New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	4542682 =	23 (0.820)	7 (0.270)	7/246	NT	26.2%	intergenic (+49/‑433)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	4542996 =	18 (0.690)					intergenic (+363/‑119)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit

CCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTA  >  NC_000913/4542859‑4543124                                                                                                                                          |                                                                                                                                 tcTCATTCTTCTCTCCAAAAACCACCTCATTTAATATAAACATCTATAAATATAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGttt                                                                                                                             <  1:43503/142‑1 (MQ=255)            tctcCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCACGATGCTTTCCTCTATAAGTCAAAAAGACCCCAAATGTTTCATCTTTTggg                                                                                                                  >  2:28165/1‑143 (MQ=255)             taaattactttacaatagaaataatttacatatcaaacagttatatgctttttgtagttttttaatatttttaggcttgagaaaaaatacgtaacttatttatgatatggacagtttggccccaaATGTTTCATCTTTTgggg                                                                                                                 <  1:211732‑M2/18‑1 (MQ=255)              aaattaatttacaatagaaataatttacatatcaaacagttagatgctttttgtcgttttttaatatttttatgcttgagaaaaaatacgtaacttatttatgatatggaaagtttggccccaaATGTTTCATATTttgggtg                                                                                                                >  2:143064‑M2/125‑141 (MQ=255)                     tccttcTCATTCAATATAAATATTTATAAATAAAGATAAAAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACtg                                                                                                         <  1:64111/138‑1 (MQ=255)                      ttacaatagaaataatttacatatcaaacagttagatgctttttgtcgttttttaatatttttatgcttgagaaaaaatacgtaacttatttatgatatggacagtttggccccaaATGTTTCATCTTTTGGGGGAAAACtgt                                                                                                        <  2:542666‑M2/27‑1 (MQ=255)                         ccTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAACTGTTTCATCGTTTGGGCGCAAACTGTGCa                                                                                                     >  2:58480/1‑143 (MQ=255)                         ccTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCATCCATGAGTCAAAATGGCAACACATGTTTCATCTTTTGGGGGACAACTGTGCa                                                                                                     >  2:428778/1‑143 (MQ=255)                         caatagaaataaattacatatcaaagtgttagatgctttttgtcgttttttaatatttttatgcttgagaaaaaatacgtaacttatttatgatatggacagtttggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCa                                                                                                     <  2:85864‑M2/30‑1 (MQ=255)                               gCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGCGTTg                                                                                               >  2:65589/1‑143 (MQ=255)                               gCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTATTAGGGGAAAAATGTGCAgaattg                                                                                               >  1:257893/1‑138 (MQ=255)                                                     ttctatgctttgtgtcgttttttaatatgtttatgcttgagaaaaaatacgtatcttatttatgatatggacagtttggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTacaaaa                                                                         <  2:1365‑M2/58‑1 (MQ=255)                                                     aaGATAACAATAGAATATTAAGCCAACAAATAATCTGAATATTTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTacaaaa                                                                         <  1:460264/143‑1 (MQ=255)                                                         tAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATAGCACCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTacaaaacaaa                                                                     >  1:192537/1‑143 (MQ=255)                                                           gctttttgtcgttttttaatatttttatgcttgagaaaaaatacgtaacttatttatgatatggacagtttggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGGAGTGTTGGCAGTGAAACTTGGtgacaaaacaaaaa                                                                   >  2:365565‑M2/80‑141 (MQ=255)                                                                 gAATATTAAGCCACCAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAg                                                             <  2:280733/143‑1 (MQ=255)                                                                      ttAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCTAATGTTTCATCTATTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGa                                                        <  1:141026/143‑1 (MQ=255)                                                                            caacaaATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAACTGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTGTACAAAACAAAGTGTACAGAACGACTAccc                                                  >  2:10522/1‑143 (MQ=255)                                                                              acaaATAAACTGAAAAAGTTTGTCGGCGATACTTTCCTCTAAGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAGAACTGTACCGTGTCAGCAGTCAAACTCGTTTCAAAAAAAAACTATACAGAACAACTGCCGAt                                                >  2:191994/1‑143 (MQ=255)                                                                                                        taacttatttatgatatggatagtttggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTgaaa                      <  1:486272‑M2/109‑1 (MQ=255)                                                                                                        cgATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCCGTCAAACTCGTTTCCAAAACAAAGTGTACAAAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTgaaa                      >  1:559196/1‑143 (MQ=255)                                                                                                        cgATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTgaaa                      <  2:22452/143‑1 (MQ=255)                                                                                                                  ctctATGAGTCAAAATGGCCCCAAGTGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAagcagc            <  2:96810/143‑1 (MQ=255)                                                                                                                         aGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGAGTTAGAAATAGTTTTAGGAAAGGAAAGCAGCACGaaaa     >  2:157082/1‑143 (MQ=255)                                                                                                                          gTCAAAATGGCTCTAAATGTTTCATCTTTAAGGTGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAAt    <  1:544903/143‑1 (MQ=255)                                                                                                                            cAAAATTGCCCCAAATGTTTCATCTTTTGGTGGAAAACTGTGTAGTGTTGGCAGTCAATCTTGTAGACAAAACAGGGTGTGCAGAGCGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTa  <  1:447317/143‑1 (MQ=255)                                                                                                                                      ccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGaaa      <  2:335735‑M2/125‑1 (MQ=255)                                                                                                                                      ccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGaaa      >  1:335735‑M2/5‑129 (MQ=255)                                                                                                                                          |                                                                                                                                 CCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTA  >  NC_000913/4542859‑4543124

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 22 ≤ 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.