Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,546,846	(A)5→4	coding (1751/2637 nt)	fimD →	type I fimbriae usher protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,546,842	0	A	.	100.0%	158.0 / NA	35	coding (1747/2637 nt)	fimD	type I fimbriae usher protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (22/13);  total (22/13)

GTAATGTCGATGAGCAATTCCAGGCTGGATTAAATACTGCGTTCGAAGATATCAACTGGACGCTCAGCTATAGCCTGACGAAAAACGCCTGGCAAAAAGGACGGGATCAGATGTTAGCGCTTAACGTCAATATTCCTTTCAGCCACTGGCTGCGTTC  >  NC_000913/4546762‑4546918                                                                                 |                                                                             gTAATGTCGATGAGCAATTCCAGGCTGGATTAAATACTGCGTTCGAAGATATCAACTGGACGCTCAGCTATAGCCTGACGa                                                                              <  1:863459/81‑1 (MQ=255)   aaTGTCGATGAGCAATTCCAGGCTGGATTAAATACTGCGTTCGAAGATATCAACTGGACGCTCAGCTATAGCCTGACGaa                                                                             >  1:863506/1‑80 (MQ=255)         gATGAGCAATTCCAGGCTGGATTAAATACTGCGTTCGAAGATATCAACTGGACGCTCAGCTATAGCCTGACGaaaacgcc                                                                       <  2:863460/80‑5 (MQ=255)         gATGAGCAATTCCAGGCTGGATTAAATACTGCGTTCGAAGATATCAACTGGACGCTCAGCTATAGCCTGACG‑AAAACGCCt                                                                     >  1:863508/1‑81 (MQ=255)             aGCAATTCCAGGCTGGATTAAATACTGCGTTCGAAGATATCAACTGGACGCTCAGCTATAGCCTGACG‑AAAACGCCTGGc                                                                  >  1:863502/1‑80 (MQ=255)             aGCAATTCCAGGCTGGATTAAATACTGCGTTCGAAGATATCAACTGGACGCTCAGCTATAGCCTGACG‑AAAACGCCTGGc                                                                  >  2:863501/1‑80 (MQ=255)             aGCAATTCCAGGCTGGATTAAATACTGCGTTCGAAGATATCAACTGGACGCTCAGCTATAGCCTGACG‑AAAACGCCTGGc                                                                  >  2:863495/1‑80 (MQ=255)               cAATTCCAGGCTGGATTAAATACTGCGTTCGAAGATATCAACTGGACGCTCAGCTATAGCCTGACG‑AAAACGCCTGGCaaa                                                               <  2:863461/81‑1 (MQ=255)                aaTTCCAGGCTGGATTAAATACTGCGTTCGAAGATATCAACTGGACGCTCAGCTATAGCCTGACG‑AAAACGCCTGGCaaa                                                               >  2:863507/1‑80 (MQ=255)                 aTTCCAGGCTGGATTAAATACTGCGTTCGAAGATATCAACTGGACGCTCAGCTATAGCCTGACG‑AAAACGCCTGGCaaa                                                               >  2:863498/1‑79 (MQ=255)                      aGGCTGGATTAAATACTGCGTTCGAAGATATCAACTGGACGCTCAGCTATAGCCTGACG‑AAAACGCCTGGCAAAAAGGACg                                                        >  1:863515/1‑81 (MQ=255)                         cTGGATTAAATACTGCGTTCGAAGATATCAACTGGACGCTCAGCTATAGCCTGACG‑AAAACGCCTGGCAAAAAGGACGGGa                                                     <  2:863462/81‑1 (MQ=255)                          tGGATTAAATACTGCGTTCGAAGATATCAACTGGACGCTCAGCTATAGCCTGACG‑AAAACGCCTGGCAAAAAGGACGGGAt                                                    >  2:863513/1‑81 (MQ=255)                           ggATTAAATACTGCGTTCGAAGATATCAACTGGACGCTCAGCTATAGCCTGACG‑AAAACGCCTGGCAAAAAGGACGGGAt                                                    >  2:863504/1‑80 (MQ=255)                            gATTAAATACTGCGTTCGAAGATATCAACTGGACGCTCAGCTATAGCCTGACG‑AAAACGCCTGGCAAAAAGGACGGGATc                                                   <  2:863463/80‑1 (MQ=255)                             aTTAAATACTGCGTTCGAAGATATCAACTGGACGCTCAGCTATAGCCTGACG‑AAAACGCCTGGCAAAAAGGACGGGAt                                                    >  1:863521/1‑78 (MQ=255)                               tAAATACTGCGTTCGAAGATATCAACTGGACGCTCAGCTATAGCCTGACG‑AAAACGCCTGGCAAAAAGGACGGGATCAGAt                                               >  2:863511/1‑81 (MQ=255)                                  aTACTGCGTTCGAAGATATCAACTGGACGCTCAGCTATAGCCTGACG‑AAAACGCCTGGCAAAAAGGACGGGATCAGATGtt                                            <  2:863464/81‑1 (MQ=255)                                     cTGCGTTCGAAGATATCAACTGGACGCTCAGCTATAGCCTGACG‑AAAACGCCTGGCAAAAAGGACGGGATCAGATGTTAg                                          <  1:863465/80‑1 (MQ=255)                                         gTTCGAAGATATCAACTGGACGCTCAGCTATAGCCTGACG‑AAAACGCCTGGCAAAAAGGACGGGATCAGATGTTAGCGCtt                                     <  2:863466/81‑1 (MQ=255)                                         gTTCGAAGATATCAACTGGACGCTCAGCTATAGCCTGACG‑AAAACGCCTGGCAAAAAGGACGGGATCAGATGTTAGCGCtt                                     <  1:863467/81‑1 (MQ=255)                                          ttCGAAGATATCAACTGGACGCTCAGCTATAGCCTGACG‑AAAACGCCTGGCAAAAAGGACGGGATCAGATGTTAGCGCTTa                                    <  2:863469/81‑1 (MQ=255)                                          ttCGAAGATATCAACTGGACGCTCAGCTATAACCTGACG‑AAAACGCCTGGCAAAAAGGACGGGATCAGATGTTAGCGCTTa                                    <  2:863468/81‑1 (MQ=255)                                             gAAGATATCAACTGGACGCTCAGCTATAGCCTGACG‑AAAACGCCTGGCAAAAAGGACGGGATCAGATGTTAGCGCTTAACg                                 >  2:863519/1‑81 (MQ=255)                                              aaGATATCAACTGGACGCTCAGCTATAGCCTGACG‑AAAACGCCTGGCAAAAAGGACGGGATCAGATGTTAGCGCTTAACGt                                >  2:863530/1‑81 (MQ=255)                                              aaGATATCAACTGGACGCTCAGCTATAGCCTGACG‑AAAACGCCTGGCAAAAAGGACGGGATCAGATGTTAGCGCTTAACGt                                >  1:863526/1‑81 (MQ=255)                                                    tCAACTGGACGCTCAGCTATAGCCTGACG‑AAAACGCCTGGCAAAAAGGACGGGATCAGATGTTAGCGCTTAACGTCAata                           <  2:863470/80‑1 (MQ=255)                                                     cAACTGGACGCTCAGCTATAGCCTGACG‑AAAACGCCTGGCAAAAAGGACGGGATCAGATGTTAGCGCTTAACGTCAATAtt                         >  1:863531/1‑81 (MQ=255)                                                      aaCTGGACGCTCAGCTATAGCCTGACG‑AAAACGCCTGGCAAAAAGGACGGGATCAGATGTTAGCGCTTAACGTCAATAtt                         <  1:863473/80‑1 (MQ=255)                                                      aaCTGGACGCTCAGCTATAGCCTGACG‑AAAACGCCTGGCAAAAAGGACGGGATCAGATGTTAGCGCTTAACGTCAATAtt                         <  1:863472/80‑1 (MQ=255)                                                      aaCTGGACGCTCAGCTATAGCCTGACG‑AAAACGCCTGGCAAAAAGGACGGGATCAGATGTTAGCGCTTAACGTCAATAtt                         <  1:863471/80‑1 (MQ=255)                                                              gCTCAGCTATAGCCTGACG‑AAAACGCCTGGCAAAAAGGACGGGATCAGATGTTAGCGCTTAACGTCAATATTCCTTTCAGc                >  1:863523/1‑81 (MQ=255)                                                                tCAGCTATAGCCTGACG‑AAAACGCCTGGCAAAAAGGACGGGATCAGATGTTAGCGCTTAACGTCAATATTCCTTTCAGCCa              >  1:863534/1‑81 (MQ=255)                                                                 cAGCTATAGCCTGACG‑AAAACGCCTGGCAAAAAGGACGGGATCAGATGTTAGCGCTTAACGTCAATATTCCTTTCAGCCAc             >  1:863514/1‑81 (MQ=255)                                                                 cAGCTATAGCCTGACG‑AAAACGCCTGGCAAAAAGGACGGGATCAGATGTTAGCGCTTAACGTCAATATTCCTTTCAGCCAc             >  2:863509/1‑81 (MQ=255)                                                                      ataGCCTGACG‑AAAACGCCTGGCAAAAAGGACGGGATCAGATGTTAGCGCTTAACGTCAATATTCCTTTCAGCCACTGGCt        >  1:863525/1‑81 (MQ=255)                                                                        aGCCTGACG‑AAAACGCCTGGCAAAAAGGACGGGATCAGATGTTAGCGCTTAACGTCAATATTCCTTTCAGCCACTGGCTGc      >  1:863528/1‑81 (MQ=255)                                                                            tGACG‑AAAACGCCTGGCAAAAAGGACGGGATCAGATGTTAGCGCTTAACGTCAATATTCCTTTCAGCCACTGGCTGCGTTc  >  2:863516/1‑81 (MQ=255)                                                                                 |                                                                             GTAATGTCGATGAGCAATTCCAGGCTGGATTAAATACTGCGTTCGAAGATATCAACTGGACGCTCAGCTATAGCCTGACGAAAAACGCCTGGCAAAAAGGACGGGATCAGATGTTAGCGCTTAACGTCAATATTCCTTTCAGCCACTGGCTGCGTTC  >  NC_000913/4546762‑4546918

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: ‑