Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,486,291	T→A	I25N (ATC→AAC)	lptF →	lipopolysaccharide transport system protein LptF

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,486,291	0	T	A	100.0%	110.0 / NA	31	I25N (ATC→AAC)	lptF	lipopolysaccharide transport system protein LptF
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base A (12/19);  total (12/19)

AGTGATAATCATAAGATATCTGGTGCGGGAGACGCTCAAAAGCCAGCTGGCGATACTCTTCATCTTGCTTTTGATCTTCTTCTGTCAAAAGTTAGTGAGGATCCTCGGCGCAGCGGTTGACGGCGATATTCCGGCGAATCTGGTGCTCTCC  >  NC_000913/4486217‑4486367                                                                           |                                                                             aGTGATAATCATAAGATATCTGGTGCGGGAGACGCTCAAAAGCCAGCTGGCGATACTCTTCATCTTGCTTTTGAacttctt                                                                        <  1:858782/81‑1 (MQ=255)   tGATAATCATAAGATATCTGGTGCGGGAGACGCTCAAAAGCCAGCTGGCGATACTCTTCATCTTGCTTTTGAacttcttct                                                                      >  1:858835/1‑81 (MQ=255)     aTAATCATAAGATATCTGGTGCGGGAGACGCTCAAAAGCCAGCTGGCGATACTCTTCATCTTGCTTTTGAACTTCTTCTGt                                                                    <  2:858782/81‑1 (MQ=255)           aTAAGATATCTGGTGCGGGAGACGCTCAAAAGCCAGCTGGCGATACTCTTCATCTTGCTTTTGAACTTCTTCTGTCAAAAg                                                              >  1:858830/1‑81 (MQ=255)             aaGATATCTGGTGCGGGAGACGCTCAAAAGCCAGCTGGCGATACTCTTCATCTTGCTTTTGAACTTCTTCTGTCAAAAGt                                                             >  2:858837/1‑80 (MQ=255)              aGATATCTGGTGCGGGAGACGCTCAAAAGCCAGCTGGCGATACTCTTCATCTTGCTTTTGAACTTCTTCTGTCAAAAGtt                                                            <  2:858783/80‑1 (MQ=255)               gATATCTGGTGCGGGAGACGCTCAAAAGCCAGCTGGCGATACTCTTCATCTTGCTTTTGAACTTCTTCTGTCAAAAGTTAg                                                          <  2:858784/81‑1 (MQ=255)               gATATCTGGTGCGGGAGACGCTCAAAAGCCAGCTGGCGATACTCTTCATCTTGCTTTTGAACTTCTTCTGTCAAAAGTTAg                                                          >  1:858829/1‑81 (MQ=255)                 tatCTGGTGCGGGAGACGCTCAAAAGCCAGCTGGCGATACTCTTCATCTTGCTTTTGAACTTCTTCTGTCAAAAGTTAGTg                                                        <  2:858785/81‑1 (MQ=255)                      ggTGCGGGAGACGCTCAAAAGCCAGCTGGCGATACTCTTCATCTTGCTTTTGAACTTCTTCTGTCAAAAGTTAGTGAGGAt                                                   >  2:858845/1‑81 (MQ=255)                       gTGCGGGAGACGCTCAAAAGCCAGCTGGCGATACTCTTCATCTTGCTTTTGAACTTCTTCTGTCAAAAGTTAGTGAg                                                      <  2:858786/77‑1 (MQ=255)                       gTGCGGGAGACGCTCAAAAGCCAGCTGGCGATACTCTTCATCTTGCTTTTGAACTTCTTCTGTCAAAAGTTAGTGAGGAt                                                   <  2:858787/80‑1 (MQ=255)                         gCGGGAGACGCTCAAAAGCCAGCTGGCGATACTCTTCATCTTGCTTTTGAACTTCTTCTGTCAAAAGTTAGTGAGGATCCt                                                >  2:858856/1‑81 (MQ=255)                          cGGGAGACGCTCAAAAGCCAGCTGGCGATACTCTTCATCTTGCTTTTGAACTTCTTCTGTCAAAAGTTAGTGAGGATCCTc                                               >  1:858843/1‑81 (MQ=255)                            ggAGACGCTCAAAAGCCAGCTGGCGATACTCTTCATCTTGCTTTTGAACTTCTTCTGTCAAAAGTTAGTGAGGATCCTCgg                                             <  1:858789/81‑1 (MQ=255)                                 cGCTCAAAAGCCAGCTGGCGATACTCTTCATCTTGCTTTTGAACTTCTTCTGTCAAAAGTTAGTGAGGATCCTCGGCGCAg                                        <  1:858790/81‑1 (MQ=255)                                  gCTCAAAAGCCAGCTGGCGATACTCTTCATCTTGCTTTTGAACTTCTTCTGTCAAAAGTTAGTGAGGATCCTCGGCGCAGc                                       <  1:858791/81‑1 (MQ=255)                                  gCTCAAAAGCCAGCTGGCGATACTCTTCATCTTGCTTTTGAACTTCTTCTGTCAAAAGTTAGTGAGGATCCTCGGCGCAGc                                       <  1:858793/81‑1 (MQ=255)                                  gCTCAAAAGCCAGCTGGCGATACTCTTCATCTTGCTTTTGAACTTCGTCTGTCAAAAGTTAGTGAGGATCCTCGGCGCAGc                                       <  2:858791/81‑1 (MQ=255)                                   cTCAAAAGCCAGCTGGCGATACTCTTCATCTTGCTTTTGAACTTCTTCTGTCAAAAGTTAGTGAGGATCTTCGGCGCAGCg                                      >  1:858832/1‑81 (MQ=255)                                         aGCCAGCTGGCGATACTCTTCATCTTGCTTTTGAACTTCTTCTGTCAAAAGTTAGTGAGGATCCTCGGCGCAGCGGTTGAc                                >  2:858857/1‑81 (MQ=255)                                         aGCCAGCTGGCGATACTCTTCATCTTGCTTTTGAACTTCTTCTGTCAAAAGTTAGTGAGGATCCTCGGCGCAGCGGTTGAc                                <  2:858793/81‑1 (MQ=255)                                              gCTGGCGATACTCTTCATCTTGCTTTTGAACTTCTTCTGTCAAAAGTTAGTGAGGATCCTCGGCGCAGCGGTTGACGGCGa                           <  1:858795/81‑1 (MQ=255)                                                 ggCGATACTCTTCATCTTGCTTTTGAACTTCTTCTGTCAAAAGTTAGTGAGGATCCTCGGCGCAGCGGTTGACGGCGatat                        >  2:858843/1‑81 (MQ=255)                                                   cGATACTCTTCATCTTGCTTTTGAACTTCTTCTGTCAAAAGTTAGTGAGGATCCTCGGCGCAGCGGTTGACGGCGATATTc                      <  2:858796/81‑1 (MQ=255)                                                   cGATACTCTTCATCTTGCTTTTGAACTTCTTCTGTCAAAAGTTAGTGAGGATCCTCGGCGCAGCGGTTGACGGCGATATTc                      <  1:858796/81‑1 (MQ=255)                                                                cTTGCTTTTGAACTTCTTCTGTCAAAAGTTAGTGAGGATCCTCGGCGCAGCGGTTGACGGCGATATTCCGGCGAATCTGGt         >  2:858840/1‑81 (MQ=255)                                                                   gCTTTTGAACTTCTTCTGTCAAAAGTTAGTGAGGATCCTCGGCGCAGCGGTTGACGGCGATATTCCGGCGAATCTGGt         <  1:858798/78‑1 (MQ=255)                                                                   gCTTTTGAACTTCTTCTGTCAAAAGTTAGTGAGGATCCTCGGCGCAGCGGTTGACGGCGATATTCCGGCGAATCTGGt         <  1:858799/78‑1 (MQ=255)                                                                     ttttGAACTTCTTCTGTCAAAAGTTAGTGAGGATCCTCGGCGCAGCGGTTGACGGCGATATTCCGGCGAATCTGGTGctct    >  1:858873/1‑81 (MQ=255)                                                                       ttGAACTTCTTCTGTCAAAAGTTAGTGAGGATCCTCGGCGCAGCGGTTGACGGCGATATTCCGGCGAATCTGGTGCTCTcc  >  2:858851/1‑81 (MQ=255)                                                                        tGAACTTCTTCTGTCAAAAGTTAGTGAGGATCCTCGGCGCAGCGGTTGACGGCGATATTCCGGCGAATCTGGTGCTCTcc  <  2:858799/80‑1 (MQ=255)                                                                        tGAACTTCTTCTGTCAAAAGTTAGTGAGGATCCTCGGCGCAGCGGTTGACGGCGATATTCCGGCGAATCTGGTGCTCTcc  <  2:858800/80‑1 (MQ=255)                                                                           |                                                                             AGTGATAATCATAAGATATCTGGTGCGGGAGACGCTCAAAAGCCAGCTGGCGATACTCTTCATCTTGCTTTTGATCTTCTTCTGTCAAAAGTTAGTGAGGATCCTCGGCGCAGCGGTTGACGGCGATATTCCGGCGAATCTGGTGCTCTCC  >  NC_000913/4486217‑4486367

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: ‑