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%	39.9 / NA	11	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 . (5/6);  total (5/6)

TTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATAT  >  NC_000913/4542570‑4542895                                                                                                                  |                                                                                                                                                                                                                     ttttGCCGGATTATGGGAAAGAAATANTCTCATNNACNAAAAATTAAAAAGAGAAGANGTNNNANNNANCTTATNGANNATAAAGTTANAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGNTACGTATTTNNTCTCAAGCATAAAAATATTAANAAANNANNANAAGNAtn                                                                                                                                      >  2:50076/1‑192 (MQ=255) ttttGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTc                                                                                           <  1:50076/236‑1 (MQ=255)         nannaagngnNANNAATNATCTCATAAACGAAAAATTAANNAGAGAAGAGNTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAN‑GGGGCCAAANNGTNCATAGNANNNANNNGTNACGTATTTTTTCTCAAGCANAANNATATTANAAAACGACAAAAAGCATCTAACTGtt                                                                                                                              <  2:45368/187‑1 (MQ=255)                             ctcATAAACGAAAAATTAAAACGAGAAGAGGATTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTACATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCg                                                >  1:187337/1‑251 (MQ=255)                               cATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGGTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTAt                                                                                                                                                                                 <  1:123757/120‑1 (MQ=255)                                                 aagagaagagGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCGAACTGTTTGATATGTAAAGTATTTCTATTGTAAATTAATTTCTCAGCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCAttcttc                            <  1:90696/251‑1 (MQ=255)                                                 aagagaagagGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGACCAAACTGTCCATATCATAAATAAGTTACGTATATTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCTCCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCAttcttc                            <  1:219609/251‑1 (MQ=255)                                                              tGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAacc                <  1:36659/250‑1 (MQ=255)                                                                    aaCTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATCAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTATTCTCTACAAAAACCACCTCAt         >  1:33739/1‑251 (MQ=255)                                                                      cTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTCTTTTTTCTCAAGCATAACAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTACTTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGc       >  1:97837/1‑251 (MQ=255)                                                                            gATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATAATACATAAGTTACGTATTTTTTCTCAAGCATAAAACTCTTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACCTCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAatat  >  1:138496/1‑250 (MQ=255)                                                                                                                  |                                                                                                                                                                                                                     TTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATAT  >  NC_000913/4542570‑4542895

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑