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%	66.3 / NA	17	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 . (11/6);  total (11/6)

GTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAGGATTATCTCGGGCATCGAAATATTCGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATT  >  NC_000913/4542447‑4542929                                                                                                                                                                                                                                             |                                                                                                                                                                                                                                                       gTTAAGGCATGCTTGGGGTTATGAATGGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAGGATTATCTCGGGCATCGAAATATTCGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATGAAAAAGAGAAGAGGTTTTATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTc                                                                                                                                                                                                                                          <  1:162893/250‑1 (MQ=255)                               ggAGCGTGGTGCAGATACTCGTTTAATTAAGGATTATCGCGGGCATCGAAAAATTCTCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGGGTAAGGGAAAGAAATAATCGCATAAACGAAAAATTAAAAAGACAAGAGGTTTTATTTAACTTATCGATAATAAAGTTAAAAAAACAAATAAACACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTtctc                                                                                                                                                                                                           <  1:331662/251‑1 (MQ=255)                                                                                                  cGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGACATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGt                                                                                                                                        >  1:271414/1‑251 (MQ=255)                                                                                                  cGTTATACCGCCAGTAATGATGCTCGTTTTGCAGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGt                                                                                                                                        >  1:271419/1‑251 (MQ=255)                                                                                                   gTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTTTGGGAAAGAAATAATCTCATAAACGACAAATTAAAAAGAGAAGAGGTTTGATTTACCTTATTGATAATACAGTTAAAAAAAAAAATAAATACAAGACAAT‑GGGGCCATACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGt                                                                                                                                        >  1:217992/1‑250 (MQ=255)                                                                                                                    nctgctCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCAc                                                                                                                      >  1:57416/2‑251 (MQ=255)                                                                                                                                   ggATTATGGGAAAGAAATACTCTAATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAACTAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTa                                                                                                        >  1:272210/1‑250 (MQ=255)                                                                                                                                                naaaTAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCt                                                                                          >  1:202107/2‑251 (MQ=255)                                                                                                                                                  aataatCTCATAAACGAAAAATTAAAAAGAGCAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAACCTGTCCATATCATAAATACGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTaa                                                                                                                                      >  1:290496/1‑205 (MQ=255)                                                                                                                                                          cATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCg                                                                                  <  1:271910/249‑1 (MQ=255)                                                                                                                                                              aaCGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATGTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCac                                                                            <  1:49276/251‑2 (MQ=255)                                                                                                                                                                 gAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGata                                                                                                                                                           >  1:207362/1‑169 (MQ=255)                                                                                                                                                                                                               aGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCCTAACTCAGTTACGTATTTTTTCTCACGCATAAAAATATTAAAAAACGCCAAAAAGAATCTAACTGTTTGATATGTAACTTATTTCTCTTGTAACTTAATTTCACATCACCTCCGCTATATg                                                                                                          >  1:159634/1‑172 (MQ=255)                                                                                                                                                                                                                         ncAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTACAAAACGACAAAAAGCATCTCACTGTTTGATATGTAAATTATTTCTATTGTAaatt                                                                                                                                   >  1:39601/2‑137 (MQ=255)                                                                                                                                                                                                                                aataCAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGAATAACAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCCTCTTCCTCATTCTTCTCTCCACAAacc                                                  >  1:70074/1‑211 (MQ=255)                                                                                                                                                                                                                                   aCAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTGAATTAATTTCACATCACCTCCGc                                                                                                                <  1:97727/146‑1 (MQ=255)                                                                                                                                                                                                                                      aGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCGCCTCCGc                                                                                                                <  1:113911/143‑1 (MQ=255)                                                                                                                                                                                                                                          caatGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTACCTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGATTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCCAAAACCACCTCATGCAATATAAACATCAATAAATAAAGATAAAAATAGAATAtt  >  1:233407/4‑250 (MQ=255)                                                                                                                                                                                                                                             |                                                                                                                                                                                                                                                       GTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAGGATTATCTCGGGCATCGAAATATTCGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATT  >  NC_000913/4542447‑4542929

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: ‑