New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	1293124 =	0 (0.000)	52 (1.330)	39/284	0.1	100%	intergenic (‑202/‑403)	hns/tdk	global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
	?	NC_000913_3_pae_tpiA	= 1300693	NA (NA)					intergenic (+1448/‑489)	ychE/oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein

GCTCTTATTGCGACTGTTCTACTTTTCATCATTCGCTTAATAGGGAATTCTCGTAAACACAACTAATACAGAAGACTGAAAGGTCGTCAGCCTACGATAATCTCCCCATAAAATGTGACATGAATCAGGAAGTTTTAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_pae_tpiA/1293261‑1293124 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCAGTTTTT  <  NC_000913_3_pae_tpiA/1300693‑1300546                                                                                                                                                                                                                                                                                                GCTCTTATTGCGACTGTTCTACTTTTCATCATTCGCTTAATAGGGAATTCTCGTAAACACAACTAATACAGAAGACTGAAAGGTCGTCAGCCTACGATAATCTCCCCATAAAATGTGACATGAATCAGGAAGTTTTAAGGAAGGTGCGA                                                                                                                                           >  1:433074/1‑149     TTATTGCGACTGTTCTACTTTTCATCATTCGCTTAATAGGGAATTCTCGTAAACACAACTAATACAGAAGACTGAAAGGTCGTCAGCCTACGATAATCTCCCCATAAAATGTGACATGAATCAGGAAGTTTTAAGGAAGGTGCGAATAA                                                                                                                                       >  2:269032/1‑149         TGCGACTGTTCTACTTTTCATCATTCGCTTAATAGGGAATTCTCGTAAACACAACTAATACAGAAGACTGAAAGGTCGTCAGCCTACGATAATCTCCCCATAAAATGTGACATGAATCAGGAAGTTTTAAGGAAGGTGCGAATAAGCGG                                                                                                                                   <  1:687415/149‑1            GACTGTTCTACTTTTCATCATTCGCTTAATAGGGAATTCTCGTAAACACAACTAATACAGAAGACTGAAAGGTCGTCAGCCTACGATAATCTCCCCATAAAATGTGACATGAATCAGGAAGTTTTAAGGAAGGTGCGAATAAGCGGGGA                                                                                                                                <  2:516446/149‑1              CTGTTCTACTTTTCATCATTCGCTTAATAGGGAATTCTCGTAAACACAACTAATACAGAAGCCTGAAAGGTCGTCAGCCTACGATAATCTCCCCATAAAATGTGACATGAATCAGGAAGTTTTAAGGAAGGTGCGAATAAGCGGCGAAA                                                                                                                              >  1:297885/1‑149                GTTCTACTTTTCATCATTCGCTTAATAGGGAATTCTCGTAAACACAACTAATACAGAAGACTGAAAGGTCGTCAGCCTACGATAATCTCCCCATAAAATGTGACATGAATCAGGAAGTTTTAAGGAAGGTGCGAATAAGCGGGGAAATT                                                                                                                            >  1:295626/1‑149                 TTCTACTTTTCATCATTCGCTTAATAGGGAATTCTCGTAAACACAACTAATACAGAAGACTGAAAGGTCGTCAGCCTACGATCACCTCCCCATAAAATGTTACATGAATCTGGGAGTTTTAAGGAAGGTGCGAATAAGCGGGGAAATTC                                                                                                                           >  1:201541/1‑149                 TTCTACTTTTCATCATTCGCTTAATAGGGAATTCTCGTAAACACAACTAATACAGAAGACTGAAAGGTCGTCAGCCTACGATAATCTCCCCATAAAATTTGACATGAATCAGGAAGGTTTAAGGACGTTGCGAATAAGCGGGGAAATTC                                                                                                                           >  2:595813/1‑149                 TTCTACTTTTCATCATTCGCTTAATAGGGAATTCTCGTAAACACAACTAATACAGAAGACTGAAAGGTCGTCAGCCTACGATAATCTCCCCATAAAATGTGACATGAATCAGGAAGTTTTAAGGAAGGTGCGAATAAGCGGGGGAATTC                                                                                                                           >  2:45268/1‑149                    TACTTTTCATCATTCGCTTAATAGGGAATTCTCGTAAACACAACTAATACAGCAGACTGAAAGGTCGCCAGCCTACGATAATCTCCCCATAAAATGTGACATGAATCAGGAAGTGTTAAGGAAGGTGCGAATAAGCGGGGAACTTCTTC                                                                                                                        >  1:140015/1‑149                       TTTTCATCATTCGCTTAATAGGGAATTCTCGTAAACACAACTAATACAGAAGACTGAAAGGTCGTCAGCCTACGATAATCTCCCCATAAAATGTGACATGAATCAGGAAGTTTTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCG                                                                                                                     <  2:433074/149‑1                        TTTCATCATTCGCTTAATAGGGAATTCTCGTAAACACAACTAATACAGAAGACTGAAAGGTCGTCAGCCTACGATAATCTCCCCATAAAATGTGACATGAATCAGGAAGTTTTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGG                                                                                                                    <  2:593476/149‑1                                  CGCTTAATAGGGAATTCTCGTAAACACAACTAATACAGAAGACTGAAAGGTCGTCAGCCTACGATAATCTCCCCATAAAATGTGACATGAATCAGGAAGTTTTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGT                                                                                                          <  1:113863/149‑1                                  CGCTTAATAGGGAATTCTCGTAAACACAACTAATACAGAAGACTGAAAGGTCGTAAGCCTACGATAGTCTATACATAGAATGTGACATGAATCAGGAAGTTTTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGT                                                                                                          >  2:596984/1‑149                                       AATAGGGAATTCTCGTAAACACAACTAATACAGAAGACTGAAAGGTCGTCAGCCTACGATAATCTCCCCATAAAATGTGACATGAATCAGGAAGTTTTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTT                                                                                                     <  1:559725/149‑1                                       AATAGGGAATTCTCGTAAACACAACTAATACAGAAGACTGAAAGGTCGTCAGCCTACGATAATCTCCCCATAAAATGTGACATGAATCAGGAAGTTTTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTT                                                                                                     <  1:656645/149‑1                                       AATAGGGAATTCTCGTAAACACAACTAATACAGAAGACTGAAAGGTCGTCAGCCTACGATAATCTCCCCATAAAATGTGACATGAATCAGGAAGTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGCCTCAGTCATTT                                                                                                     >  2:620691/1‑149                                            GGAATTCTCGTAAACACAACTAATACAGAAGACTGAAAGGTCGTCAGCCTACGATAATCTCCCCATAAAATGTGACATGAATCAGGAAGTTTTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTT                                                                                                >  1:480973/1‑149                                               ATTCTCGTAAACACAACTAATACAGAAGACTGAAAGGTCGTCAGCCTACGATAATCTCCCCATAAAATGTGACATGAATCAGGAAGTTTTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTT                                                                                             <  1:234071/149‑1                                                TTCTCGTAAACACAACTAATACAGAAGACTGAAAGGTCGTCAGCCTACGATAATCTCCCCATAAAATGTGACATGAATCAGGAAGTTTTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTC                                                                                            <  2:476444/149‑1                                                  CTCGTAAACACAACTAATACAGAAGACTGAAAGGTCGTCAGCCTACGATAATCTCCCCGTAAAATGTGACATGAATCAGGAAGTTTTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCAT                                                                                          <  2:395256/149‑1                                                   TCGTAAACACAACTAATACAGAAGACTGAAAGGTCGTCAGCCTACGATAATCTCCCCATAAAATGTGACATGAATCAGGAAGTTTTAAGGAAGGTGCGAATAAGCGCGGAAATACTTCTCGGCTGACTCAGTCATTTCATTTCTTCATG                                                                                         >  2:493814/1‑149                                                        AACACAACTAATACAGAAGACTGAAAGGTCGTCAGCCTACGATAATCTCCCCATAAAATGTGACATGAATCAGGAAGTTTTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGc                                                                                    >  2:689790/1‑148                                                           cCAACTAATACAGAAGACTGAAAGGTCGTCAGCCTACGATAATCTCCCCTTAAAATGGGACATGAATCAGGAAGTTTTAAGGAAGGTACGAATACGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCC                                                                                 >  2:526777/2‑149                                                           ACAACTAATACAGAAGACTGAAAGGTCGTCAGCCTACGATAATCTCCCCATAAAATGTGACATGAATCAGGAAGTTTTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCC                                                                                 >  1:74101/1‑149                                                                    ACAGAAGACTGAAAGGTCGTCAGCCTACGATAATCTCCCCATAAAATGTGACATGAATCAGGAAGTTTTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTC                                                                        <  1:607296/149‑1                                                                        AAGACTGAAAGGTCGTCAGCCTACGATAATCTCCCCATAAAATGTGACATGAATCAGGAAGTTTTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCC                                                                    >  1:372974/1‑149                                                                         AGACTGAAAGGTCGTCAGCCTACGATAATCTCCCCATAAAATGTGACATGAATCAGGAAGTTTTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCAT                                                                                          <  1:44146/126‑1                                                                         AGACTGAAAGGTCGTCAGCCTACGATAATCTCCCCATAAAATGTGACATGAATCAGGAAGTTTTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCAT                                                                                          >  2:44146/1‑126                                                                              GAAAGGTCGTCAGCCTACGATAATCTCCCCATAAAATGTGACATGAATCAGGAAGTTTTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAAT                                                              >  1:21231/1‑149                                                                               AAAGGTCGTCAGCCTACGATAATCTCCCCATAAAATGTGACATGAATCCGGAAGTTTTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATG                                                             >  1:207938/1‑149                                                                               AAAGGTCGTCAGCCTACGATAATCCCCCCATAAAATGTGACATGAATCAGGAAGTTTTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATG                                                             <  2:301593/149‑1                                                                                   GTCGTGAGCCTACGATAATCTCCCCATAAAATGTGACATGAATCAGGAAGTTTTAAGGAAGGTGCGAATAAGCGGGGTAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTT                                                         <  1:57799/149‑1                                                                                   GTCGTCAGCCTACGATAATCTCCCCATAAAATGTGACATGAATCAGGAAGTTTTAAGGAAGGTGCGAATAAGCGGGGA                                                                                                                                <  2:151895/78‑1                                                                                   GTCGTCAGCCTACGATAATCTCCCCATAAAATGTGACATGAATCAGGAAGTTTTAAGGAAGGTGCGAATAAGCGGGGA                                                                                                                                >  1:151895/1‑78                                                                                         AGCCTACGAAAATCTCCCCATAAAATGTGACATGAATCAGGAAGTTTTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCA                                                   <  2:15363/149‑1                                                                                         AGCCCACAATAACCGCCCCATAAAATGTGACATGAATCAGGAAGTTTTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCA                                                   <  1:535831/149‑1                                                                                            CTACGATAATCTCCCCATAAAATGTGACATGAATCAGGAAGTTTTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATACCTTGAATtaccc                                                >  2:31828/1‑144                                                                                               CGATAATCTCCCCATAAAATGTGACATGAATCAGGAAGAATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTAT                                             >  2:497003/1‑149                                                                                                    ATCTCCCCATAAAATGTGACATGAATCAGGAAGTTTTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGA                                        <  2:21231/149‑1                                                                                                    ATCTCCACATAAAATGTGACATGAATCAGGAAGTTTTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGA                                        <  2:22034/149‑1                                                                                                     TCTCCCCATAAAATGTGACATGAATCAGGAAGTTTTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGAC                                       <  2:372974/149‑1                                                                                                        CCCCATAAGATGGGACAGGAATCAGGAAGTTTTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCGTCATGTTTGAGCCGATTTTTTCTCCGGTAAAGGCCGTGAATCAGCCTATTTAGACCGT                                    <  2:499036/149‑1                                                                                                         CCCATAAAATGTGACATGAATCAGGAAGTTTTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTACCGTAAATGCCTTGAATCAGCCTATTTAGACCGTT                                   >  1:538519/1‑149                                                                                                          CCATAAAATGTGACATGAATCAGGAAGTTTTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCGGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGACTCAGCCTATTTGAACCGTTT                                  >  1:567060/1‑149                                                                                                             TAAAATGTGACATGAATCAGGAAGTTTTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACGCTTTCTT                               >  2:403608/1‑149                                                                                                                                    tgtcTAACGAAGGTGCGAGTAACCGGCGAAAATCTTCTCGCCTGACTCAGGTATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTACTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCA        <  2:145713/145‑1                                                                                                                                     TTTTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCAG       >  1:44168/1‑149                                                                                                                                       TTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGGAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCAGTT     <  2:605193/149‑1                                                                                                                                          AGGAAGGTGCGACTAAGGGGGGAAATTCTTCTCGGCTAACTCAGTCATTTCATTTCTGCTTGTTTGAGCCGATTTTTTCTCCCGTAAATGCGTTGAATCTGTCTATTTAGACCGTTTCTTCGCGATTTAAGGCGTTATCCACAATTTTT  >  2:539600/1‑149                                                                                                                                          AGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCAGTTTTT  >  2:518401/1‑149                                                                                                                                          AGGAAGGGGCGAATAAGCGGGGAATTTCTTCCCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGATCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTCACTTCGCCATATAAGGCGTTAACCCCCGTTTTT  <  2:599920/149‑1                                                                                                                                                                                                                                                                                                GCTCTTATTGCGACTGTTCTACTTTTCATCATTCGCTTAATAGGGAATTCTCGTAAACACAACTAATACAGAAGACTGAAAGGTCGTCAGCCTACGATAATCTCCCCATAAAATGTGACATGAATCAGGAAGTTTTAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_pae_tpiA/1293261‑1293124 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCAGTTTTT  <  NC_000913_3_pae_tpiA/1300693‑1300546

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.