New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 1469240	NA (NA)	42 (0.930)	31/276	NT	100%	intergenic (‑91/‑1)	insC1/ydbA	IS2 repressor TnpA/pseudogene, autotransporter homolog; interrupted by IS2 and IS30
	?	NC_000913	= 1652258	0 (0.000)					pseudogene (708/1158 nt)	intQ	pseudogene, Qin prophage; phage integrase family;Phage or Prophage Related

TTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/1469097‑1469240 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CTTAATAAGATGAATGACCCGATTGGTTCCCGCCTGTGTTTTTGGTACCGTGAAACGGTCT‑TTTGCTAAATTTCTCCTGATCATCATTGTTCCATTTTTCAGATCTATGTCCTCCCATCCAAGTGCACACAGCTCACCAGGGCG  <  NC_000913/1652258‑1652115                                                                                                                                                                                                                                                                                                   TTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTCCTTAA                                                                                                                                              >  1:69667/1‑149             GTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTACTTAATAAGATGAATGA                                                                                                                                  >  2:377189/1‑149                         CGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTACTTAATAAGATGAATGACCCGATTGGTTC                                                                                                                      >  2:779069/1‑149                                      ccAAGACATCCACTATCGTTTTTCCAATGACTAGTCTAAAAACTATTATTAAGACTATCACTTATTTAAGTGTTATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTACTTAATAAGATGAATGACCCGATTGGTTCCCGCCTGTGTTTT                                                                                                         <  1:138647/147‑1                                       TAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCGGGGGGCCAGTTTACTTAATAAGATGAATGACCCGATTGGTTCCCGCCTGTGTTTTT                                                                                                        >  2:25678/1‑149                                       TAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTACTTAATAAGATGAATGACCCGATTGGTTCCCGCCTGTGTTTTT                                                                                                        >  2:690231/1‑149                                       TAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTACTTAATAAGATGAATGACCCGATTGGTTCCCGCCTGTGTTTTT                                                                                                        <  1:511553/149‑1                                             ATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTGTTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTACTTAATAAGATGAATGACCCGATTGGTTCCCGCCTGTGTTTTTGTTACC                                                                                                  >  1:430284/1‑149                                                  TCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTGTGGAGATTCACGGGGCCAGGCTACTTAATAAGATGAATGACCCGGTTGGTTCTGGCATGTATGTTTAGTACaagaaa                                                                                             >  2:397592/1‑143                                                  TCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTACTTAATAAGATGAATGACCCGATTGGTTCCCGCCTGTGTTTTTGGTACCGTGAA                                                                                             >  1:8919/1‑149                                                   cagCTGTTCCCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTACTTAATAAGATGAATGACCCGATTGGTTCCCGCCTGTGTTTTTGGTACCGTGAAA                                                                                            <  1:3935/146‑1                                                     TCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTACTTAATAAGATGAATGACCCGATTGGTTCCCGCCTGTGTTTTTGGTACCGTGAAACG                                                                                          <  1:272546/149‑1                                                     TCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTACTTAATAAGATGAATGACCCGATTGGTTCCCGCCTGTGTTTTTGGTACCGTGAAACG                                                                                          <  1:29189/149‑1                                                        GTTCTCCAATGACTAGTCTAAAATCTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTACTTAATAAGATGAATGACCCGATTGGTTCCCGCCTGTGTTTTTGGTACCGTGAAACGGTC                                                                                       >  1:421450/1‑149                                                        GTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTGTACTTAATAAGATGAATGACCCCGTTGGTTCCCGCGTGTGTTTTTGGTACCGTGAAACGGTC                                                                                       >  1:542544/1‑149                                                          cCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTACTTAATAAGATGAATGACCCGATTGGTTCCCGCCTGTGTTTTTGGTACCGTGAAACGGTCT‑T                                                                                    <  2:394499/148‑1                                                            TCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTACTTAATAAGATGAATGACCCGATTGGTTCCCGCCTGTGTTTTTGGTACCGTGAAACGGTCT‑TTT                                                                                  <  1:493482/149‑1                                                            TCCAAGGACTACTCTAAAAACTAGAATTAAGACTAGCACTTATTTAAGTGATATTGGTTGTCTGGAGAGTCAGGGGGCCAGTCTTCTTAATAAGATGAATGCCCCGATTTGTTCCCGCCTGTGTTTTTGGTACCGTGAAACGGTCT‑TTT                                                                                  <  2:657773/149‑1                                                             caAATGAATAGGCTAAAAAATAGTATTAATACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGACTCAGGGGGCCAGTCTACCTAATAAGATGAATGACCCGATTGGTTCCCGCCTGTGTTTTTGGTACCGTGAAACGGTCT‑TTTG                                                                                 <  2:30696/147‑1                                                                   ACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTACTTAATAAGATGAATGACCCGATTGGTTCCCGCCTGTGTTTTTGGTACCGTGAAACGGTCT‑TTTGCTAAAT                                                                           >  1:144240/1‑149                                                                    CTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTACTTAATAAGATGAATGACCCGATTGGTTCCCGCCTGTGTTTTTGGTACCGTGAAACGGTCT‑TTTGCTAAATT                                                                          >  2:186132/1‑149                                                                                   GTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTACTTAATAAGATGAATGACCCGATTGGTTCCCGCCTGTGTTTTTGGTACCGTGAAACGGTCT‑TTTGCTAAATTTCTCCTGATCATCAT                                                           <  1:246755/149‑1                                                                                    TATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTACTTAATAAGATGAATGACCCGATTGGTTCCCGCCTGTGTTTTTGGTACCGTGAAACGGTCT‑TTTGCTAAATTTCTCCTGATCATCATT                                                          <  1:779069/149‑1                                                                                           ACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTACTTAATAAGATGAATGACCCGATTGGTTCCCGCCTGTGTTTTTGGTACCGTGAAACGGTCT‑TTTGCTACATTCACCCGGACCATCAATGTTCCAT                                                   >  1:145987/1‑149                                                                                           ACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTACTTAATAAGATGAATGACCCGATTGGTTCCCGCCTGTGTTTTTGGTACCGTGAAACGGTCT‑TTTGCTAAATTTCTCCTGATCATCATTGTTCCAT                                                   >  1:467223/1‑149                                                                                               TCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTACTTAATAAGATGAATGACCCGATTGGTTCCCGCCTGTGTTTTTGGTACCGTGAAACGGTCT‑TTTGCTAAATTTCTCCTGATCATCATTGTTCCATTTTT                                               <  2:574439/149‑1                                                                                                 ACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTACTTAATAAGATGAATGACCCGATTGGTTCCCGCCTGTGTTTTTGGTACCGTGAAACGGTCT‑TTTGCTAGATTTCTCCTGATCATCATTGTGCCATTTTTCA                                             >  2:185236/1‑149                                                                                                 ACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTACTTAATAAGATGAATGACCCGATTGGTTCCCGCCTGTGTTTTTGGTACCGTGAAACGGTCT‑TTTGCTAAATTTCTCCTGATCATCATTGTTCCATTTTTCA                                             <  2:69667/149‑1                                                                                                     aaaTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTACTTAATAAGATGAATGACCCGATTGGTTCCCGCCTGTGTTTTTGGTACCGTGAAACGGTCT‑TTTGCTAAATTTCTCCTGATCATCATTGTTCCATTTTTCAGATC                                         >  1:396165/4‑149                                                                                                     aaaTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTACTTAATAAGATGAATGACCCGATTGGTTCCCGCCTGTGTTTTTGGTACCGTGAAACGGTCT‑TTTGCTAAATTTCTCCTGATCATCATTGTTCCATTTTTCAGATC                                         >  2:490675/4‑149                                                                                                          AGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTACTTAATAAGATGAATGACCCGATTGGTTCCCGCCTGTGTTTTTGGTACCGTGAAACGGTCT‑TTTGCTAAATTTCTCCTGATCATCATTGTTCCATTTTTCAGATCTATGT                                    >  2:536835/1‑149                                                                                                              ATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTACTTAATAAGATGAATGACCCGATTGGTTCCCGCCTGTGTTTTTGGTACCGTGAAACGGTCT‑TTTGCTAAATTTCTCCTGATCATCATTGTTCCATTTTTCAGATCTATGTCCTC                                <  2:8919/149‑1                                                                                                              ATATTGGTTGTCGGGAGATTCAGGGGGCCAGTCTACTTAATTAGATGAATGACCCGATTGGTTCCCGCCTGTGTTTTTGGTACCGTGAATCGGTCT‑TTTGCTAAATTTCTCCTGATCATCATTGTTCCATTTTTCAGATCTATGTCCTC                                <  1:397592/149‑1                                                                                                                ATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTACTTAATAAGATGAATGACCCGATTGGTTCCCGCCTGTGTTTTTGGTACCGTGAAACGGTCT‑TTTGCTAAATTTCTCCTGATCATCATTGTTCCATTTTTCAGATCTATGTCCTCCC                              >  1:375516/1‑149                                                                                                                ATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTACTTAATAAGATGAATGACCCGATTGGTTCCCGCCTGTGTTTTTGGTACCGTGAAACGGTCT‑TTTGCTAAATTTCTCCTGATCATCATGGTTCCATTTTTCGGATCTATGTCCTCCC                              >  2:706889/1‑149                                                                                                                  TGGTTGTCTGGAGATTCAGGGGGCCAGTCTACTTAATAAGATGAATGACCCGATTGGTTCCCGCCTGTGTTTTTGGTACAGTG‑GCCTTTCTGTTAGCTAAATTTCTCCTGATCATCATTGTTCCATTTTTCAGATCTATGTCCTCCCAT                            >  1:786497/1‑149                                                                                                                   GGTTGTCTGGAGATTCAGGGGGCCAGTCTACTTAATAAGATGAATGACCCGATTGGTTCCCGCCTGTGTTTTTGGTACCGTGAAACGGTCT‑TTTGCTAAATTTCTCCTGATCATCATTGTTCCATTTTTCAGATCTATGTCCTCCCATC                           <  2:234678/149‑1                                                                                                                      TGTCTGGAGATTCAGGGGGCCAGTCTACTTAATAAGATGAATGACCCGATTGGTTCCCGCCTGTGTTTTTGGTACCGTGAAACGGTCT‑TTTGCTAAATTTCTCCTGATCATCATTGTTCCATTTTTCAGATCTATGTCCTCCCATCCAA                        <  1:729608/149‑1                                                                                                                        TCTGGAGATTCAGGGGGCCAGTCTACTTAATAAGATGAATGACCCGATTGGTTCCCGCCTGTGTTTTTGGTACCGTGAAACGGTCT‑TTTGCTAAATTTCTCCTGATCATCATTGTTCCATTTTTCAGATCTATGTCCTCCCATCCACGT                      >  2:419363/1‑149                                                                                                                         CTGGAGATTTCGGGGGCCAGTCTACTTTATTGGATGGATGCCCGGTTTGGTTCCCGCGTGTGTTTTTTGTACCGTGAAGCGGTCT‑TGTGCTAAATTTCTCCTGATCATCATTGTTCCTTTTTTCAGATCTATGTCCTCCCATCCAAGTG                     <  2:270294/149‑1                                                                                                                         CTGGAGATTCAGGGGGCCAGTCTACTTAATAAGATGAATGACCCGATTGGTTCCCGCCTGTGTTTTTGGTACCGTGAAACGGTCT‑TTTGCTAAATTTCTCCTGATCATCATTGTTCCATTTTTCAGATCTATGTCCTCCCATCCAAGTG                     <  2:144240/149‑1                                                                                                                          TGGAGATTCAGGGGGCCAGTCTACTTAATAAGATGAATGACCCGATTGGTTCCCGCCTGTGTTTTTGGTACCGTGAAACGGTCT‑TTTGCTAAATTTCTCCTGATCATCATTGTTCCATTTTTCAGATCTATGTCCTCCCATCCAAGTGC                    >  1:756415/1‑149                                                                                                                                TTCAGGGGGCCAGTCTACTTAATAAGATGAATGACCCGATTGGTTCCCGCCTGTGTTTTTGGTACCGTGAAACGGTCT‑GTTGCTAAATTTCTCCTGATCATCATTGTTCCATTTTTCAGATCTATGTCCTCCCATCCAAGTGCACACAG              <  1:377189/149‑1                                                                                                                                            GTCTACTTAATTAGATGAATGACCCGATTGGTTCCCGCCTGTGTTTTTGGTACCGTGAAACGGTCT‑TTTGCTAAATTTCTCCTGATCAGCATTGTTCCATTTTTCAGATCTATGTCCTCCCATCCAAGTGCACACAGCTCACCAGGGCG  <  1:67240/149‑1                                                                                                                                                                                                                                                                                                   TTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/1469097‑1469240 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CTTAATAAGATGAATGACCCGATTGGTTCCCGCCTGTGTTTTTGGTACCGTGAAACGGTCT‑TTTGCTAAATTTCTCCTGATCATCATTGTTCCATTTTTCAGATCTATGTCCTCCCATCCAAGTGCACACAGCTCACCAGGGCG  <  NC_000913/1652258‑1652115

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ 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.