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%	87.6 / NA	21	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 . (12/9);  total (12/9)

TGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAGGATTATCTCGGGCATCGAAATAT‑TCG‑CCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAA  >  NC_000913/4542456‑4542917                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                           ttcTTGCGGTTATGAAGTGGCGGAGCGTGGTGAAGATACTCGTTTAATTCAGGATTATCTCGGGCATCGAAATAT‑TCG‑CCTTACTGTGCGTTATCCCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGGTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCata                                                                                                                                                                                                                     <  1:180810/248‑1 (MQ=255)   cTTGCGGTTATAAAATGGAGGAGCGTGGTGCAGATACTCGTTTAATTCAGGATTATCTCGGGCATCGAAATAT‑TCG‑CCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGCTTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCata                                                                                                                                                                                                                     >  2:180810/1‑248 (MQ=255)                       gaggggggtgCAGATACTCGTTTAATTCAGAATTATCTCGGGCATCGAAATAT‑TCG‑CCATACTGGGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCa                                                                                                                                                                                              <  1:257233/245‑1 (MQ=255)                        gacgtggtgtatttccTCGTTTAATTCAGGATTATCTCGGTATTCGAA‑TATGTCGTCCCT‑CTTGGCTTTATACCGCCAGTAATGCGGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAACTAAAAAGAGAAGAGGTGTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAATACAAT‑GGGGCCAAAATGTCCATATCATAAATAAGTTACGTAttttggcttaa                                                                                                                                                                                             <  2:2511/236‑8 (MQ=255)                           gtggtgcagatatgattttAATTAAGGATTAGCTCGGACATGGAAATTT‑TCG‑CCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATATAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCa                                                                                                                                                                                          <  2:57932/235‑1 (MQ=255)                           gtggtgCAGATACTCGCATAAGTCAGGATTATCTCGGGCATAGAAATAT‑TCG‑CCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGATTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑CGGGCCAAAATGTCCATATCATCAATAAGTTACGTCTTTGTTCTCaatc                                                                                                                                                                                           >  2:129987/1‑248 (MQ=255)                               ggCAGATATCCGTTTATTTCAGGATTATCTCGGGCATCGAAATAT‑TCG‑CCATATTGGGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATaaa                                                                                                                                                                                      <  2:270118/250‑1 (MQ=255)                                                                          at‑TCG‑CAATACTGTGCGTTATGCCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGt                                                                                                                                            <  2:219681/250‑1 (MQ=255)                                                                                 ccATACTGTGCTTTATACCGCCCGTCATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTAATAAACGAAAAATTCCAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAACTAAATACAAGACAAT‑GGGGCCAAACTGTCAATATCATAAATAAGTTACGTATTTTTTCTCAAGCATATAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAatt                                                                                                                                       >  2:174769/1‑250 (MQ=255)                                                                                    tACTGTGCGTTATACCGCCAGGAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTAttt                                                                                                                                   >  2:79372/1‑251 (MQ=255)                                                                                                             gctgctCGTGTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTATCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCa                                                                                                           <  2:228469/250‑1 (MQ=255)                                                                                                                 ctCGTTTTGCCGGAGTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGCGAAGAGGTTTGATTTAACTTATTGATAATAAAGTAAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATCTCATAAATACGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCCCCTcc                                                                                                      >  2:245351/1‑251 (MQ=255)                                                                                                                     ttttGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCt                                                                                                   >  2:18058/1‑250 (MQ=255)                                                                                                                                                                 tAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCAtt                                                      >  1:75802/1‑251 (MQ=255)                                                                                                                                                                         gaagagGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTtctctc                                              >  2:58501/1‑251 (MQ=255)                                                                                                                                                                                           ttATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGcc                            >  2:21120/1‑250 (MQ=255)                                                                                                                                                                                               tGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATAATAAATAAGTTACGTATTTTTTCTCAAGCATAACAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTAGACGCATCTTCCTCATTCTTATCTCCAAAACCAACCTCATGCAatat                        >  2:148106/1‑251 (MQ=255)                                                                                                                                                                                                      aaaGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATc                 <  1:5035/251‑1 (MQ=255)                                                                                                                                                                                                          ttAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCtat              >  1:12485/1‑250 (MQ=255)                                                                                                                                                                                                                     aataaataCAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAATCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACATTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATaa  <  2:109205/251‑1 (MQ=255)                                                                                                                                                                                                                     aaaaaaaaCAAGAAAAT‑GGGGCCAAACTGTACATATCATAAATAAGTTACGGATTTTTTCTCAAGCATAAAAATATTAAAAAACGACCAAAAGCATCTAACTGTTTGATATGAAAATTATTTCTAGTGTAAATTAATTTCACATCAACTCCGCTATGTGTAAAGCTAACATTTCTGTGGCTCGACGCATTTTCCTCCTTCTTCTCTCCAAAAACCGCATCATGCAATATAAACATCTATACATAAAGATa   >  2:141004/8‑250 (MQ=255)                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                           TGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAGGATTATCTCGGGCATCGAAATAT‑TCG‑CCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAA  >  NC_000913/4542456‑4542917

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑