New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_hsa_pgi	4542710 =	43 (0.810)	5 (0.100)	5/252	NT	10.9%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913_3_hsa_pgi	4543024 =	42 (0.840)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)

ATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAA  >  NC_000913_3_hsa_pgi/4542564‑4542856                                                                                                                                                   |                                                                                                                                                   aacgattgccagagttttaattttcatgctgctttcctttcaaaaaactatttctaaatcgacatgggcagtcgttctgtacactttgttttgtaaacgagtttgactgccaacatcgcacatggtgcccccaaaagatgaaacatTTg                                                                                                                                                  >  2:972129‑M1/147‑149 (MQ=255) aacgattgccagagttttaattttcatgctgctttcccttcaaaaaactatttctaaatcgacatgggcagtcgttctgtacactttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTg                                                                                                                                                  >  1:4013‑M1/147‑149 (MQ=255)  actgttgcgagagttttaagtttcatgctgtttaccttttaaaaaactatttctaaatcgacatgggcagtcgttctgtacactttgttttgtaaacgagtttgacggccaacactgcacagttttcccccaaaagatgaaacatTTgg                                                                                                                                                 >  2:430526‑M1/146‑149 (MQ=255)  acgattgccaggttttttattttcatgctgctttcctttcaaaaaactatttctaaatcgacttgggcagtcgttctgtacactttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTgg                                                                                                                                                 >  1:511814‑M1/146‑149 (MQ=255)    cTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTgggg                                                                                                                                               <  1:394418/149‑1 (MQ=255)       tgCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCa                                                                                                                                            >  1:825799/1‑149 (MQ=255)         ccagagttttaattttcatgctgctttcctttcaaaaaactatttctaaatcgacatgggcagtcgttctgtacactttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCaaa                                                                                                                                          <  2:786999‑M1/11‑1 (MQ=255)           ttATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGAAAATAGGGTCCAAACt                                                                                                                                        >  2:932605/1‑149 (MQ=255)                   ccAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAATAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTACAAAACAAAATAAATACAAACAAATTGGGACCAACATGTCCatct                                                                                                                                >  1:872781/1‑147 (MQ=255)                   ccAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCatat                                                                                                                                <  2:659446/149‑1 (MQ=255)                    cAGTAAGGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGATAAATTACAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAATACAATTGGGGCCAAACTGTCCTTATc                                                                                                                               <  2:764343/149‑1 (MQ=255)                     aGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCa                                                                                                                              <  2:181316/149‑1 (MQ=255)                      gTAAGGCTGCTCGTTTTGACGGATTATGGGAAAGAAATAATCTGATAAACTAAAAATTATAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCat                                                                                                                             <  2:840269/149‑1 (MQ=255)                       tAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCAATATCata                                                                                                                            >  1:427711/1‑149 (MQ=255)                             gtatCGTTTTGCCGGATTATGAGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAg                                                                                                                      <  1:155606/146‑1 (MQ=255)                                ctttcctttcaaaaaactatttctaaatcgacatgggcagtcgttctgtacactttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTa                                                                                                                   >  1:569911‑M1/116‑149 (MQ=255)                                   ttttGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCAAAACTGTCCATATCATAAATAAGTTACGt                                                                                                                >  2:270547/1‑149 (MQ=255)                                         cGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAATTACGTAttttt                                                                                                          >  1:872615/1‑149 (MQ=255)                                         cGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTAGGGCCAAACTGTCCATATCATAAATAAGTTACGTCttttt                                                                                                          >  2:817201/1‑149 (MQ=255)                                         cGGATTATGGGAAAGAAATAATCTCATAAACGAAAAAATAAAAAGAGAAAAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTAttttt                                                                                                          >  2:157406/1‑149 (MQ=255)                                            aTTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTtct                                                                                                       <  2:825799/149‑1 (MQ=255)                                               aggggAAAAAACAAATCTCATAAACAAAAAATAAAAAAGAGAAAAGGGTTGACTTAATTTATTGATAAAAAAAAAAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCaa                                                                                                    <  2:355304/147‑1 (MQ=255)                                               aTGGGAAATAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCaa                                                                                                    <  1:169914/149‑1 (MQ=255)                                                        aaaTAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAAATTATTGATAATAAAGTTAAAAAAACAAATAAATAAAAGAAAATTGGGGCTAAACTGTCTATATAATAAATAAGTTAAGTATTTTTTTTTAAGTATaaaaa                                                                                           >  1:367313/1‑149 (MQ=255)                                                             gacatgggcagtcgttctgtacactttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTa                                                                                      <  2:168965‑M1/63‑1 (MQ=255)                                                              tctcATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTAGAGCCAAACTATCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATACAAATATTaa                                                                                     >  2:80183/1‑149 (MQ=255)                                                                acgggcagtcgttctgtaaaccttgttgtgtagacgagtttgactgccaacacttcacagttttccaccaaaagatgaaacatTTGGGCCCAAACTGTACACATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTaaaa                                                                                   >  2:166437‑M1/84‑149 (MQ=255)                                                                                aaaaaGAGTAGATGTGCGATGTCACTTATTGATAATAAAGTTAAAATAACAATTTAACACAAGATAAATAGTGACAAACGATCATTATGATAAAAGAGTTATGGATTGTTTATAAATCAGAAAAATATTAAAAAATGACAAAAAACAtt                                                                   >  2:648244/1‑148 (MQ=255)                                                                                   aagagaagagGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTaa                                                                >  2:556850/1‑149 (MQ=255)                                                                                         ttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGttt                                                          >  1:592588‑M1/59‑149 (MQ=255)                                                                                         agagGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACCTCTTAAATCCCTAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGttt                                                          <  2:920925/149‑1 (MQ=255)                                                                                          gagGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTg                                                         <  1:382935/149‑1 (MQ=255)                                                                                              tttGATTTAACTTATTGTTAAAAAAGTGAAATAAACAAATAAATACAAGCCAATTGGGGCAAAACTTTCCATATCATAAATAAGTTACGTATTTTTTTTTAAGCATAAAAATATTAAAAAACGACAAAAAGCATTTAACTGTTTGatat                                                     <  2:599524/149‑1 (MQ=255)                                                                                                 acgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTa                                                  >  1:168965‑M1/51‑149 (MQ=255)                                                                                                         ttATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTAttt                                          <  1:167929/149‑1 (MQ=255)                                                                                                            tttataataAAGTTAAAAAAACAAAGAAACACAAGTCAATTGTGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAATAAGCATCTAACTGTTTGATATGTAAATTATTTCTa                                       <  2:553584/146‑1 (MQ=255)                                                                                                              gATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTTGGGCCAAACTGTCAATATCATAAATAAGTTACGTATTTTTTCTCAAGCAAAAAAATATTAACACACGACAAAACGCATCTAAGTGTTTTATATTTAAATTATATCTAtt                                     >  2:448315/1‑149 (MQ=255)                                                                                                              gATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAACCTGTCCATATCATAAATAAGTTACGTATTTTTTCTGAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTCTTTGATCTGTAAATTATTTCTAtt                                     >  2:524698/1‑149 (MQ=255)                                                                                                              gATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTAtt                                     >  1:310737/1‑149 (MQ=255)                                                                                                               ataataAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTg                                    >  2:728309/1‑149 (MQ=255)                                                                                                                  ataaAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGATACGTCTTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTaa                                 >  1:881236/1‑149 (MQ=255)                                                                                                                  ataaAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCAAATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTATGATATGTAAATTATTTCTATTGTaa                                 >  2:660084/1‑149 (MQ=255)                                                                                                                           aaaaaaaaaaTAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTc                        <  1:558/149‑1 (MQ=255)                                                                                                                           aaaaaaCAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTc                        >  2:839708/1‑149 (MQ=255)                                                                                                                           aaaaaaCAAACAACTAAAAGACAATTGGGGACAAACTGGCCATAGCATAAATAAGTTACGTATTTGTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTc                        <  1:455312/149‑1 (MQ=255)                                                                                                                            aaaaaCAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTca                       <  1:358877/149‑1 (MQ=255)                                                                                                                            aaaaaCAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTca                       >  2:177466/1‑149 (MQ=255)                                                                                                                             aaaaCAAATAAATACAACACAATGGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTcac                      <  1:454078/149‑1 (MQ=255)                                                                                                                                aCAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATAATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTACTTTAaatttattcaaccag                   >  2:247834/1‑142 (MQ=255)                                                                                                                                     taaataCAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTc              <  1:270547/149‑1 (MQ=255)                                                                                                                                     taaataCAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATAGTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACAtgtcctg              >  1:142103/1‑143 (MQ=255)                                                                                                                                            aaGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTATCTGTCTGCCGTTGGAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCtata       <  1:236922/149‑1 (MQ=255)                                                                                                                                            aaGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACTTCCGCtata       >  1:774444/1‑149 (MQ=255)                                                                                                                                                 aaTTGGGGCCAAACTGTTCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTaa  <  2:310737/149‑1 (MQ=255)                                                                                                                                                 aaTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTTTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATAACTTCCGCTATATGTaa  >  1:583049/1‑149 (MQ=255)                                                                                                                                                   |                                                                                                                                                   ATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAA  >  NC_000913_3_hsa_pgi/4542564‑4542856

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ 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.