New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	4542682 =	11 (0.630)	3 (0.180)	3/274	1.6	18.6%	intergenic (+49/‑433)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	4542996 =	16 (0.970)					intergenic (+363/‑119)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
Rejected: Frequency below/above cutoff threshold.

TGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGTTCACTTTAAAGGGGAAGTTGTTAACGCC  >  NC_000913/4542772‑4543240                                                                                                                                                                                                                                 |                                                                                                                                                                                                                                                     tGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCAACTCCGCTATATGTAAAGCTAAAGTTTCTGTGGCTCGACGCATATTCCTCATTCTTTTCTACAAAAAACACATAATGCAATATAAACATCTTTAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGAGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATGTTTTGGGGGAAAACtgt                                                                                                                                                                                                                            >  1:198682/1‑251 (MQ=255)    gatttttatattgcatgaggtggtttttggagagaagaatgaggaagatgcgtcgagccacagaaacgttagctttacatatagcggaggtgatgtgaaattaatttacaatagaaataatttacatatcaaacagttagattctttttgtcgttttttaatatttttatgcttgagaaaaaatacgtaacttatttatgatatggacagtttggccccaaATGTTTCATCTTTTggg                                                                                                                                                                                                                                      <  1:382521‑M2/17‑1 (MQ=255)                                        agaatgaggaagatgcgtcgagccacagaaacgttagctttacatatagcggaggtgatgtgaaattaatttacaatagaaataatttacatatcaaacagttagatgctttttgtcgttttttaatatttttatgcttgagaaaaatacgtaacttatttatgatatggacagtttggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAgtgt                                                                                                                                                                                     <  1:142670‑M2/66‑1 (MQ=255)                                                          aGCTAACGTTTCTGTGGCTCGACTCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCGATGAGTCAAAATTGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGttt                                                                                                                                                                                                   <  1:297609/219‑1 (MQ=255)                                                                          gNTCGAAGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGttt                                                                                                                                                                                                                                                 >  1:349868/1‑157 (MQ=255)                                                                             cGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATACACATCTATAAATACAGCTAAACATAAAATATTACGCACACCAATAAAATGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAACACTGTGCAGTGTTGGCAGTCAAACTCGTTTacaaaac                                                                                                                                                                                            >  1:400451/1‑207 (MQ=255)                                                                                       tCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTgaaagg                                                                                                                                        <  1:213730/249‑1 (MQ=255)                                                                                               cttctCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGtt                                                                                                                                                                                                                                                  <  1:399689/135‑1 (MQ=255)                                                                                               cttctCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGACAACAAATAAACTGAAAAAGTTTGTCCGCGCTGCTTTCCTATATGAGTAACAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCAt                                                                                                                              >  1:71229/1‑251 (MQ=255)                                                                                                 tctctcCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGGTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCAtn                                                                                                                             <  1:46655/250‑2 (MQ=255)                                                                                                      ccaaaccccaccTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTACGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTc                                                                                                                                                                                                                                                >  1:102702/8‑130 (MQ=255)                                                                                                                      gCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCg                                                                                                       >  1:386405/1‑251 (MQ=255)                                                                                                                            taAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGt                                                                                                                                                                                                                                                   >  1:35085/1‑105 (MQ=255)                                                                                                                                     ataaatnnAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGt                                                                                                                                                                                                                                                   <  2:35085/96‑1 (MQ=255)                                                                                                                                                                  ccAACAAATAAACTGAAAAAGTGTGTCCGCGATGCTTTCATCTATGAGTCACAATGGCCCCAACTGTTTCCTCTTTTGGGGGAAAACTGTGCCGTGTTGGCAGTCAAACTCGTTTACAAACCAAAGTGTACAGAACGAATGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCCGCATGAAAATTACAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTCAAGCGGCTCTGGcc                                                           >  1:308860/1‑251 (MQ=255)                                                                                                                                                                                          gTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCtttt                                                                                                                                                                                                                                         >  1:440306/1‑53 (MQ=255)                                                                                                                                                                                          gTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCgg                                                                                           <  1:294043/195‑1 (MQ=255)                                                                                                                                                                                                  cttatttatgatatggacagtttggccccaaATGTTTCATCTTTTGGGGGAAAAc                                                                                                                                                                                                                               <  1:413551‑M2/24‑1 (MQ=255)                                                                                                                                                                                                                aGTCAAAATGGCCCCAAATGTATCATCTTTTGGTGGAAAACTGTGCAGTGTTGGCATTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTTCCCATTTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGt                                                                                              <  1:445825/170‑1 (MQ=255)                                                                                                                                                                                                                           ccccAAATGTTTCATCTTTTGGGGGAACACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAAAGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGTTCACTTTAAAGGGGAAGTTGTTAAcgcc  >  1:379293/1‑251 (MQ=255)                                                                                                                                                                                                                             ccAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAACCTAGTTTACAAAACAAAGTGTAAAGACAGACTGCCCATGACGATTTCGAAATAGTTTTTTGCAAGGAAAGCAGCATGTAAATTAAAACTATGGCACTCGTTGTTCTGTCGGCTCTGTCCTTCAGTTCTAAAGCGGCTTTgg                                                             >  1:66899/1‑190 (MQ=255)                                                                                                                                                                                                                                 |                                                                                                                                                                                                                                                     TGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGTTCACTTTAAAGGGGAAGTTGTTAACGCC  >  NC_000913/4542772‑4543240

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 18 ≤ 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.