Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,542,683	Δ1 bp	intergenic (+50/‑432)	fimE → / → fimA	regulator for fimA/type 1 fimbriae major subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,542,683	0	T	.	100.0%	30.4 / NA	9	intergenic (+50/‑432)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (6/3);  total (6/3)

TAATTCAGGATTATCTCGGGCATCGAAATATTCGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCT  >  NC_000913/4542500‑4542867                                                                                                                                                                                        |                                                                                                                                                                                         tAATTCAGGATTATCTCGGGCATCGAAATTTTCGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGGTTTGCCGGATTATGGGAAAGAAATAATCTCAAAAACGAAAAAGTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAATTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAAc                                                                                                                       <  1:54955/250‑1 (MQ=255)                                 cGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGCTTTGCCGGATTATGGGAAAGCAATAATCTCATAACCGACAAATTCAACAGAGAAGCGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAAc                                                                                                                       >  1:151645/1‑218 (MQ=255)                                                             aTGCTGCTCGTTTTTCCGGATTATGTGAAAGAAAGAATCTCAGAAACGAAAAATTAAAAAGAGAAGATGTTTGATTTAACTTAGTGATAATAAAGTTAAAAATACAAATAAATACAATACAAT‑GGGGCCAAACTGTCCAGATCATAAATAATTTACGTATTTTGTCTCAATCATAAATATATGAAAAAACTACAAAAAGCATCTAACTGTTGGATATGTAAATTATTTCTATTGTAAATTAATTTCACATc                                                          <  1:170663/251‑1 (MQ=255)                                                                ctgctCGTTTTGCAGGATTATGGGAAAGAAATAATCTCATAGACGAAAAATTAAAAAGTGAAGAGGCTTGATTGCACTTATTGATAATAAAGTTGAAAACACCAATACAGAAATGACAAT‑GGGGCCAAACTGTACATATGATAAATAGGTTACGTATTTTTTGTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAAATGTTTGATATGTAAATTATTTCTATTGTAATTTAATTTCACATCAcc                                                       >  1:124833/1‑251 (MQ=255)                                                                           gCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACg                                                                                                                      >  1:58718/1‑177 (MQ=255)                                                                                    tGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTCAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAg                                       >  1:165879/1‑247 (MQ=255)                                                                                                aatCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTgg                        <  1:27281/250‑1 (MQ=255)                                                                                                                     aaaaGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAACACAAT‑GGGGCCAAACTGTACATCTCATAGATACGTTACGTATTTTTTCTCAAGCATCAAAATAATACAAAACGACAAAAAGCATCTAACTGTTTGCTATGTAAATTATTTCTCTTGTAACTTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCAttct  >  1:162554/1‑251 (MQ=255)                                                                                                                                                                              aCAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTAACTATTTTTTATCAAGCATAAAAATATTAACAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTgg                        >  1:22369/1‑172 (MQ=255)                                                                                                                                                                                        |                                                                                                                                                                                         TAATTCAGGATTATCTCGGGCATCGAAATATTCGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCT  >  NC_000913/4542500‑4542867

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑