGTACAAATACTGCGCGCGCGGTTCCAGCGTTTGGGTATAACCCGGAGCCAGCA  >  NC_000913/55345‑55614

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑