New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	4542682 =	33 (0.750)	7 (0.180)	6/116	1.8	17.2%	intergenic (+49/‑433)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	4542996 =	39 (1.020)					intergenic (+363/‑119)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
Rejected: Frequency below/above cutoff threshold.

GCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTA  >  NC_000913/4542932‑4543062                                                                 |                                                                   gCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGt                                                                 >  1:1072876/1‑68 (MQ=255) gCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGt                                                                 >  1:1779006/1‑68 (MQ=255)        aaTAAACTGAAAAAGTTTGTCCTCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCt                                                          <  1:2452110/68‑1 (MQ=255)           tatgcttgagaaaaaatacgtaacttatttatgatatggacagtttggccccaaATGTTTCATCtttt                                                       >  1:195431‑M2/55‑68 (MQ=255)             aCTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTgg                                                     >  1:1208612/1‑68 (MQ=255)             aCTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTgg                                                     >  1:1578358/1‑68 (MQ=255)              cTGAAGAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTATCATCTTTTggg                                                    <  1:2130777/68‑1 (MQ=255)              cTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTggg                                                    <  1:1006597/68‑1 (MQ=255)              cTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTggg                                                    <  1:736451/68‑1 (MQ=255)                   aaaGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGaaa                                               <  1:833454/68‑1 (MQ=255)                   aaaGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGaaa                                               <  1:2444228/68‑1 (MQ=255)                   aaaGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGaaa                                               <  1:3003844/68‑1 (MQ=255)                   aaaGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGaaa                                               <  1:1781288/68‑1 (MQ=255)                   aaaGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGaaa                                               <  1:3301497/68‑1 (MQ=255)                   aaaGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGaaa                                               <  1:591597/68‑1 (MQ=255)                     aGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAAc                                             >  1:2733494/1‑68 (MQ=255)                     aGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAAc                                             >  1:2648700/1‑68 (MQ=255)                        ttGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACtgt                                          <  1:1394764/68‑1 (MQ=255)                        ttGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACtgt                                          <  1:1700460/68‑1 (MQ=255)                        aaatacgtaacttatttatgatatggacagtttggccccaaATGTTTCATCTTTTGGGGGAAAACtgt                                          <  1:1732295‑M2/27‑1 (MQ=255)                            ccGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAg                                      <  1:1099732/68‑1 (MQ=255)                            ccGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAg                                      <  1:2290589/68‑1 (MQ=255)                            ccGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAg                                      <  1:3094686/68‑1 (MQ=255)                            ccGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAg                                      <  1:818255/68‑1 (MQ=255)                             cgtaacttatttatgatatggacagtttggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAgt                                     <  1:225700‑M2/32‑1 (MQ=255)                              gcgATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAgtg                                    <  1:947880/68‑1 (MQ=255)                              gcgATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAgtg                                    <  1:346167/68‑1 (MQ=255)                              gcgATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAgtg                                    <  1:888378/68‑1 (MQ=255)                              gcgATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAgtg                                    <  1:27947/68‑1 (MQ=255)                              gcgATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAgtg                                    <  1:98885/68‑1 (MQ=255)                              gcgATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAgtg                                    <  1:2299243/68‑1 (MQ=255)                               cgATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAgtgt                                   <  1:1146701/68‑1 (MQ=255)                               cgATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAgtgt                                   <  1:2311425/68‑1 (MQ=255)                                      ttCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGt                            <  1:529137/68‑1 (MQ=255)                                      ttCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGt                            <  1:2199539/68‑1 (MQ=255)                                        ccTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCa                          >  1:2679967/1‑68 (MQ=255)                                        ccTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCa                          >  1:685196/1‑68 (MQ=255)                                          tctATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCaaa                        >  1:3466280/1‑68 (MQ=255)                                            tATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACt                      <  1:3421086/68‑1 (MQ=255)                                                  tCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTa                >  1:2062493/1‑68 (MQ=255)                                                  acagtttggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTa                >  1:1319573‑M2/16‑68 (MQ=255)                                                  acagtttggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTa                >  1:1416269‑M2/16‑68 (MQ=255)                                                    agtttggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTaca              >  1:2902726‑M2/14‑68 (MQ=255)                                                       ttggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTacaaaa           >  1:3107973‑M2/11‑68 (MQ=255)                                                       aTGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTacaaaa           >  1:1072562/1‑68 (MQ=255)                                                       aTGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTacaaaa           >  1:810434/1‑68 (MQ=255)                                                          gccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTacaaaacaa        <  1:3063158‑M2/61‑1 (MQ=255)                                                             ccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAgt     <  1:3409507‑M2/64‑1 (MQ=255)                                                             ccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAgt     <  1:229834‑M2/64‑1 (MQ=255)                                                             ccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAgt     <  1:3097471‑M2/64‑1 (MQ=255)                                                             ccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAgt     <  1:1573379‑M2/64‑1 (MQ=255)                                                             ccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAgt     <  1:2324745‑M2/64‑1 (MQ=255)                                                             acaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAgt     <  1:3459135‑M2/64‑1 (MQ=255)                                                              caaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAgtg    <  1:2705502‑M2/65‑1 (MQ=255)                                                               aaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAgtgt   <  1:2121911‑M2/66‑1 (MQ=255)                                                               aaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAgtgt   <  1:835695‑M2/66‑1 (MQ=255)                                                                aATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTa  >  1:3081814‑M2/2‑68 (MQ=255)                                                                 |                                                                   GCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTA  >  NC_000913/4542932‑4543062

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ 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.