New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	3583428 =	NA (NA)	25 (1.000)	23/492	0.2	100%	noncoding (1/768 nt)	IS1	repeat region
	?	NC_000913	= 4542158	0 (0.000)					coding (122/597 nt)	fimE	regulator for fimA

AATTGACTGATAGCCACATCACTCCGTGTGTGGTTATCTTTTTATCTATTGGGCTAATTTTGACCGATTGAGGTTTCCTATAGGTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACGGGAGCCAGAGATTATTGTCTTATTCTGTTGGCATATCGGCATGGGATGCGTATTAGTGAACTGCTTGATCTGCATTATCAGGACCTTGACCTTAATGAAGGTAGAATAAATATTCGCCGACTGAAGAACGGATTTTCTACCGTTCACCCGTTACGTTTTGATGAGCGTGAAGCCGTGGAACGCTGGACCCAGGAACGTGCTAACTGGAAAGGCGCTGACCGGACTGACGCTATATTTATTTCTCGCCGCGGGAGTCGGCTTTCTCGCCAGCAGGCCTATCGCATTATTCGCGATGCC  >  NC_000913/4541914‑4542405                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                                        aaTTGACTGATAGCCACATCACTCCGTGTGTGGTTATCTTTTTATCTATTGGGCTAATTTTGACCGATTGAGGTTTCCTATAGGTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACGGGAGCCAGCGATTATTGTCTTATTCTGTTGGCATATCGGCATGGGATGCGggggat                                                                                                                                                                                                                                                   <  1:35822‑M2/251‑7 (MQ=255)          ctaGCCATATCACTCAGTGTGTGGATATCTTTTTATCTATTGGGCTACTTTTGACCGATTGAGGTTTCCTATAGGTCTTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACGGGAGCCAGAGATTATTGTCTTATTCTGTTGGAATATCGGCATGGGGTGAGggtgatgctgccaac                                                                                                                                                                                                                                          <  2:26379‑M2/250‑16 (MQ=255)                    cACTCCGTGTGTGGTTATCTTTTTATCTATTGGGCTAATTTTGACCGATTGAGGTTTCCTATAGGTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACGGGAGCCAGAGATTATTGTCTTATTCTGTTGGCATATCGGCATGGGATGCGggtgatgctgccaacttactgatt                                                                                                                                                                                                                                 >  2:26033‑M2/1‑226 (MQ=255)                                 gTTATCTTTTTATCTATTGGGCTAATTTTGACCGATTGAGGTTTCCTATAGGTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACGGGAGCCAGAGATTATTGTCTTATTCTGTTGGCATATCGGCATGGGATGCGggtgatgctgcccacttactgatttagtgtatgatggg                                                                                                                                                                                                                   <  2:111587‑M2/251‑39 (MQ=255)                                                                  gATTGAGGTTTCCTATAGGTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACGGGAGCCAGAGATTATTGTCTTATTCTGTTGGCATATCGGCATGGGATGCGggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggtgctccagtggcttctgtttct                                                                                                                                                                                   <  1:114171‑M2/250‑71 (MQ=255)                                                                                         cattcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACGGGAGCCAGAGATTAGTGTCGTATTCTGTTGGCATATCGGCATGGGATGCGggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggggctccagtggcttctgtttctatcagctgtccctcctgttcagct                                                                                                                                                           >  1:14237‑M2/1‑157 (MQ=255)                                                                                                          gTTAGGAGTACTACTATTGTGCGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACGGGCGCCAGAGATTATTGTCTTATTCTGTTGGCATATAGGCATGGGATGCGggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggtgctccagtggcttctgtttctatcagctgtccctcctgttcagctactgacgggggggtgcg                                                                                                                                          <  2:236962‑M2/251‑112 (MQ=255)                                                                                                              ggAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACGGGAGCCAGAGATTATTGTCTTATTCTGTTGGCATATCGGCATGGGATGCGggtgatgctgccaac                                                                                                                                                                                                                                          >  2:62182‑M2/1‑136 (MQ=255)                                                                                                              ggAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACGGGAGCCAGAGATTATTGTCTTATTCTGTTGGCATATCGGCATGGGATGCGggtgatgctgccaac                                                                                                                                                                                                                                          <  1:62182‑M2/151‑16 (MQ=255)                                                                                                                                 tAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACGGGAGCCAGAGATTATTGTCTTATTCTGTTGGCATATCGGCATGGGATGCGggtgatgctgccaacttactga                                                                                                                                                                                                                                   >  1:196323‑M2/1‑117 (MQ=255)                                                                                                                                 tAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACGGGAGCCAGAGATTATTGTCTTATTCTGTTGGCATATCGGCATGGGATGCGggtgatgctgccaacttactga                                                                                                                                                                                                                                   <  2:196323‑M2/139‑23 (MQ=255)                                                                                                                                   aaCGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGCTGCAGGCGGTTTGTTACGGGGCAACGGGAGCCAGAGATTATTGTCTTATTCTGTTGGCATATAGGCATGGGATGCGggtgatgctgccaacttactgatttagtgtatgatggggtttttgaggtgctccagtggcttctgtttctatcagctgtccctcctgttcagctactgacggggtggtgcgtaacggcaaaagcaccgccggaca                                                                                                                  <  1:113987‑M2/250‑136 (MQ=255)                                                                                                                                                       aaaGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACGGGAGCCAGAGATTATTGTCTTATTCTGTTGGCATATCGGCATGGGATGCGggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggtgctccagtggcttctgtttctatcagctgtccctcctgttcagctactgacggggtggtgcgtaacggcaaaagcaccgccggacatcagcgctatctctgctctc                                                                                              >  1:192821‑M2/1‑95 (MQ=255)                                                                                                                                                       aaaGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGAGGCAACGGGAGCCAGAGATTATTGTCTTATTCTGTTGGCATATCGGCATGGGATGCGggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggtgctccagtggcttctgtttctatcagctgtccctcctgttcagctactgactgggtgatgcgtaacggcaaaatcaccgccggacatcagcgctatctctgctctc                                                                                              >  1:192823‑M2/1‑95 (MQ=255)                                                                                                                                                                 aGGCCATGATGCAGGCGGTTTGTTACGGGGCAACGGGAGCCAGAGATTATTGTCTTATTCTGTTGGCATATCGGCATGGGATGCGggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggtgctccagtggcttctgtttctatcagctgtccctcctgttcagctactgacggggtggtgcgtaacggcaaaagcaccgccggacatcagcgctatctctgctctcactgccgtaa                                                                                    <  1:114979‑M2/250‑166 (MQ=255)                                                                                                                                                                        gatgCAGGCGGTTTGTTACGGGGCAACGGGCGCCCGAGATTATTATCTTATTCTGTTGGCATATCGGCATGGGATGCGggtgatgccgccaacttactgatttagtgtatgatggtgtttttgaggtgctccagtggcttctgtttctatcagctgtccctcctgttcagctactgacggggtggtgcgtaacggcaaaagaaccgccggaaatcagcgctatctctgctctcactgccgtaaaacatggc                                                                            <  1:232173‑M2/251‑174 (MQ=255)                                                                                                                                                                             aGGCGGTTTGTTACGGGGCAACGGGAGCCAGAGATTATTGTCTTATTCTGTTGGCATATCGGCATGGGATGCGggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggtgctccagtggcttctgtttctatcagctgtccctcctgttcagctactgacggggtggtgcgtaacggcaaaagcaccgccggacatcagcgctatctctgctctcactgccgtaaaacatggcaactg                                                                       >  1:236962‑M2/1‑73 (MQ=255)                                                                                                                                                                                      gTTACGGGGCAACGGGAGCCAGAGATTATTGTCTTATTCTGTTGGCATATCGGCATGGGATGCGggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggtgctccagtggcttctgtttctatcagctgtccctcctgttcagctactgacggggtggtgcgtaacggcaaaagcaccgccggacatcagcgctatctctgctctcactgccgtaaaacatggcaactgcagttcact                                                              >  1:89963‑M2/1‑64 (MQ=255)                                                                                                                                                                                             ggCAACGGGAGCCAGAGATTATTGTCTTATTCTGTTGGCATATCGGCATGGGATGCGggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggtgctccagtggcttctgtttctatcagctgtccctcctgttcagctactgacggggtggtgcgtaacggcaaaagcaccgccggacatcagcgctatctctgctctcactgccgtaaaacatggcaactgcagttcacttacaccg                                                       >  1:98742‑M2/1‑57 (MQ=255)                                                                                                                                                                                             ggCAACGGGAGCCAGAGATTATTGTCTTATTCTGTTGGCATATCGGCATGGGATGCGggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggtgctccagtggcttctgtttctatcagctgtccctcctgttcagctactgacggggtggtgcgtaacggcaaaagcaccgccggacatcagcgctatctctgctctcactgccgtaaaacatggcaactgcagttcacttacaccg                                                       <  1:230967‑M2/251‑195 (MQ=255)                                                                                                                                                                                                  cGGGAGCCAGAGATTATTGTCTTATTCTGTTGGCATATCGGCATGGGATGCGggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggtgctccagtggcttctgtttctatcagctgtccctcctgttcagctactgacggggtggtgcgtaacggcaaaagcaccgccggacatcagcgctatctctgctctcactgccgtaaaacatggcaactgcagttcacttacaccgcttct                                                  >  2:202242‑M2/1‑52 (MQ=255)                                                                                                                                                                                                     gAGCCAGAGATTATTGTCTTATTCTGTTGGCATATCGGCATGGGATGCGggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggtgctccagtggcttctgtttctatcagctgtccctcctgttcagctactgacggggtggtgcgtaacggcaaaagcaccgccggacatcagcgctatctctgctctcactgccgtaaaacatggcaactgcagttcacttacaccgcttctca                                                <  1:144123‑M2/250‑202 (MQ=255)                                                                                                                                                                                                          agagATTATTGTCTTATTCTGTTGGCATATCGGCATGGGATGCGggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggtgctccagtggcttctgtttctatcagctgtccctcctgttcagctactgacggggtggtgcgtaacggcaaaagcaccgccggacatcagcgctatctctgctctcactgccgtaaaacatggcaactgcagttcacttacaccgcttctcaacccgg                                          <  1:188259‑M2/251‑208 (MQ=255)                                                                                                                                                                                                                                               ggATGCGggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggtgctccagtggcttctgtttctatcagctgtccctcctgttcagctactgacggggtggtgcgtaacggcaaaagcaccgccggacatcagcgctatctctgctctcactgccgtaaaacatggcaactgcagttcacttacaccgcttctcaacccggtacgcaccagaaaatcattgatatggccatgaatggc     <  1:66311‑M2/251‑245 (MQ=255)                                                                                                                                                                                                                                                  tGCGggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggtgctccagtggcttctgtttctatcagctgtccctcctgttcagctactgacggggtggtgcgtaacggcaaaagcaccgccggacatcagcgctatctctgctctcactgccgtaaaacatggcaactgcagttcacttacaccgcttctcaacccggtacgcaccagaaaatcattgatatggccatgaatggcgtt  <  1:95488‑M2/251‑248 (MQ=255)                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                                        AATTGACTGATAGCCACATCACTCCGTGTGTGGTTATCTTTTTATCTATTGGGCTAATTTTGACCGATTGAGGTTTCCTATAGGTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACGGGAGCCAGAGATTATTGTCTTATTCTGTTGGCATATCGGCATGGGATGCGTATTAGTGAACTGCTTGATCTGCATTATCAGGACCTTGACCTTAATGAAGGTAGAATAAATATTCGCCGACTGAAGAACGGATTTTCTACCGTTCACCCGTTACGTTTTGATGAGCGTGAAGCCGTGGAACGCTGGACCCAGGAACGTGCTAACTGGAAAGGCGCTGACCGGACTGACGCTATATTTATTTCTCGCCGCGGGAGTCGGCTTTCTCGCCAGCAGGCCTATCGCATTATTCGCGATGCC  >  NC_000913/4541914‑4542405

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 35 ≤ 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.