Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,543,047	T→G	intergenic (+414/‑68)	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	4,543,047	0	T	G	97.0%	98.4 / NA	34	intergenic (+414/‑68)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
Reads supporting (aligned to +/- strand):  ref base T (1/0);  major base G (21/11);  minor base A (1/0);  total (23/11)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.92e-01

ATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTT‑GGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGTTCACTTTAAAGGGGAAGTTGTTAACGCCGCTTGCGCAGTTGATGCAGGCTCTGTTGATCAAACCGTTC  >  NC_000913/4542802‑4543280                                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                          attTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTT‑GGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTGacaa                                                                                                                                                                                                                                       >  2:133277/1‑250 (MQ=255)   ttCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTT‑GGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTGacaaaac                                                                                                                                                                                                                                    >  1:416007/1‑251 (MQ=255)             cTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTT‑GGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTGACAAAACAAAGTGTAc                                                                                                                                                                                                                           >  1:370942/1‑250 (MQ=255)               ccGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTT‑GGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTGACAAAACAAAGTGTAc                                                                                                                                                                                                                           >  1:461718/1‑248 (MQ=255)                     tatGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTT‑GGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTGACAAAACAAAGTGTACAGAACGaat                                                                                                                                                                                                                  >  1:408760/1‑249 (MQ=255)                                        tgtgGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTAATGAAATATAAACATCTATAAATAAAGATAAAAATAGAATATTAAACCAACAAAAAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCAAAATGTTTCATCTTTT‑GGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTGACAAAACAAAGAGTACAGAACGACTGCCCATGTCGAATTAGaa                                                                                                                                                                                                >  1:25865/1‑250 (MQ=255)                                                gACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTT‑GGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTGACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGttttt                                                                                                                                                                                       >  2:122691/1‑251 (MQ=255)                                                             cATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTT‑GGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTGACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAagca                                                                                                                                                                          <  1:426549/251‑1 (MQ=255)                                                                                          aaTAAAAACATCTATAAATAAAGATAACAATAGAATATGAAGCCAACAAAGAAACTGAAAAAGTTTGTCCGCGATGCTTCCCACTATGAGTCAAAATGGCCTCAAATGTTTCATCTTTT‑GGGTGAAAACTGTGCAGTGTTGGGAGTCAAACTCGTTGACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCgtt                                                                                                                                             <  1:31567/251‑1 (MQ=255)                                                                                           atatAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTT‑GGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTGACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCgttg                                                                                                                                            <  1:343119/251‑1 (MQ=255)                                                                                               aaaCATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTT‑GGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTGACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTc                                                                                                                                         <  2:461718/250‑1 (MQ=255)                                                                                               aaaCATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTT‑GGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTGACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCt                                                                                                                                        >  1:266153/1‑251 (MQ=255)                                                                                                      tataAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGATTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTT‑GTGGGAAAACTGTGCAGAGTTGGCAGTCAAACTCGTTAACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGct                                                                                                                                 >  2:381755/1‑251 (MQ=255)                                                                                                                aaTAACAATAGAATATTAAGCCAACAAAGAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTT‑GGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTGACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCa                                                                                                                       <  1:396171/250‑1 (MQ=255)                                                                                                                     cAATAGAATATTAAGCCAACAAATAACCTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTT‑GGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTGACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCt                                                                                                                  >  1:194085/1‑251 (MQ=255)                                                                                                                       aTAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCTCGATGCTTGCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTT‑GGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTGACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTAc                                                                                                                <  1:377047/251‑1 (MQ=255)                                                                                                                           aaTATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTT‑GGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTGACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTGAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGTCTCTGTCCCTCAGTTCTACAGCg                                                                                                            <  2:39563/251‑1 (MQ=255)                                                                                                                              atTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTT‑GGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTGACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGATCTGTCCCTCAGTTCTACAGCGGct                                                                                                         >  2:353479/1‑251 (MQ=255)                                                                                                                                                   aaaaaGTTTGTCCGTGATGCTTTCCTCGAGGAGTCAAAATGGCCCCAAATGTTTCATCATTT‑GGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTGACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGtt                                                                                    <  2:152376/251‑1 (MQ=255)                                                                                                                                                    aaaaGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTT‑GGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTGACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTa                                                                                   <  1:353479/251‑1 (MQ=255)                                                                                                                                                             tCCGCGTTGCTTACCACTATGAGTCAACATGGCCCCAATTGTTTCATATTTT‑GGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTAGCCAAAACAAAGTGTACGGCACGACTGCCCATGTCGCTTTAGCAATAGTTTTTTGGAAGGAAAGCAGCATGAAGATTAAACATCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTAAAGCGGCTCTGGACGCTGCCACGCCGGATAATGGTgggg                                                                          >  2:313087/1‑250 (MQ=255)                                                                                                                                                             tCCGCGATGCTTTCCTCTATGAGTCGAAATGGCCCCAAATGTTTCATCTTTT‑GGGGGAATACTGTGCAGTGTTGGCAGTCAAACTCGTTGACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGCAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCCCGACGGTTGATGGTgggg                                                                          >  2:170284/1‑250 (MQ=255)                                                                                                                                                                 agATGCTGTCCTCTATGAGTCAAACTGGCCCCAAATGTTTCAGCTTGT‑GGGGGCAAACTGCGCAATGTTGCCAGTCAAGCTCGTTGACACAACAACGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGAAAAGCAGCATGCAAATTAAAACTCTGGCAATCGTTGTTCAGTAGGCTCTGTCCCTCAGTTCTCAAGCGCCTCTGGCCGCTCCCACGGCGGATAATGGAGGGACCgc                                                                      >  2:123236/2‑250 (MQ=255)                                                                                                                                                                    tGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTT‑GGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTGACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGttg                                                                    >  1:304518/1‑249 (MQ=255)                                                                                                                                                                     gCTTTCCTCTATGAGTCAAAATGTCCCCAAATGTTTCATCTTTT‑GGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTGACAAAACAAAGTTTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGttga                                                                   <  2:304518/250‑3 (MQ=255)                                                                                                                                                                         tCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTT‑GGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTGACAAAACAAAGTGTACAGAACGAATGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGTTCTCttt                                                               >  2:308879/1‑250 (MQ=255)                                                                                                                                                                             ctATGAGTCAAAATGGCCCCAAATGTTTCATCTTTT‑GGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTGACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGcc                                                                                             <  1:16495/216‑1 (MQ=255)                                                                                                                                                                             ctATGAGTCAAAATGGCCCCAAATGTTTCATCTTTT‑GGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTGACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGcc                                                                                             >  2:16495/1‑216 (MQ=255)                                                                                                                                                                                               ccAAATGTTTCATCTTTT‑GGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTGACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGTTCACTTTAAAGGGGAAGTTGTTAAagccgc                                        >  1:158795/1‑251 (MQ=255)                                                                                                                                                                                                cAAATGTTTCATCTTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAACCAAAGTGTACAGAACGACTGCCCATGTCGCTTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGTTCCCTTTAAAGGGGAAGTTGTTAAcgccgc                                        >  1:64230/1‑251 (MQ=255)                                                                                                                                                                                                                             gtgCAGTGTTGGCAGTCAAACTCGTTGACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGTTCACTTTAAAGGGGAAGTTGTTAACGCCGCTTGCGCAGTTGATGCAGGCTCTGTTGATc           >  1:104858/1‑251 (MQ=255)                                                                                                                                                                                                                               gCAGTGTTGGCAGTCAAACTCGTTGACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGTTCACTTTAAAGGGGAAGTTGTTAACGCCGCTTGCGCAGTTGATGAAGGCTCTGTTGATCa          >  2:397676/1‑250 (MQ=255)                                                                                                                                                                                                                                     ttGGCAGTCAAACTCGTTGACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGTTCACTTTAAAGGGGAAGTTGTTAACGCCGCTTGCGCAGTTGATGCAGGCTCTGTTGATAAAACCGtt   >  1:462517/1‑251 (MQ=255)                                                                                                                                                                                                                                        gCAGTCAAACTCGTTGACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAACTAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTATACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGTTCACTTTAAGGGGGACGTTGTTAACGCCGCTTGCGCAGTTGATGCAGGATCTGTTGATCAAACCGTTc  >  2:427492/1‑249 (MQ=255)                                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                          ATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTT‑GGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGTTCACTTTAAAGGGGAAGTTGTTAACGCCGCTTGCGCAGTTGATGCAGGCTCTGTTGATCAAACCGTTC  >  NC_000913/4542802‑4543280

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: ‑