Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,543,024	C→G	intergenic (+391/‑91)	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	4,543,024	0	C	G	100.0%	52.4 / NA	16	intergenic (+391/‑91)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base G (9/7);  total (9/7)

TAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGTTCACTTTAAAGGGGAAGTTGTTAACGCCGCTTGCGCAGTTGATGCAGGCTC  >  NC_000913/4542795‑4543263                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                tggtttttggagagaagaatgaggaagatgcgtcgagccacagaaacgttagctttacatatagcggaggtgatgtgaaattaatttacaatagaaataatttacatatcaaacagttagatgctttttgtcgttttttaatatttttatgcttgagaaaaaatacgtaacttatttatgatatggacagtttggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGGAGTGTTGGCAGTCAAAc                                                                                                                                                                                                                                <  1:12608‑M2/46‑1 (MQ=255) tggtttttggagagaagaatgaggaagatgcgtcgagccacagaaacgttagctttacatatagcggaggtgatgtgaaattaatttacaatagaaataatttacatatcaaacagttagatgctttttgtcgttttttaatatttttatgcttgagaaaaaatacgtaacttatttatgatatggacagtttggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGGAGTGTTGGCAGTCAAAc                                                                                                                                                                                                                                >  2:12608‑M2/202‑247 (MQ=255)                        gaagatgcgtcgagccacagaaacgttagctttacatatagcggaggtgatgtgaaattaatttacaatagaaataatttacatatcaaacagttagatgctttttgtcgttttttaatatttttatgcttgagaaaaaatacgtaacttatttatgatatggacagtttggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGGAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAAc                                                                                                                                                                                                     <  1:176397‑M2/73‑1 (MQ=255)                          tataTGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACCATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGGAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACg                                                                                                                                                                                                    >  1:126942/1‑250 (MQ=255)                               gTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGGAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGc                                                                                                                                                                                               <  2:121326/250‑1 (MQ=255)                                  cgagccacagaaacgttagctttacatatagcggaggtgatgtgaaattaatttacaatagaaataatttacatatcaaacagttagatgctttttgtcgttttttaatatttttatgcttgagaaaaaatacgtaacttatttatgatatggacagtttggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGGAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCa                                                                                                                                                                                            <  1:114192‑M2/82‑1 (MQ=255)                                                        aCGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGGAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGtttttt                                                                                                                                                                     <  1:221985/251‑1 (MQ=255)                                                                                                                                    cgttttttaatatttttatgcttgagaaaaaatacgtaacttatttatgatatggacagtttggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGGAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGc                                                                                         >  2:37622‑M2/71‑251 (MQ=255)                                                                                                                                       tAAGCCAACAAATAAACTGAAAAAGATTGTCAGCGATGCTTTACTCTCCGAGTCAACACGGCCCCAAATGTTTCATCTTTTGGGGGAACACTGAGGAGTGTTGGCAGTCAAACTCGTTTACAAAGCAAAGAGTAAAGAACGACTGCCCATGTCGATTTAGGAATAGTTTTTTGAGAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTAAAGCGGctct                                                                                      >  2:211434/1‑251 (MQ=255)                                                                                                                                                  tttatgcttgagaaaaaatacgtaacttatttatgatatggacagtttggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGGAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGcc                                                                            >  2:133248‑M2/57‑250 (MQ=255)                                                                                                                                                           aaaaGTTTGTCCGCGATACTTTCCTCTATGAGTCAAAATGGCCCCACATGCTTCCTCTTTTGGGGGAAAACTGTGGAGTGTTGCCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGNtt                                                                   >  2:203242/1‑250 (MQ=255)                                                                                                                                                                   atacgtaacttatttatgatatggacagtttggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGGAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTggg                                                          >  2:49034‑M2/40‑251 (MQ=255)                                                                                                                                                                      cgcgATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGGAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCGGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGAcc                                                       <  1:134641/251‑1 (MQ=255)                                                                                                                                                                                         aGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGGAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGTTCACTTTAAAGGGGAAg                                    <  1:179466/251‑1 (MQ=255)                                                                                                                                                                                                              ttCATCTTTTGGGGGAAAACTGTGGAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGTATTCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGTTCACTTTAAAGGGGAAGTTGTTAACGCCGCTTgcgc                 >  1:141992/1‑249 (MQ=255)                                                                                                                                                                                                                           ggAAAACTGTGGAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGAGGGACCGTTCACTTTAAAGGGTAAGTTGTTAACGCCGCTTGCGCTGTTGCTGCAGGctc  >  2:222147/1‑251 (MQ=255)                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                TAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGTTCACTTTAAAGGGGAAGTTGTTAACGCCGCTTGCGCAGTTGATGCAGGCTC  >  NC_000913/4542795‑4543263

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑