New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	= 1755758	1 (0.030)	29 (0.740)	19/280	1.3	96.7%	coding (61/1413 nt)	pykF	pyruvate kinase I
	?	NC_000913_3_pae_tpiA	2101749 =	NA (NA)					intergenic (‑5/+146)	wbbL/insH1	pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator

GTAATACCGGATTCGCTTTCCGGCAGTGCGCCCAGAAAGCAAGTTTCTCCCATCCTTCTCAACTTAAAGACTAAGACTGTCATGAAAAAGACCAAAATTGTTTGCACCATCGGACCGAAAACCGAATCTGAAGAGATGTTAG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913_3_pae_tpiA/1755617‑1755758 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCAGTT  >  NC_000913_3_pae_tpiA/2101749‑2101893                                                                                                                                                                                                                                                                                                 GTAATACCGGATTCGCTTTCCGGCAGTGCGCCCAGAAAGCAAGTTTCTCCCATCCTTCTCAACTTAAAGACTAAGCCTGTCATGAAAAAGACCAAAATTGTTTGCACCATCGGACCGAAAACCGAATCTGAAGAGATAGAAGGGAAGGT                                                                                                                                            >  1:10587/1‑149     TACCGGATTCGCCTTCCGGCAGTGCGCCCAGAAAGCAAGTTTCTCCCATCCTTCTCAACTTAAAGACTAAGACTGTCATGAAAAAGACCAAAATTGTTTGCACCATCGGACCGAAAACCGAATCTGAAGAGATGTTAGGGAAGGTGCGA                                                                                                                                        <  1:637178/149‑1             TCGCTTTCCGGCAGTGCGCCCAGAAAGCAAGTTTCTCCCATCCTTCTCAACTTAAAGACTAAGACTGTCATGAAAAAGACCAAAATTGTTTGCACCTTCGGACCGAAAACCGAATCTGAAGAGATGTTAGGGAAGGTGCGAATAAGCGG                                                                                                                                <  1:199087/149‑1                 TTTCCGGCAGTGCGCCCAGAAAGCAAGTTTCTCCCATCCTTCTCAACTTAAAGACTAAGACTGTCATGAAAAAGACCAAAATTGTTTGCACCATCGGACCGAAAACCGAATCTGAAGAGATGTTAGGGAAGGTGCGAATAAGCGGGGAA                                                                                                                            >  1:222815/1‑149                 TTTCCGGCAGTGCGCCCAGAAAGCAAGTTTCTCCCATCCTTCTCAACTTAAAGACTAAGACTGTCATGAAAAAGACCAAAATTGTTTGCACCATCGGACCGAAAACCGAATCTGAAGAGATGTTAGGGAAGGTGCGAATAAGCGGGGAA                                                                                                                            >  2:459170/1‑149                 TTTCCGGCAGTGCGCCCAGAAAGCAAGTTTCTCCCATCCTTCTCAACTTAAAGACTAAGAACGTCATGAAAAAGCCCAAAATTGTTTGCACCATCGGACCGAAAACCGAATCTGAAGAGATGTTAGGGACGGTGCGAATAAGCGGGGca                                                                                                                            >  1:657251/1‑147                        CAGTGCGCCCAGAAAGCAAGTTTCTCCCATCCTTCTCAACTTAAAGACTAAGACTGTCATGAAAAAGACCAAAATTGTTTGCACCATCGGACCGAAAACCGAATCTGAAGAGATGTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTC                                                                                                                     >  1:540878/1‑149                                            TTTCTCCCATCCTTCTCAACTTAAAGACTAAGACTGTCATGAAAAAGACCAAAATTGTTTGCACCATCGGACCGAAAACCGAATCTGAAGAGATGTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTC                                                                                                 >  2:605827/1‑149                                            TTTCTCCCATCCTTCTCAACTTAAAGACTAAGACTGTCATGAAAAAGACCAAAATTGTTTGCACCATCGGACCGAAAACCGAATCTGAAGAGATGTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTC                                                                                                 >  1:565755/1‑149                                                TCCCATCCTTCTCAACTTAAAGACTAAGACTGTCATGAAAAAGACCAAAATTGTTTGCACCATCGGACCGAAAACCGAATCTGAAGAGATGTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTT                                                                                             <  1:534613/149‑1                                                   CATCCTTCTCAACTTAAAGACTAAGACTGTCATGAAAAAGACCAAAATTGTTTGCACCATCGGACCGAAAACCGAATCTGAAGAGATGTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTT                                                                                          <  1:459170/149‑1                                                            CAACTTAAAGACTAAGACTGTCATGAAAAAGACCAAAATTGTTTGCACCATCGGACCGAAAACCGAATCTGAAGAGATGTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGA                                                                                 <  1:568021/149‑1                                                                            ACTGCCATGAAAAAGACCAAAATTGTTTGCACCATCGGACCGAAAACCGAATCTGAAGAGATGTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCC                                                                 <  2:312724/149‑1                                                                                TCATGAAAAAGACCAAAATTGTTTGCACCATCGGACCGAAAACCGAATCTGAAGAGATGTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAA                                                             >  1:343040/1‑149                                                                                          GACCAAAATTGTTTGCACCATCGGACCGAAAACCGAATCTGAAGAGATGTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCTTGTTTGTGCCGATTTTTTCTTCCGTGAATGCCTTGAc                                                   >  1:179725/1‑148                                                                                                    gttgtCACCAGCGGACCGAAAACCGAATCTGAAGAGATGTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATT                                         <  2:676998/144‑1                                                                                                          ACCATCGGACCGAAAACCGAATCTGAAGAGATGTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGCATCAGCCTATTTAGACC                                   >  2:93390/1‑149                                                                                                                    CGAAAACCGAATCTGAAGAGATGTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCA                                                                                                     <  1:121078/73‑1                                                                                                                    CGAAAACCGAATCTGAAGAGATGTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCA                                                                                                     >  2:121078/1‑73                                                                                                                      AAAACCGAATCTGAAGAGATGTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCA                       <  2:540878/149‑1                                                                                                                      AAAACCGAATCTGAAGAGATGTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGAT                                                                           <  1:296656/97‑1                                                                                                                           CGAATCTGAAGAGATGTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAA                  >  1:496221/1‑149                                                                                                                              acCTGAAGAGATGTTAGGGAAGGCGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTCGACCGTTTCTTCGCCATTTAAGGC               <  2:378534/147‑1                                                                                                                                         TGTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAA                  <  1:618847/135‑1                                                                                                                                         TGTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAA                  >  2:618847/1‑135                                                                                                                                          atagGGGAAGGTGCGAATAAGCGGGGAAATTTTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCAGT   <  2:105842/145‑1                                                                                                                                          GTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCACGTAAATGCCTTGAATCAGCCTATTTAAACCGTTTCTTCGCCATTTAAGGCATTATCCCCAGT   >  1:4468/1‑149                                                                                                                                          GTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTAAGTCATTTCATTTCTTCATGTTTGAGCCGAATTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCAGT   <  2:528689/149‑1                                                                                                                                           TTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCAGTT  >  2:568945/1‑149                                                                                                                                                                                                                                                                                                 GTAATACCGGATTCGCTTTCCGGCAGTGCGCCCAGAAAGCAAGTTTCTCCCATCCTTCTCAACTTAAAGACTAAGACTGTCATGAAAAAGACCAAAATTGTTTGCACCATCGGACCGAAAACCGAATCTGAAGAGATGTTAG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913_3_pae_tpiA/1755617‑1755758 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCAGTT  >  NC_000913_3_pae_tpiA/2101749‑2101893

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.