New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	4497494 =	294 (1.080)	5 (0.020)	4/246	NT	1.7%	pseudogene (820/1266 nt)	intB	pseudogene, integrase homology;IS, phage, Tn; Phage‑related functions and prophages; KpLE2 phage‑like element; P4‑like integrase
	?	NC_000913	4497532 =	292 (1.130)					pseudogene (858/1266 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.

TATTTACCGTATTCTCACTCATGGGTTTGTGCGAATCGTGATCACCAATAAATATCAAGTCATGGGCCCCATAAAACTGTTTTATCTGCTTTAAAATTGCAAGAGCTTGCGTTGAAAGAGGCACTAGATGCGTTGTACGCATTTTTGAGCCTCT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/4497647‑4497494 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gcctctTTCAACGCAAGCTCTTGCAATTTTAAAGCAGATAAAACAGTTTTATGGGGCCCATGACTTGATATTTATTGGTGATCACGATTCGCACAAACCCATGAGTGAGAATACGGTAAATAGTGCGTTACGGGTCATGGGGTATGATACAAAA  >  NC_000913/4497532‑4497679                                                                                                                                                                                                                                                                                                                TATTTACCGTATTCTCACTCATAGGTTTGTGCGAATCGTGATCACCAATAAATATCAAGTCATGGGCCCCATAAAACTGTTTTATCTGCTTTAAAATTGCAAGAGCTTGCGTTGAAAGAGGCACTAGATGCGTTGTACGCATTTTTGAG                                                                                                                                                           >  3:128496/1‑149   TTTACCGTATTCTCACTCATGGGTTTGTGCGAATCGTGATCACCAATAAATATCAAGTCATGGGCCCCATAAAACTGTTTTATCTGATTTAAAATTGCAAGAGCTTGCGTTGAAAGAGGCACTAGATGCGTTGTACGCATTTTTGAGCC                                                                                                                                                         >  4:1594526/1‑149    TTACCGTATTCTCACTCATGGGTTTGTGCGAATCGTGATCACCAATAAATATCAAGTCATGGGCCCCATAAAACTGTTTTATCTGCTTTAAAATTGCAAGAGCTTGCGTTGAAAGAGGCACTAGATGCGTTGTACGCATTTTTGAGCCT                                                                                                                                                        <  3:991880/149‑1         GTATTCACACTCATGGGTTTGTGCGAATCGTGATCACCAATAATGATCAAGTCATGGGACCCATAAAACCATGTCATCTGCGTTAAAATTGCAAAAGATTGCATTGAAAGAGTCACTAGATGCGTTGTACGCATTTTTGAACCTCTTTg                                                                                                                                                   >  2:2095983/1‑148                                CGAATCGTGATCACCAATAAATATCAAGTCATGGGCCCCATAAAACTGTTTTATCTGCTTTAAAATTGCAAGAGCTTGCGTTGAAAGAGGCACTAGATGCGTTGTACGCATTTTTGAGC                                                                                                                                                          <  3:1393007/119‑1                                CGAATCGTGATCACCAATAAATATCAAGTCATGGGCCCCATAAAACTGTTTTATCTGCTTTAAAATTGCAAGAGCTTGCGTTGAAAGAGGCACTAGATGCGTTGTACGCATTTTTGAGC                                                                                                                                                          >  4:1393007/1‑119                                                ATAAATATCAAGTCATGGGCCCCATAAAACTGTTTTATCTGCTTTAAAATTGCAAGAGCTTGCGTTGAAAGAGGCACTAGATGCGTTGTACGCATTTTTGAGCC                                                                                                                                                         >  2:2002871/1‑104                                                ATAAATATCAAGTCATGGGCCCCATAAAACTGTTTTATCTGCTTTAAAATTGCAAGAGCTTGCGTTGAAAGAGGCACTAGATGCGTTGTACGCATTTTTGAGCC                                                                                                                                                         <  1:2002871/104‑1                                                          AGTCATGGGCCCCATAAAACTGTTTTATCTGCTTTAAAATTGCAAGAGCTTGCGTTGAAAGAGGCACTAGATGCGTTGTACGCATTTTTGAG                                                                                                                                                           >  1:1200222/1‑92                                                          AGTCATGGGCCCCATAAAACTGTTTTATCTGCTTTAAAATTGCAAGAGCTTGCGTTGAAAGAGGCACTAGATGCGTTGTACGCATTTTTGAG                                                                                                                                                           <  2:1200222/92‑1                                                               TGGGCCCCATAAAACTGTTTTATCTGCTTTAAAATTGCAAGAGCTTGCGTTGAAAGAGGCACTAGATGCGTTGTACGCATTTTTGAGCCTC                                                                                                                                                       >  4:2085260/1‑91                                                               TGGGCCCCATAAAACTGTTTTATCTGCTTTAAAATTGCAAGAGCTTGCGTTGAAAGAGGCACTAGATGCGTTGTACGCATTTTTGAGCCTC                                                                                                                                                       <  3:2085260/91‑1                                                                                          TTTAAAATTGCAAGAGCTTGCGTTGAAAGAGGCACTAGATGCGTTGTACGCATTTTTGAG                                                                                                                                                           >  3:1159572/1‑60                                                                                          TTTAAAATTGCAAGAGCTTGCGTTGAAAGAGGCACTAGATGCGTTGTACGCATTTTTGAG                                                                                                                                                           <  4:1159572/60‑1                                                                                                               GTTGAAAGAGGCACTAGATGCGTTGTACGCATTTTTGAGCCTCTTTCAACGCAAGCTCTTGCAATTTTAAAGCAGATAAAACAGTTTTATGGGGCCCATGACTTGATATTTATTGGTGATCACGATTCGCACAAACCCATGAGTGAGAA                                             >  3:2094432/1‑149                                                                                                                      GAGGCACTAGATGCGTTGTACGCATTTTTGAGCCTCTTTCAACGCAAGCTCTTGCAATTTTAAAGCAGATAAAACAGTTTTATGGGGCCCATGACTTGATATTTATTG                                                                               >  3:537590/1‑108                                                                                                                      GAGGCACTAGATGCGTTGTACGCATTTTTGAGCCTCTTTCAACGCAAGCTCTTGCAATTTTAAAGCAGATAAAACAGTTTTATGGGGCCCATGACTTGATATTTATTG                                                                               <  4:537590/108‑1                                                                                                                           ACTAGATGCGTTGTACGCA‑TTTAGTGCCTCTTTCAACGCAAGCTCTTGCAATTTTAAAGCAGATAAAACAGTTTTATGGGGCCCATGACTTGATATTTATTG                                                                               >  4:1761538/1‑102                                                                                                                           ACTAGATGCGTTGTACGCA‑TTTAGTGCCTCTTTCAACGCAAGCTCTTGCAATTTTAAAGCAGATAAAACAGTTTTATGGGGCCCATGACTTGATATTTATTG                                                                               <  3:1761538/102‑1                                                                                                                                                     GCCTCTTTCAACGCAAGCTCTTGCAATTTTAAAGCAGATAAAACAGTTTTATGGGGCCCATGACTTGATATTTATTGGTGATCACGATTCGCACAAACCCATGAGTGAGAATACGGTAAATAGTGCGTTACGGGTCATGGGGTATGATA       >  4:2122483/1‑149                                                                                                                                                     GCCTCTTTCAACGCAAGCTCTTGCAATTTTAAAGCAGATAAAACAGTTTTATGGGGCCCATGACTTGATATTTATTGGTGATCACGATTCGCACAAACCCATGAGTGAGAATACGGTAAATAGTGCGTTACGGGTCATGGGGTATGATA       <  1:1544467/149‑1                                                                                                                                                      CCTCTTTCAACGCAAGCTCTTGCAATTTTAAAGCAGATAAAACAGTTTTATGGGGCCCATGACTTGATATTTATTGGTGATCACGATTCGCACAAACCCATGTGTGAGAATACGGTAAATAGTGCGTTACGGGTCATGGGGTATGATAC      >  2:162522/1‑149                                                                                                                                                      CCTCTTTCAACGCAAGCTCTTGCAATTTTAAAGCAGATAAAACAGTTTTATGGGGCCCATGACTTGATATTTATTGGTGATCACGATTCGCACAAACCCATGAGTGAGAATACGGTAAATAGTGCGTTACGGGTCATGGGGTATGATAC      >  3:2409835/1‑149                                                                                                                                                      CCTCTTTCAACGCAAGCTCTTGCAATTTTAAAGCAGATAAAACAGTTTTATGGGGCCCATGACTTGATATTTATTGGTGATCACGATTCGCACAAACCCATGAGTGAGAATACGGTAAATAGTGCGTTACGGGTCATGGGGTATGATAC      >  1:1698926/1‑149                                                                                                                                                      CCTCTTTCAACGCAAGCTCTTGCAATTTTAAAGCAGATAAAACAGTTTTATGGGGCCCATGACTTGATATTTATTGGTGATCACGATTCGCACAAACCCATGAGTGAGAATACGGTAAATAGTGCGTTACGGGTCATGGGGTATGATAC      >  2:580441/1‑149                                                                                                                                                      CCTCTTTCAACGCAAGCTCTTGCAATTTTAAAGCAGATAAAACAGTTTTATGGGGCCCATGACTTGATATTTATTGGTGATCACGATTCGCACAAACCCATGAGTGAGAATACGGTAAATAGTGCGTTACGGGTCATGGGGTATGATAC      >  2:665311/1‑149                                                                                                                                                      CCTCTTTCAACGCAAGCTCTTGCAATTTTAAAGCAGATAAAACAGTTTTATGGGGCCCATGACTTGATATTTATTGGTGATCACGATTC                                                                  >  2:610645/1‑89                                                                                                                                                      CCTCTTTCAACGCAAGCTCTTGCAATTTTAAAGCAGATAAAACAGTTTTATGGGGCCCATGACTTGATATTTATTGGTGATCACGATTC                                                                  <  1:610645/89‑1                                                                                                                                                       CTCTTTCAACGCAAGCTCTTGCAATTTTAAAGCAGATAAAACAGTTTTATGGGGCCCATGACTTGATATTTATTGGTGATCACGATTCGCACAAACCCATGAGTGAGAATACGGTAAATAGTGCGTTACGGGTCATGGGGTATGATACA     >  1:1820629/1‑149                                                                                                                                                       CTCTTTCAACGCAAGCTCTTGCAATTTTAAAGCAGATAAAACAGTTTTATGGGGCCC                                                                                                 >  2:727655/1‑57                                                                                                                                                       CTCTTTCAACGCAAGCTCTTGCAATTTTAAAGCAGATAAAACAGTTTTATGGGGCCC                                                                                                 <  1:727655/57‑1                                                                                                                                                        TCTTTCAACGCAAGCTCTTGCAATTTTAAAGCAGATAAAACAGTTTTATGGGGCCCATGACTTGATATTTATTGGTGATCACGATTCGCACAAACCCATGAGTGAGAATACGGTAAATAGTGCGTTACGGGTCATGGGGTATGATACAA    >  4:461741/1‑149                                                                                                                                                        TCTTTCAACGCAAGCTCTTGCAATTTTAAAGCAGATAAAACAGTTTTATGGGGCCCATGACTTGATATTTATTGGTGATCACGATTCGCACAAACCCATGAGTGAGAATACGGTAAATAGTGCGTTACGGGTCATGGGGTATGATACAA    >  1:1891663/1‑149                                                                                                                                                        TCTTTCAACGCAAGCTCTTGCAATTTTAAAGCAGATAAAACAGTTTTATGGGGCCCATGACTTGATATTTATTGGTGATCACGATTCGCACAAACCCATGAGTGAGAATACGGTAAATAG                                 <  4:2172875/120‑1                                                                                                                                                        TCTTTCAACGCAAGCTCTTGCAATTTTAAAGCAGATAAAACAGTTTTATGGGGCCCATGACTTGATATTTATTGGTGATCACGATTCGCACAAACCCATGAGTGAGAATACGGTAAATAG                                 >  3:2172875/1‑120                                                                                                                                                          TTTCAACGCAAGCTCTTGCAATTTTAAAGCAGATAAAACAGTTTTATGGGGCCCATGACTTGATATTTATTGGTGATCACGATTCGCACAAACCCATGAGTGAGAATACGGTAAATAGTGCGTTACGGGTCATGGGGTATGATACAAAA  <  3:1258776/149‑1                                                                                                                                                          TTTCAACGCAAGCTCTTGCAATTTTAAAGCAGATAAAACAGTTTTATGGGGCCCATGACTTGATATTTATTGGTGATCACGATTCGCACAAACCCATGAGTGAGAATACGGTAAATAGTGCGTTACGGGTCATGGGGTATGATACAAAA  >  1:1750356/1‑149                                                                                                                                                          TTTCAACGCAAGCTCTTGCAATTTTAAAGCAGATAAAACAGTTTTATGGGGCCCATGACTTGATATTTATTGGTGATCACGATTCGCACAAACCCATGAGTGAGAATACGGTAAATAGTGCGTTACGGGTCATGGGGTATGATACAAAA  <  1:2400545/149‑1                                                                                                                                                          TTTCAACGCAAGCTCTTGCAATTTTAAAGCAGATAAAACAGTTTTATGGGGCCCATGACTTGATATTTATTGGTGATCACGATTCGCACAAACCCATGAGTGAGAATACGGTAAATAGTGCGTTACGGGTCATGGGGTATGATACAAAA  <  1:278790/149‑1                                                                                                                                                          TTTCAACGCAAGCTCTTGCAATTTTAAAGCAGATAAAACAGTTTTATGGGGCCCATGACTTGATATTTATTGGTGATCACGATTCGCACAAACCCATGAGTGAGAATACGGTAAATAGTGCGTTACGGGTCATGGGGTATGATACAAAA  <  4:960154/149‑1                                                                                                                                                          TTTCAACGCAAGCTCTTGCAATTTTAAAGCAGATAAAACAGTTTTATGGGGCCCATGACTTGATATTTATTGGTGATCACGATTCGCACAAACCCATGAGTGAGAATACGGTAAATAGTGCGTTACGGGTCATGGGGTATGATACAAAA  >  2:1123739/1‑149                                                                                                                                                          TTTCAACGCAAGCTCTTGCAATTTTAAAGCAGATAAAACAGTTTTATGGGGCCCATGACTTGATATTTATTGGTGATCACGATTCGCACAAACCCATGAGTGAGAATACGGTAAATAGTGCGTTACGGGTCATGGGGTATGATACAAAA  <  2:1318784/149‑1                                                                                                                                                          TTTCAACGCAAGCTCTTGCAATTTTAAAGCAGATAAAACAGTTTTATGGGGCCCATGACTTGATATTTATTGGTGATCACGATTCGCACAAACCCATGAGTGAGAATACGGTAAATAGTGCGTTACGGGTCATGGGGTATGATACAAAA  <  4:634366/149‑1                                                                                                                                                          TTTCAACGCAAGCTCTTGCAATTTTAAAGCAGATAAAACAGTTTTATGGGGCCCATGACTTGATATTTATTGGTGATCACGATTCGCACAAACCCATGAGTGAGAATACGGTAAATAGTGCGTTACGGGTCATGGGGTATGATACAAAA  <  2:2500652/149‑1                                                                                                                                                          TTTCAACGCAAGCTCTTGCAATTTTAAAGCAGATAAAACAGTTTTATGGGGCCCATGACTTGATATTTATTGGTGATCACGATTCGCACAAACCCATGAGTGAGAATACGGTAAATAGTGCGTTACGGGTCATGGG               >  3:573912/1‑136                                                                                                                                                          TTTCAACGCAAGCTCTTGCAATTTTAAAGCAGATAAAACAGTTTTATGGGGCCCATGACTTGATATTTATTGGTGATCACGATTCGCACAAACCCATGAGTGAGAATACGGTAAATAGTGCGTTACGGGTCATGGG               <  4:573912/136‑1                                                                                                                                                          TTTCAACGCAAGCTCTTGCAATTTTAAAGCAGATAAAACAGTTTTATGGGGCCCATGACTTGATATTTATTGGTGATCACGATTCGCACAAACCCATGAGTGAGAATACGGTAAATAGTGCGTT                           >  1:148910/1‑124                                                                                                                                                          TTTCAACGCAAGCTCTTGCAATTTTAAAGCAGATAAAACAGTTTTATGGGGCCCATGACTTGATATTTATTGGTGATCACGATTCGCACAAACCCATGAGTGAGAATACGGTAAATAGTGCGTT                           <  2:148910/124‑1                                                                                                                                                          TTTCAACGCAAGCTCTTGCAATTTTAAAGCAGATAAAACAGTTTTATGGGGCCCATGACTTGATATTTATTGGTGATCACGATGCGCACAAGCCCATGAGTGAGAATACGGTAAATAGTGCGTTACGGGTCATTGGGTATGATACAAAt  <  2:690456/149‑2                                                                                                                                                          TTTCAACGCAAGCTCTTGCAATTTTAAAGCAGATAAAACAGTTTTATGGGGCCCATGACTTGATATTTAT                                                                                 <  2:550763/70‑1                                                                                                                                                          TTTCAACGCAAGCTCTTGCAATTTTAAAGCAGATAAAACAGTTTTATGGGGCCCATGACTTGATATTTAT                                                                                 >  1:550763/1‑70                                                                                                                                                                                                                                                                                                                TATTTACCGTATTCTCACTCATGGGTTTGTGCGAATCGTGATCACCAATAAATATCAAGTCATGGGCCCCATAAAACTGTTTTATCTGCTTTAAAATTGCAAGAGCTTGCGTTGAAAGAGGCACTAGATGCGTTGTACGCATTTTTGAGCCTCT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/4497647‑4497494 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gcctctTTCAACGCAAGCTCTTGCAATTTTAAAGCAGATAAAACAGTTTTATGGGGCCCATGACTTGATATTTATTGGTGATCACGATTCGCACAAACCCATGAGTGAGAATACGGTAAATAGTGCGTTACGGGTCATGGGGTATGATACAAAA  >  NC_000913/4497532‑4497679

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ 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.