New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 4497499	152 (0.810)	7 (0.040)	6/226	NT	4.7%	pseudogene (825/1266 nt)	intB	pseudogene, integrase homology;IS, phage, Tn; Phage‑related functions and prophages; KpLE2 phage‑like element; P4‑like integrase
	?	NC_000913	= 4497525	139 (0.780)					pseudogene (851/1266 nt)	intB	pseudogene, integrase homology;IS, phage, Tn; Phage‑related functions and prophages; KpLE2 phage‑like element; P4‑like integrase
Rejected: Frequency below/above cutoff threshold.

AACCCGATGGGCGATAGAACTCACTTTGCTGATCTTTATTCGGTCCAGTGAGCTGCGTTTTGCTCGTTGGTCAGAGATCGATTTCGAAGCGTCTATATGGACTATCCCACCGGAGCGGGAGCCTATTCCTGGAGTGAAACATTCCCATAGAGGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/4497346‑4497499 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑agaggcACTAGATGCGTTGTACGCATTTTTGAGCCTCTATGGGAATGTTTCACTCCAGGAATAGGCTCCCGCTCCGGTGGGATAGTCCATATAGACGCTTCGAAATCGATCTCTGACCAACGAGCAAAACGCAGCTCACTGGACCGAATAAA  <  NC_000913/4497525‑4497380                                                                                                                                                                                                                                                                                                              AACCCGATGGGCGATAGAACTCACTTTGCTGATCTTTATTCGGTCCAGTGAGCTGCGTTTTGCTCGTTGGTCAGAGATCGATTTCGAAGCGTCTATATGGACTATCCCACCGGAGCGGGAGCCTATTCCTGGAGTGAAACATTCCCATA                                                                                                                                                         <  2:1033645/149‑1   CCCGATGGGCGATAGAACTCACTTTGCTGATCTTTATTCGGTCCAGTGAGCTGCGTTTTGCTCGTTGGTCAGAGATCGATTTCGAAGCGTCTATATGGACTATCCCACCGGAGCGGGAGCCTATTCCTGGAGTGAAACATTCCCATAGA                                                                                                                                                       >  1:456521/1‑149   CCCGATGGGCGATAGAACTCACTTTGCTGATCTTTATTCGGTCCAGTGAGCTGCGTTTTGCTCGTTGGTCAGAGATCGATTTCGAAGCGTCTATATGGACTATCCCACCGGAGCGGGAGCCTATTCCTGGAGTGAAACATTCCCATAGA                                                                                                                                                       <  4:1650828/149‑1     CGATGGGCGATAGAACTCACTTTGCTGATCTTTATTCGGTCCAGTGAGCTGCGTTTTGCTCGTTGGTCAGAGATCGATTTCGAAGCGTCTATATGGACTATCCCACCGGAGCGGGAGCCTATTCCTGGAGTGAAACATTCCCATAGAGG                                                                                                                                                     >  4:587552/1‑149     CGATGGGCGATAGAACTCACTTTGCTGATCTTTATTCGGTCCAGTGAGCTGCGTTTTGCTCGTTGGTCAGAGATCGATTTCGAAGCGTCTATATGGACTATCCCACCGGAGCGGGAGCCTATTCCTGGAGTGAAACATTCCCATAGAGG                                                                                                                                                     >  2:956880/1‑149      GATGGGCGATAGAACTCACTTTGCTGATCTTTATTCGGTCCAGTGAGCTGCGTTTTGCTCGTTGGTCAGAGATCGATTTCGAAGCGTCTATATGGACTATCCCACCGGAGCGGGAGCCTATTCCTGGAGTGAAACATTCCCATAGAGGC                                                                                                                                                    <  4:263516/149‑1      GATGGGCGATAGAACTCACTTTGCTGATCTTTATTCGGTCCAGTGAGCTGCGTTTTGCTCGTTGGTCAGAGATCGATTTCGAAGCGTCTATATGGACTATCCCACCGGAGCGGGAGCCTATTCCTGGAGTGAAACATTCCCATAGAGGC                                                                                                                                                    <  4:1624539/149‑1                   ACTCACTTTGCTGATCTTTATTCGGTCCAGTGAGCTGCGTTTTGCTCGTTGGTCAGAGATCGATTTCGAAGCGTCTATATGGACTATCCCACCGGAGCGGGAGCCTATTCCTGGAGTGAAACATTCCCATAGAGGCACTAGATGCGTTG                                                                                                                                       >  2:72283/1‑149                   ACTCACTTTGCTGATCTTTATTCGGTCCAGTGAGCTGCGTTTTGCTCGTTGGTCAGAGATCGATTTCGAAGCGTCTATATGGACTATCCCACCGGAGCGGGAGCCTATTCCTGGAGTGAAACATTCCCATAGAGGCACTAGATGCGTTG                                                                                                                                       >  4:398325/1‑149                     TCACTTTGCTGATCTTTATTCGGTCCAGTGAGCTGCGTTTTGCTCGTTGGTCAGAGATCGATTTCGAAGCGTCTATATGGACTATCCCACCGGAGCGGGAGCCTATTCCTGGAGTGAAACCTTCCCATAGAG                                                                                                                                                      <  3:1080419/132‑1                     TCACTTTGCTGATCTTTATTCGGTCCAGTGAGCTGCGTTTTGCTCGTTGGTCAGAGATCGATTTCGAAGCGTCTATATGGACTATCCCACCGGAGCGGGAGCCTATTCCTGGAGTGAAACATTCCCATAGAG                                                                                                                                                      >  4:1080419/1‑132                                ATCTTTATTCGGTCCAGTGAGCTGCGTTTTGCTCGTTGGTCAGAGATCGATTTCGAAGCGTCTATATGGACTATCCCACCGGAGCGGGAGCCTATTCCTGGAGTGAAACATTCCCATAGAGGCACTAGATGCGTTGTACGCATTTTTGA                                                                                                                          <  3:398325/149‑1                                ATCTTTATTCGGTCCAGTGAGCTGCGTTTTGCTCGTTGGTCAGAGATCGATTTCGAAGCGTCTATATGGACTATCCCACCGGAGCGGGAGCCTATTCCTGGAGTGAAACATTCCCATAGAGG                                                                                                                                                     >  3:1830899/1‑122                                ATCTTTATTCGGTCCAGTGAGCTGCGTTTTGCTCGTTGGTCAGAGATCGATTTCGAAGCGTCTATATGGACTATCCCACCGGAGCGGGAGCCTATTCCTGGAGTGAAACATTCCCATAGAGG                                                                                                                                                     <  3:1422002/122‑1                                ATCTTTATTCGGTCCAGTGAGCTGCGTTTTGCTCGTTGGTCAGAGATCGATTTCGAAGCGTCTATATGGACTATCCCACCGGAGCGGGAGCCTATTCCTGGAGTGAAACATTCCCATAGAGG                                                                                                                                                     >  4:1422002/1‑122                                ATCTTTATTCGGTCCAGTGAGCTGCGTTTTGCTCGTTGGTCAGAGATCGATTTCGAAGCGTCTATATGGACTATCCCACCGGAGCGGGAGCCTATTCCTGGAGTGAAACATTCCCATAGAGG                                                                                                                                                     <  4:1830899/122‑1                                ATCTTTATTCGGTCCAGTGAGCTGCGTTTTGCTCGTTGGTCAGAGATCGATTTCGAAGCGTCTATATGGACTATCCCACCGGAGCGGGAGCCTATTCCTGGAGTGAAACATTCCCATAGAG                                                                                                                                                      >  3:375036/1‑121                                ATCTTTATTCGGTCCAGTGAGCTGCGTTTTGCTCGTTGGTCAGAGATCGATTTCGAAGCGTCTATATGGACTATCCCACCGGAGCGGGAGCCTATTCCTGGAGTGAAACATTCCCATAGAG                                                                                                                                                      <  4:375036/121‑1                                        TCGGTCCAGTGAGCTGCGTTTTGCTCGTTGGTCAGAGATCGATTTCGAAGCGTCTATATGGACTATCCCACCGGAGCGGGAGCCTATTCCTGGAGTGAAACATTCCCATAGAGGCACTAGATGCGTTGTACGCATTTTTGAGCCTCTAT                                                                                                                  <  3:879782/149‑1                                         CGGTCCAGTGAGCTGCGTTTTGCTCGTTGGTCAGAGATCGATTTCGAAGCGTCTATATGGACTATCCCACCGGAGCGGGAGCCTATTCCTGGAGTGAAACATTCCCATAGAGGCACTAGATGCGTTGTACGCATTTTTGAGCCTCTATG                                                                                                                 <  1:72283/149‑1                                                                TCGTTGGTCAGAGATCGATTTCGAAGCGTCTATATGGACTATCCCACCGGAGCGGGAGCCTATTCCTGGAGTGAAACATTCCCATAGAGGCACTAGATGCGTTGTACGCATTTTTGAGCCTCTATGG                                                                                                                <  4:1109715/127‑1                                                                TCGTTGGTCAGAGATCGATTTCGAAGCGTCTATATGGACTATCCCACCGGAGCGGGAGCCTATTCCTGGAGTGAAACATTCCCATAGAGGCACTAGATGCGTTGTACGCATTTTTGAGCCTCTATGG                                                                                                                >  3:1109715/1‑127                                                                                                                                                       AGGCACTAGATGCGTTGTACGCATTTTTGAGCCTCTATGGGAATGTTTCACTCCAGGAATAGGCTCCCGCTCCGGTGGGATAGTCCATATAGACGCTTCGAAATCGATCTCTGACCAACGAGCAAAACGCAGCTCACTGGACCGAATAA   >  2:1561302/1‑149                                                                                                                                                        GGCACTAGATGCGTTGTACGCATTTTTGAGCCTCTATGGGAATGTTTCACTCCAGGAATAGGCTCCCGCTCCGGTGGGATAGTCCATATAGACGCTTCGAAATCGATCTCTGACCAACGAGCAAAACGCAGCTCACTGGACCGAATAAA  <  4:1107014/149‑1                                                                                                                                                        GGCACTAGATGCGTTGTACGCATTTTTGAGCCTCTATGGGAATGTTTCACTCCAGGAATAGGCTCCCGCTCCGGTGGGATAGTCCATATAGACGCTTCGAAATCGATCTCTGACCAACGAGCAAAACGCAGCTCACTGGACCGAATAAA  >  4:1786315/1‑149                                                                                                                                                         GCACTAGATGCGTTGTACGCATTTTTGAGCCTCTATGGGAATGTTTCACTCCAGGAATAGGCTCCCGCTCCGGTGGGATAGTCCATATAGACGCTTCGAAATCGATCTCTGA                                      <  2:1664768/112‑1                                                                                                                                                         GCACTAGATGCGTTGTACGCATTTTTGAGCCTCTATGGGAATGTTTCACTCCAGGAATAGGCTCCCGCTCCGGTGGGATAGTCCATATAGACGCTTCGAAATCGATCTCTGA                                      >  1:1664768/1‑112                                                                                                                                                          CACTAGATGCGTTGTACGCATTTTTGAGCCTCTATGGGAATGTTTCACTCCAGGAATAGGCTCCCGCTCCGGTGGGATAGTCCATATAGACGCTTCGAAATCG                                              >  4:355095/1‑103                                                                                                                                                          CACTAGATGCGTTGTACGCATTTTTGAGCCTCTATGGGAATGTTTCACTCCAGGAATAGGCTCCCGCTCCGGTGGGATAGTCCATATAGACGCTTCGAAATCG                                              <  3:355095/103‑1                                                                                                                                                                                                                                                                                                              AACCCGATGGGCGATAGAACTCACTTTGCTGATCTTTATTCGGTCCAGTGAGCTGCGTTTTGCTCGTTGGTCAGAGATCGATTTCGAAGCGTCTATATGGACTATCCCACCGGAGCGGGAGCCTATTCCTGGAGTGAAACATTCCCATAGAGGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/4497346‑4497499 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑agaggcACTAGATGCGTTGTACGCATTTTTGAGCCTCTATGGGAATGTTTCACTCCAGGAATAGGCTCCCGCTCCGGTGGGATAGTCCATATAGACGCTTCGAAATCGATCTCTGACCAACGAGCAAAACGCAGCTCACTGGACCGAATAAA  <  NC_000913/4497525‑4497380

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ 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.