New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	= 1217417	51 (0.650)	31 (0.400)	29/246	2.5	37.8%	coding (90/1524 nt)	ycgG	putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
	?	NC_000913_3_pae_tpiA	1467910 =	NA (NA)					intergenic (+6/+11)	ydbA/insD1	pseudogene, autotransporter homolog; interrupted by IS2 and IS30/IS2 transposase TnpB

AATGGCATTTTCATGTATTAAACCCTTTGGCCGGGACAAGCAAATGCGCAATACACTCATACCCATCCTCGTTGCGATATGCTTGTTTATTACCGGTGTCGCTATTTTGAACATCCAGCTCTGGTATTCCGCA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913_3_pae_tpiA/1217285‑1217417 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCT  >  NC_000913_3_pae_tpiA/1467910‑1468042                                                                                                                                                                                                                                                                            AATGGCATTTTCATGTATTAAACCCTTTGGCCGGGACAAGCAAATGCGCAATACACTCATACCCATCCTCGTTGCGATATGCTTGTTTATTACCGGTGTCGCTATTTTGAACATCCAGCTCTGGTATTCCGCATGGATTTGCCCCTATAT                                                                                                                      >  3:243450/1‑150        TTTTCATGTATTAAACCCTTTGGCCGGGACAAGCAAATGCGCAATACACTCATACCCATCCTCGTTGCGATATGCTTGTTTATTACCGGTGTCGCTATTTTGAACATCCAGCTCTGGTATTTGGCATGGATTTGCCCCTATATTTCCAGA                                                                                                               >  1:447662/1‑150                TATTAAACCCTTTGGCCGGGACAAGCAAATGCGCAATACACTCATACCCATCCTCGTCGCGATATGCTTGTTTATTACCGGTGTCGCTATTTTGAACATCCAGCTCTGGTATTCCGCATGGATTTGCCCCTATATTTCCAGACATCTGTT                                                                                                       >  1:968897/1‑150                  TTAAACCCTTTGGCCGGGACAAGCAAATGCGCAATACACTCATACCCATCCTCGTTGCGATATGCTTGTTTATTACCGGTGTCGCTATTTTGAACATCCAGCTCTGGTATTCCGCATGGATTTGCCCCTATATTTCCAGACATCTGTTAT                                                                                                     >  3:496435/1‑150                     AACCCTTTGGCCGGGACAAGCAAATGCGCAATACACTCATACCCATCCTCGTTGCGATATGCTTGTTTATTACCGGTGTCGCTATTTTGAACATCCAGCTCTGGTATTCCGCATGGATTTGCCCCTATATTTCCAGACATCTGTTATCAC                                                                                                  >  1:974938/1‑150                                CGGGACAAGCAAATGCGCAATACACTCATACCCATCCTCGTTGCGATATGCTTGTTTATTACCGGTGTCGCTATTTTGAACATCCAGCTCTGGTATTCCGCATGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTA                                                                                       <  1:797423/150‑1                                  GGACAAGCAAATGCGCAATACACTCATACCCATCCTCGTTGCGATATGCTTGTTTATTACCGGTGTCGCTATTTTGAACATCCAGCTCTGGTATTCCGCATGGATTTGCCC                                                                                                                            >  1:242959/1‑111                                  GGACAAGCAAATGCGCAATACACTCATACCCATCCTCGTTGCGATATGCTTGTTTATTACCGGTGTCGCTATTTTGAACATCCAGCTCTGGTATTCCGCATGGATTTGCCC                                                                                                                            <  2:242959/111‑1                                        GCAAATGCGCAATACACTCATACCCATCCTCGTTGCGATATGCTTGTTTATTACCGGTGTCGCTATTTTGAACATCCAGCTCTGGTATTCCGCATGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCG                                                                               >  1:89783/1‑150                                                         TCATACCCATCCTCGTTGCGATATGCTTGTTTATTACCGGTGTCGCTATTTTGAACATCCAGCTCTGGTATTCCGCATGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCC                                                                                >  1:341800/1‑132                                                         TCATACCCATCCTCGTTGCGATATGCTTGTTTATTACCGGTGTCGCTATTTTGAACATCCAGCTCTGGTATTCCGCATGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCC                                                                                <  2:341800/132‑1                                                           ATACCCATCCTCGTTGCGATATGCTTGTTTATTACCGGTGTCGCTATTTTGAACATCCAGCTCTGGTATTCCGCATGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGT                                                            <  4:496435/150‑1                                                            TACCCATCCTCGTTGCGATATGCTTGTTTATTACCGGTGTCGCTATTTTGAACATCCAGCTCTGGTATTCCGCATGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTG                                                           <  2:519871/150‑1                                                                       GTTGCGATATGCTTGTTTATTACCGGTGTCGCTATTTTGAACATCCAGCTCTGGTATTCCGCATGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAA                                                >  3:37008/1‑150                                                                        TTGCGATATGCTTGTTTATTACCGGTGTCGCTATTTTGAACATCCAGCTCTGGTATTCCGCATGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAAC                                               <  4:428151/150‑1                                                                        TTGCGATATGCTTGTTTATTACCGGTGTCGCTATTTTGAACATCCAGCTCTGGTATTCCGCATGGATTTGCCCCTATATTTCCA                                                                                                                 <  2:937185/84‑1                                                                        TTGCGATATGCTTGTTTATTACCGGTGTCGCTATTTTGAACATCCAGCTCTGGTATTCCGCATGGATTTGCCCCTATATTTCCA                                                                                                                 >  1:937185/1‑84                                                                              TATGCTTGTTTATTACCGGTGTCGCTATTTTGAACATCCAGCTCTGGTATTCCGCATGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCG                                         <  4:243450/150‑1                                                                                              CGGTGTCGCTATTTTGAACATCCAGCTCTGGTATTCCGCATGGATTTGCCCCTATATTTCCAGA                                                                                                               >  4:153486/1‑64                                                                                              CGGTGTCGCTATTTTGAACATCCAGCTCTGGTATTCCGCATGGATTTGCCCCTATATTTCCAGA                                                                                                               <  3:153486/64‑1                                                                                                GTGTCGCTATTTTGAACATCCAGCTCTGGTATTCCGCATGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATT                       >  2:310616/1‑150                                                                                                   TCGCTATTTTGAACATCCAGCTCTGGTATTCCGCATGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGC                                                     >  4:125738/1‑117                                                                                                   TCGCTATTTTGAACATCCAGCTCTGGTATTCCGCATGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGC                                                     <  3:125738/117‑1                                                                                                    CGCTATTTTGAACATCCAGCTCTGGTATTCCGCATGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAG                                                                      <  1:127880/99‑1                                                                                                    CGCTATTTTGAACATCCAGCTCTGGTATTCCGCATGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAG                                                                      >  2:127880/1‑99                                                                                                      CTATTTTGAACATCCAGCTCTGGTATTCCGCATGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTAT                 <  2:974938/150‑1                                                                                                              AACATCCAGCTCTGGTATTCCGCATGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCG         <  2:89783/150‑1                                                                                                                     AGCTCTGGTATTCCGCATGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCT  <  4:37008/150‑1                                                                                                                     AGCTCTGGTATTCCCCATGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCTTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCT  <  2:447662/150‑1                                                                                                                                     ATGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGT                                                            >  1:797159/1‑76                                                                                                                                     ATGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGT                                                            <  2:797159/76‑1                                                                                                                                                                                                                                                                            AATGGCATTTTCATGTATTAAACCCTTTGGCCGGGACAAGCAAATGCGCAATACACTCATACCCATCCTCGTTGCGATATGCTTGTTTATTACCGGTGTCGCTATTTTGAACATCCAGCTCTGGTATTCCGCA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913_3_pae_tpiA/1217285‑1217417 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCT  >  NC_000913_3_pae_tpiA/1467910‑1468042

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ 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.