Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC JC	NC_000913	4,542,042	IS1 (+) +8 bp	coding (6‑13/597 nt)	fimE →	regulator for fimA

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	3583428 =	NA (NA)	21 (0.830)	19/490	0.3	100%	noncoding (1/768 nt)	IS1	repeat region
	?	NC_000913	= 4542049	0 (0.000)					coding (13/597 nt)	fimE	regulator for fimA
*	?	NC_000913	= 3584195	NA (NA)	33 (1.300)	32/492	0.1	100%	noncoding (768/768 nt)	IS1	repeat region
	?	NC_000913	4542042 =	0 (0.000)					coding (6/597 nt)	fimE	regulator for fimA

CCCTTTGACGTGGTGATATGGATGACGGATGGCTGGCCGCTGTATGAATCCCGCCTGAAGGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCAAAAGGAAACAAAAATCATTGTAAACCATGCCATCTTTTTAGAGATTACCAGCAGAAAATTCCTTGTTCGAAATTTAGCAGTGCAAGCTAT  >  NC_000913/3583950‑3584405                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                   cccTGTGACGTGGTGATATGGATGACGGATGGCTGGCCGCTGTATGAATCCCGCCTGAAGGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCGCGAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACAt                                                                                                                                                                                                               <  2:228310/251‑1 (MQ=14)     ttGACGTGGTGATATGGATGACGGATGGCTGGCCGCTGTATGAATCCCGCCTGAAGGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGATCGGCATAACCTGAATCTGAGGCATCACCTGGCACGGCTGGGTCGGAAGTCGCTGTCGGTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTTGAGTCATTACCGACATTa                                                                                                                                                                                                             <  1:99413/249‑1 (MQ=255)     ttGACGGGGTGATATGGATGACGGATGGCTGGCCGCTGTATGAATCCCGCCTGAAGGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTaa                                                                                                                                                                                                            <  2:7421/250‑1 (MQ=18)             gtgATATGGATGACGATTGGCTGGCGGCTGGATGAATCCCGCCTGAAGGGAAAGCTGCCCGTAATCAGCAAGCGATATACGCAGCGAATTGAGGGGCATAACCTGGATCGGAGGCAGCACCTGGCGCGGCTGGGACGGAATTCGTTGTGGTTCTCAAAATCGGTTGAGCTTCATGACAAAGTTTTCGGGCATTATCTGGACATAATACTCTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACtt                                                                                                                                                                                                   <  1:244021/251‑1 (MQ=11)                          cGGATGGCTGGACGCTGTATGAATCCCGCATGAAGGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACATGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCGGACGATCTCAAAATCGGTGGAGCTGCATGACAACGTCATAGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGACATTACCGACATTAAAAGTAACTTTTTTGAAAtt                                                                                                                                                                                         >  2:169379/1‑248 (MQ=14)                             aTGGCTGGCAGCTGTATGACTCCCGCCGGAAGGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACAGTAAAAGTAACTTTTTTGAAATTAGAGat                                                                                                                                                                                   <  2:2777/251‑1 (MQ=255)                                                     gCCTGAAGGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTc                                                                                                                                                           <  1:54510/251‑1 (MQ=255)                                                                 aGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCAGTGGAGCAGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTTCCGACATTAAAAGTAACTTGTTTGAAATTAGAGATAATATTGGCACATAAAATATATTCAGTTCTTTTAGt                                                                                                                                               <  2:38886/251‑1 (MQ=255)                                                                               aGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGCCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGCCATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCAtt                                                                                                                                 >  1:241869/1‑251 (MQ=255)                                                                                     cGATATACGCAGCGAATTGAGCGGCATAAACTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTaa                                                                                                                            >  2:263007/1‑250 (MQ=255)                                                                                                       gggCGGCATAACCTGAATCTGTGGCAGCACCGGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTTATTTctct                                                                                                                                      <  2:206864/220‑1 (MQ=255)                                                                                                       gAGCGGCATAACCTGCATCTGAGGCAGCACCGGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTctct                                                                                                                                      >  1:206864/1‑222 (MQ=255)                                                                                                           ggCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTc                                                                                                      >  1:144075/1‑250 (MQ=255)                                                                                                                       aTCTTAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGAACAGTTGTTCATAATAATCaac                                                                                          >  1:15072/1‑249 (MQ=255)                                                                                                                          tGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCAAAAgg                                                                                       >  1:95116/1‑250 (MQ=255)                                                                                                                                                  gACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACGTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGGTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCAAAAGGAAACAAAAATCATTGTAACCCATGc                                                              <  2:101019/251‑1 (MQ=255)                                                                                                                                                                                   aGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCAAAAGGAAACAAAAATCATTGTAAACCATGCCATCTTTTTAGAGATTACCAGCAGAAAATTCCt                             >  1:169932/1‑251 (MQ=255)                                                                                                                                                                                                       gggCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGCAATTAGCGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCAAAAGGAAACAAAAATCATTGTAAACCATGCCATCTTTTTAGAGATTACCAGCAGAAAATTCCTTGTTCGAAATTTAGCAGTg          >  1:175294/1‑250 (MQ=255)                                                                                                                                                                                                           aTTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCAAAAGGAAACAAAAATCATTGTAAACCATGCCATCTTTTTAGAGATTACCAGCAGAAAATTCCTTGTTCGAAATTTAGCAGTGAAAGc     >  1:141180/1‑251 (MQ=255)                                                                                                                                                                                                                  gAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCAAAAGGAAACAAAAATCATTGTAAACCATGCCATCTTTTTAGAGATTACCAGCAGAAAATTCCTTGTTCGAAATTTAGCAGTGCAAGCTAt  <  1:56785/247‑1 (MQ=255)                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                   CCCTTTGACGTGGTGATATGGATGACGGATGGCTGGCCGCTGTATGAATCCCGCCTGAAGGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCAAAAGGAAACAAAAATCATTGTAAACCATGCCATCTTTTTAGAGATTACCAGCAGAAAATTCCTTGTTCGAAATTTAGCAGTGCAAGCTAT  >  NC_000913/3583950‑3584405

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.