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%	98.1 / NA	22	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 . (7/15);  total (7/15)

CCTCATATGTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGC‑AGATACTCGTTTAATTCAGGATTATCTCGGGCATCGAAATATTCGCCATACTGTG‑CGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAAT  >  NC_000913/4542439‑4542926                                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                                    ccTCATATGTAAAGGCATGCGTGCGTTTATGATTGGGCGGGGCGTGGGGC‑AGATACTCTGTTAATTCAGGATTATCTCGGGCATCGAAATTTGCGCCATAC‑GTGGAGTAATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGca                                                                                                                                                                                                                                               <  2:263947/250‑2 (MQ=255)                cATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGC‑AGATACTCGTTTAATTCAGGATTATCTCGGGCATCGAAATATTCGCCATACTGTG‑CGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCattttgactcatag                                                                                                                                                                                                                                 >  2:114923/1‑236 (MQ=255)                 aTGCTTGCGGTTATGAATGGGCGGAGCGTGGTGC‑AGATACTCGTTTAATTCAGGATTATCTCGGGCATCGAAATATTCGCCATACTGTG‑CGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCata                                                                                                                                                                                                                              <  1:200692/251‑1 (MQ=255)                     tggcgtttagtaaTTGGGGGAGCGTG‑TGCCAGATACTCTTTTAATTCAGGATTATCTCGGGAATGGAAATATTCGCAATTCTGGG‑CTTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGTGCCAAACTGTCCATATCataaat                                                                                                                                                                                                                           <  2:367932/239‑1 (MQ=255)                                    ggCGGAGCGTGGGGC‑AGATACTCGTTTAATTCAGGATTATCTCGGGCATCGAAATATTCGCCATACTGTG‑CGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTAtttttc                                                                                                                                                                                                           <  1:286480/251‑2 (MQ=255)                                            gtggtgC‑CGATACTCGTTTCATTCAGGATTATCTCGGGCATCGAAATATTCGCCATACTGTG‑CGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTT‑CTCAAGCAt                                                                                                                                                                                                  >  2:256513/1‑251 (MQ=255)                                                 gC‑AGATACTCGTTTAATTCAGGATTATCTCGGGCATCGAAATATTCGCCATACTGTG‑CGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTT‑CTCAAGCATaaaa                                                                                                                                                                                              >  1:71131/1‑250 (MQ=255)                                                                                  gCATCGAAATATTCGCCATACTGTG‑CGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTT‑CTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGtt                                                                                                                                                             <  1:242740/251‑1 (MQ=255)                                                                                                               aagaCCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTT‑CTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTaaa                                                                                                                                  <  2:320677/247‑1 (MQ=255)                                                                                                                                                              taatCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTT‑CTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGc                                                                                  >  1:196037/1‑251 (MQ=255)                                                                                                                                                                        aaCGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTT‑CTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGTCGCATc                                                                        <  2:278834/251‑1 (MQ=255)                                                                                                                                                                         aCGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTT‑CTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCt                                                                       <  2:201606/251‑1 (MQ=255)                                                                                                                                                                              aaaTTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTT‑CTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTc                                                                  <  1:117656/251‑1 (MQ=255)                                                                                                                                                                                    aaaaGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTT‑CTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCAttctt                                                            >  1:24428/1‑251 (MQ=255)                                                                                                                                                                                    aaaaGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTT‑CTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGAGATGTAAATTATTTCTATTGTAAATTAATTTCACATCGCCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCAttctt                                                            <  1:389724/251‑1 (MQ=255)                                                                                                                                                                                          gaagagGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTT‑CTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTcc                                                      >  1:178379/1‑251 (MQ=255)                                                                                                                                                                                                          aCTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTT‑CTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCGCCTCATGc                                      <  1:355357/251‑1 (MQ=255)                                                                                                                                                                                                             tATTGATACTAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTT‑CTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAat                                   >  1:81289/1‑251 (MQ=255)                                                                                                                                                                                                                    aataaAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTT‑CTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAAc                             <  2:385720/250‑1 (MQ=255)                                                                                                                                                                                                                                           ataCAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTT‑CTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTAATTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCCCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAg     <  2:198537/251‑1 (MQ=255)                                                                                                                                                                                                                                             aCAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTT‑CTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGa    <  1:286852/250‑1 (MQ=255)                                                                                                                                                                                                                                              cAAGACAAT‑GGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTT‑CTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAat  <  1:337892/251‑1 (MQ=255)                                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                                    CCTCATATGTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGC‑AGATACTCGTTTAATTCAGGATTATCTCGGGCATCGAAATATTCGCCATACTGTG‑CGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAAT  >  NC_000913/4542439‑4542926

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑