Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,542,692	+A	intergenic (+59/‑423)	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	4,542,692	1	.	A	90.0%	21.2 / ‑5.8	10	intergenic (+59/‑423)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
Reads supporting (aligned to +/- strand):  ref base . (0/0);  major base A (7/2);  minor base G (0/1);  total (7/3)
Fisher's exact test for biased strand distribution p-value = 3.00e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGCGTGGTGCAGATACTCGTTTAATTCAGGATTATCTCGGGCATCGAAATATTCGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAA‑CTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATT  >  NC_000913/4542479‑4542929                                                                                                                                                                                                                       |                                                                                                                                                                                                                                              aGCGTGGTGCAGATACTCGTTTAATTCAGGATTATCTCGGGCATCGAAATATTCGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAAACTGTCCATATCATACATAAGTTACGTATTTTTtctc                                                                                                                                                                                                           >  1:214294/1‑250 (MQ=255)          cAGATACTCGTTTAATTCAGGATTATCTCGGGCATCGAAATATTCGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATaaa                                                                                                                                                                                                  >  1:194825/1‑250 (MQ=255)                      tAATTCAGGATTATCTCGGGCATCGAAATATTCGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAACGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAAACTGTCCATATAATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTaaaaaa                                                                                                                                                                                      >  2:105773/1‑250 (MQ=255)                                    ctcGGGCATCGAAATATTCGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCt                                                                                                                                                                       >  2:30082/1‑251 (MQ=255)                                                                                                gacagATTATGAGAAATAAATAATCTCATAAACGAAAAATTAAAAAGAAAAGAGTTTTGTTTTAACTGATTGATAATAAAGTTAAAAAAACAAATAAATACAAGGCAATTGTG‑CCAAAGCAGTCCATATCATAAATAAGTTACATATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAATAAACAACTTACTGTTCACTACTTAAATTATTCCTATTGTAAATTAATTTCACATCACATCCTCTatat                                                                                                           <  2:32828/247‑1 (MQ=255)                                                                                                              aagaaaTAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGATTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAAACTGTCAATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATTTAATTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAATCTAATGtt                                                                                             >  2:137719/1‑251 (MQ=255)                                                                                                                                                gaagagGATTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAACTACAAGACAAT‑GGGGCCAAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCCTCTTCCTCATtcttctat                                                           >  1:156405/1‑249 (MQ=255)                                                                                                                                                           aTTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAAACTGTCCATATCATAAATAAGTTACGTATTTTATCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCGCCTCCGCTATATGTAAAGCTAACGTGTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAaccac                                                <  1:136921/251‑1 (MQ=255)                                                                                                                                                                             aaaGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCGTCTCTCCAAAAACCACCTCATGCAATATAAACAt                              <  2:49869/251‑1 (MQ=255)                                                                                                                                                                                                          caatGGGGCCAAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACACAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATAtt  >  1:265481/4‑251 (MQ=255)                                                                                                                                                                                                                       |                                                                                                                                                                                                                                              AGCGTGGTGCAGATACTCGTTTAATTCAGGATTATCTCGGGCATCGAAATATTCGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAA‑CTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATT  >  NC_000913/4542479‑4542929

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑