New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_pgi	= 1216556	19 (0.430)	34 (0.760)	26/278	1.0	64.1%	coding (188/267 nt)	ariR	RcsB connector protein for regulation of biofilm and acid‑resistance
	?	NC_000913_3_pae_pgi	= 1651548	NA (NA)					intergenic (+11/‑3)	insD1/intQ	IS2 transposase TnpB;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related/pseudogene, Qin prophage; phage integrase family;Phage or Prophage Related

AAGCGTTAGCAAGTTACTTTCGCAGTTCGGGTAATTTGTTAGAAGAAGAATCAGCAGTGTTAGGGCAGGCTGTCACCAATTTAATGCTTTCAGGCGATAATGTTAATAATAAAAATATTATCTTAAGTCTGATACACTCCTTGGAAAC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913_3_pae_pgi/1216409‑1216556 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTG  <  NC_000913_3_pae_pgi/1651548‑1651401                                                                                                                                                                                                                                                                                                          AAGCGGTAGCAAGTTACTTTCGCAGTGCGGGTAATTGGTTAAAAGAAGAATCAGCAGTGTTAGGGCAGGCTGTCACCAATTTAATGTTTTCAGGCGATAATGTTAATAATAAAAATATTATCTTAAGTCTGATACACTCCTTGGAAACT                                                                                                                                                     <  2:283272/149‑1     GTTAGCAAGTTACTTTCGCAGTTCGGGTAATTTGTTAGAAGAAGAATCAGCAGTGTTAGGGCAGGCTGTCACCAATTTAATGCTTTCAGGCGATAATGTTAATAATAAAAATATTATCTTAAGTCTGATACACTCCTTGGAAACTGGAT                                                                                                                                                 >  1:433912/1‑149     GTTAGCAAGTTACGTTATCACGTCGGGTAATTTGTTAGAAGAAGAATCAGCAGTGTTAGGGCAGGCTGTCACCAATTTAATGCTTTCAGGCGATAATGTTAATAATAAAAATATTATCTTATGTCTGATACCCTCCTTCGAAACTGGAT                                                                                                                                                 <  2:67908/149‑1                      GCAGTTCGGGTAATTTGTTAGAAGAAGAATCAGCAGTGTTAGGGCAGGCTGTCACCAATTTAATGCTTTCAGGCGATAATGTTAATAATAAAAATATTATCTTAAGTCTGATACACTCCTTGGAAACTGGATTTGCCCCTATATTTCCA                                                                                                                                >  1:319858/1‑149                         GTTCGGGTAATTTGTTAGAAGAAGAATCAGCAGTGTTAGGGCAGGCTGTCACCAATTTAATGCTTTCAGGCGATAATGTTAATAATAAAAATATTATCTTAACTCTGATACACTCCTTGGAAACTGGATTTGCCCCTATATTTCCAGAC                                                                                                                             <  1:709482/149‑1                             ggtTAATTTGTTAGAAGAAGAATCAGCAGTGTTAGGGCAGGCTGTCACCAATTTAATGCTTTCAGGCGATAATGTTAATAATAAAAATATTATCTTAAGTCTGATACACTCCTTGGAAACTGGATTTGCCCCTATATTTCCAGACATCT                                                                                                                         <  1:17404/146‑1                             GGGTAATTTGTTAGAAGAAGAATCAGCAGTGTTAGGGCAGGCTGTCACCAATTTAATGCTTTCAGGCGATAATGTTAATAATAAAAATATTATCTTAAGTCTGATACACTCCTTGGAAACTGGATTTGCCCCTATATTTCCAGACATCT                                                                                                                         <  2:319858/149‑1                                   TTTGTTAGAAGAAGAATCAGCAGTGTTAGGGCAGGCTGTCACCAATTTAATGCTTTCAGGCCATAATGTTAATAATAAAAATATTATCTTAAGTCTGATACACTCCTTGGAAACTGGCTTTGCCCCTATATTTCCAGACATCTGTTATC                                                                                                                   >  2:686419/1‑149                                       gTAGAAGAAGAATCAGCAGTGTTAGGGCAGGCTGTCACCAATGTAATGCTTTCAGGCGAAAATGTTAATGATAAAAATACTATCTTAAGTCTGAAACACTACTTGGAAACTGGATTTTACCCTAAGTTGCAAGACATCTGTTATCCCTT                                                                                                               >  2:596289/2‑149                                           AAGAAGAATCAGCAGTGTTAGGGCAGGCTGTCACCAATTTAATGCTTTCAGGCGATAATGTTAATAATAAAAATATTATCTTAAGTCTGATACACTCCTTGGAAACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACC                                                                                                           >  2:197043/1‑149                                                               GGGCAGGCTGTCACCAATTTAATGCTTTCAGGCGATAATGTTAATAATAAAAATATTATCTTAAGTCTGATACACTCCTTGGAAACTGGATTT                                                                                                                                               <  2:208568/93‑1                                                               GGGCAGGCTGTCACCAATTTAATGCTTTCAGGCGATAATGTTAATAATAAAAATATTATCTTAAGTCTGATACACTCCTTGGAAACTGGATTT                                                                                                                                               >  1:208568/1‑93                                                                                    ATGCTTTCCGGCGTTAATGTTAATAATAAAAATATTATCTTAAGTCTGATACACTCCTTGGAAACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGA                                                                  <  2:318123/149‑1                                                                                       CTTTCAGGCGATAATGTTAATAATAAAAATATTATCTTAAGTCTGATACACTCCTTGGAAACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATA                                                                <  2:602726/148‑1                                                                                       CTTTCAGGCGATAATGTTAATAATAAAAATATTATCTTAAGTCTGATACACTCCTTGGAAACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATA                                                                >  1:602726/1‑148                                                                                        TTTCAGGCGATAATGTTAATAATAAAAATATTATCTTAAGTCTGATACACTCCTTGGAAACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAAACCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAAC                                                              >  1:230166/1‑149                                                                                             GGCGATAATGTTAATAATAAAAATATTATCTTAAGTCTGATACACTCCTTGGAAACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGC                                                         >  2:745625/1‑149                                                                                              GCGATAATGTTAATAATAAAAATATTATCTTAAGTCTGATACACTCCTTGGAAACTGGATTTGCCCCTATATTTCCAGGCATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCG                                                        >  1:724677/1‑149                                                                                                   AATGTTAATAATAAAAATATTATCTTAAGTCTGATACACTCCTTGGAAACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTA                                                   <  2:235297/149‑1                                                                                                       TTAAGAATAAAAATATTATCTTAAGTCTGATACACTCCTTGGAAACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCG                                               <  2:161048/149‑1                                                                                                         AATAATAAAAATATTATCTTAAGTCTGATACACTCCTTGGAAACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGA                                             >  1:274800/1‑149                                                                                                         AATAATAAAAATATTATCTTAAGTCTGATACACTCCTTGGAAACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGA                                             >  2:674124/1‑149                                                                                                           TAATAAAAATATTATCTTAAGTCTGATACACTCCTTGGAAACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTCTGCGGATG                                           >  2:683190/1‑149                                                                                                            AATAAAAATATTATCTTAAGTCTGATACACTCCTTGGAAACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGC                                          <  1:745625/149‑1                                                                                                                       TATCTTAAGTCTGATACACTCCTTGGAAACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAG                                                          >  2:587110/1‑122                                                                                                                       TATCTTAAGTCTGATACACTCCTTGGAAACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAG                                                          <  1:587110/122‑1                                                                                                                                  TGATACACTCCTTGGAAACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCGCTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATCGGTATGCCGTTGTTTAT‑ATGCTCGACCGC                   >  2:147664/1‑149                                                                                                                                  TGATACACTCCTTGGAAACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTCCAAGCCCGCTGCCGCAAATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATCCCATTCCGTATAAGCATCGAACG                    >  2:147685/1‑149                                                                                                                                   GATACCCTCCTTGGAAACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATGCGTTATAATGCTCGAACGC                   <  2:663479/149‑1                                                                                                                                                 AAACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCACGGTTCT     >  2:55805/1‑149                                                                                                                                                   ACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTT   <  2:274800/149‑1                                                                                                                                                    CTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTG  >  2:558017/1‑149                                                                                                                                                    CTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTG  <  2:299736/149‑1                                                                                                                                                    CTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTG  <  1:112123/149‑1                                                                                                                                                                                                                                                                                                          AAGCGTTAGCAAGTTACTTTCGCAGTTCGGGTAATTTGTTAGAAGAAGAATCAGCAGTGTTAGGGCAGGCTGTCACCAATTTAATGCTTTCAGGCGATAATGTTAATAATAAAAATATTATCTTAAGTCTGATACACTCCTTGGAAAC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913_3_pae_pgi/1216409‑1216556 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTG  <  NC_000913_3_pae_pgi/1651548‑1651401

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ 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.