Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC JC	NC_000913	4,541,967	IS5 (–) +4 bp	intergenic (+408/‑67)	fimB → / → fimE	Type 1 fimbriae regulatory protein FimB/regulator for fimA

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	3652036 =	NA (NA)	18 (0.630)	17/484	0.5	100%	noncoding (1195/1195 nt)	IS5	repeat region
	?	NC_000913	= 4541970	0 (0.000)					intergenic (+411/‑67)	fimB/fimE	Type 1 fimbriae regulatory protein FimB/regulator for fimA
*	?	NC_000913	= 3653230	NA (NA)	28 (0.980)	27/484	0.2	100%	noncoding (1/1195 nt)	IS5	repeat region
	?	NC_000913	4541967 =	0 (0.000)					intergenic (+408/‑70)	fimB/fimE	Type 1 fimbriae regulatory protein FimB/regulator for fimA

CGGATAAGGTCGCCGGCCATTACCAGCCTTGGGGTAAAACGGCTCGATGACTTCCACCATGTTTTGCCATGGCAGAATCTGCTCCATGCGGGACAAGAAAATCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATGACAACCTTTTACGAGCAAAAGCGGAAATTGCTTCGACAATAATTAAATTTTTAGAGGCCAGGATAACCAATCTTTCATACAATGACATATTAAAATATCAGCAAGAATTCCAAAGACAATGTT  >  NC_000913/3652995‑3653468                                                                                                                                                                                                                                            |                                                                                                                                                                                                                                               cGGATAAGGTCGCCGGCCATTACCAGCCTTGGGGTAAAACGGCTCGATGACTTCCACCATGTTTTGCCATGGCAGAATCTGCTCCATGCGGGACAAGAAAATCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTAtt                                                                                                                                                                                                                                 <  1:138995/251‑1 (MQ=33) cGGATAAGGTCGCCGGCCATTACCAGCCTTGGGGTAAAACGGCTCGATGACTTCCACCATGTTTTGCCATGGCAGAATCTGCTCCATGCGGGACAAGAAAATCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTAtt                                                                                                                                                                                                                                 <  1:33602/251‑1 (MQ=33)  ggATAAGGTCGCCGGCCATTACCAGCCTTGGGGTAAAACGGCTCGATGACTTCCACCATGTTTTGCCATGGCAGAATCTGCTCCATGCGGGACAAGAAAATCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTAttt                                                                                                                                                                                                                                <  1:221277/251‑1 (MQ=33)            gCCGGCCATTACCAGCCTTGGGGTAAAACGGCTCGATGACTTCCACCATGTTTTGCCATGGCAGAATCTGCTCCATGCGGGACAAGAAAACCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTGATATCAGTTGCTTGTTCGCCCCTTCCTTAGGTGACACTATTTTTTTACATaa                                                                                                                                                                                                                      <  1:186135/251‑1 (MQ=255)             ccGGCCATTACCAGCCTTGGGGTAAAACGGCTCGATGACTTCCACCATGTTTTGCCATGGCAGAATCTGCTCCATGCGGGACAAGAAAATCTCTTTGCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGGTGATGACTCATGATGAACCCTGTGCTATGGCTCCATATGACAAACATGATCTCATATCAGGGACTTGTTCTCACCTTCCGTAGGTGACACTATTTTTTTACATa                                                                                                                                                                                                                       <  1:111824/249‑1 (MQ=255)                   aTTACCAGCCTTGGGGTAAAACGGCTCGATGACTTCCACCATGTTTTGCCATGGCAGAATCTGCTCCATGCGGGACAAGAAAATCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAATAacac                                                                                                                                                                                                               <  1:212808/251‑1 (MQ=255)                          gCCTTGGGGTAAAACGGCTCGATGACTTCCACCATGTTTTGCCATGGCAGAATCTGCTCCATGCGGGACAAGAAAATCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTAccc                                                                                                                                                                                                        <  1:214442/251‑1 (MQ=255)                                     aaaCGGCTCGATGACTTCCACCATGTTTTGCCATGGCAGAATCTGCTCCATGCGGGACAAGAAAATCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGTACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACTCTACCCCCAAATtatat                                                                                                                                                                                             <  2:57901/251‑1 (MQ=255)                                                                                                    aaTCTCTTATCTGGTCTTACGGCGCTTACTGCTGAATTCACTTTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCATCTTCCTTAGGTGACACTATTTTGTTACATAAAGAAGGCCCTACCCCCTATTTATATTAATTTGTACATTATCTTGGCAATCAATGCGAAGGTTTATGTTTAACATTATTAACCATTAAt                                                                                                                              <  2:42822/251‑1 (MQ=17)                                                                                                        tctTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATGAc                                                                                                                           >  1:312522/1‑250 (MQ=255)                                                                                                                                                 ggCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATTGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATGACAACCTTTTACGAGCAAAAGCGGAAATTGCTTCGACAATAAtt                                                                                 <  1:306816/251‑1 (MQ=255)                                                                                                                                                                atgaCTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCCCCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTAGTTTCAACATTATTAACCATTAATGACAACCTTTTACGAGCAAAAGCGGAAATTGCTTCGACAATAATTAAATTTTTAGAGGcc                                                                  <  2:97330/251‑1 (MQ=255)                                                                                                                                                                  gacgcATGATGAACCCTGTTCTATGGCTGCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATGTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCAGTAATGACAACCTTTTACGAGCAAAAGCGGAAATTGCTTCGACAATAATGAAATTTTTAGAGGcct                                                                 <  2:265038/246‑2 (MQ=255)                                                                                                                                                                            gaACCCTGTTCTAATGCTCCAGATGACAAACATGATCACATATCAGGGACTTGTTCGCTCCTTCCTTAGGTGACAATATGTTTGTACATAAAGAACACCCTACCCCCAAAGTATATAAAGATGGACAATAGCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATGACAACCTTTTACGAGCAAAAGCTTAAATAGCGTCGACAATAATTAAAGTTTGAGAGGCCAGGATAACCAAt                                                      <  2:187928/251‑1 (MQ=255)                                                                                                                                                                                     tCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATGACAACCTTTTACGAGCAAAAGCTGAAATTGCTTCGACAATAATTAAATTTTTAGATGCCAGGATAACCAATCTTTCATa                                              <  1:115871/250‑1 (MQ=255)                                                                                                                                                                                          ggCTCCAGATGACAAACATGATCTCATATCCGGGCCTTGTACGCAACTTACTTCGGTGACACTATTTTTTTACATAAAGAACACCCTACTCCCAAATCATATAAAGATGGACAATATCTTGACAAACAAATCGACGGTTTATTTTCAACATTATTAACCATTAATGACAACCTTTTAAGAGCAAAAGCGGAAATTGCTTCGACAATAATTAAATTTTTAGAGGCCAGGATAACCAATCTTTCATACAATg                                         >  1:140910/1‑250 (MQ=255)                                                                                                                                                                                                                                 ttCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATGACAACCTTTTACGAGCAAAAGCGGAAATTGCTTCGACAATAATTAAATTTTTAGAGGCCAGGATAACCAATCTTTCATACAATGACATATTAAAATATCAGCAAGAATTCCAAAGACAATGtt  >  1:198906/1‑250 (MQ=255)                                                                                                                                                                                                                                            |                                                                                                                                                                                                                                               CGGATAAGGTCGCCGGCCATTACCAGCCTTGGGGTAAAACGGCTCGATGACTTCCACCATGTTTTGCCATGGCAGAATCTGCTCCATGCGGGACAAGAAAATCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATGACAACCTTTTACGAGCAAAAGCGGAAATTGCTTCGACAATAATTAAATTTTTAGAGGCCAGGATAACCAATCTTTCATACAATGACATATTAAAATATCAGCAAGAATTCCAAAGACAATGTT  >  NC_000913/3652995‑3653468

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: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.