New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	1755687 =	0 (0.000)	48 (0.870)	37/284	0.6	100%	intergenic (‑546/‑11)	ydhZ/pykF	uncharacterized protein/pyruvate kinase I
	?	NC_000913_3_pae_tpiA	= 2102943	NA (NA)					intergenic (‑32/+1)	insH1/wbbL	IS5 transposase and trans‑activator/pseudogene, lipopolysaccharide biosynthesis protein

GCTGACCGTGTTCTGCATAGTCACCATGAGAGAAGTTCAGACGCATAACGTTCATGCCAGCGTCCAGCATTTTAGCTAACATCTCTTCAGATTCGGTTTTCGGTCCGATGGTGCAAACAATTTTGGTCTTTTTCATGACAGTCTTAG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_pae_tpiA/1755833‑1755687 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTCCC  <  NC_000913_3_pae_tpiA/2102943‑2102797                                                                                                                                                                                                                                                                                                        GCTGACCGTGTTCTGCATAGTCACCATGAGAGAAGTTCAGACGCATAACGTTCATGCCAGCGTCCAGCATTTTAGCTAACATCTCTTCAGATTCGGTTTTCGGTCCGATGGTGCAAACAATTTTGGTCTTTTTCATGACAGTCTTAGGG                                                                                                                                                   >  1:820616/1‑149    gcCCGTGTTCTGCATAGTCACCATGAGAGAAGTTCAGACGCATAACGTTCATGCCAGCGTCCAGCATTTTAGCTAACATCTCTTCAGATTCGGTTTTCGGTCCGATGGTGCAAACAATTTTGGTCTTTTTCATGACAGTCTTAGGGAAG                                                                                                                                                <  1:425723/147‑1    GACCGTGTTCTGCATAGTCACCATGTGAGAATTTCAGACGCATAACGTTCATGCCAGCGTCCAGCATTTTAGCTAACATCTCTTCAGATTCGGTTTTCGGTCCGATGGTGCAAACACTTTTGGTCTTTTTCATGACAGTCTTAGGGAAG                                                                                                                                                <  1:778868/149‑1      CCGTTTTCTGCATAGTCACCATGAGAGAAGTTCAGACGCATAACGTTCATGCCAGCGTCCAGCATTTTAGCTAACATCTCTTCAGATTCGGTTTTCGGTCCGATGGTGCAAACAATTTTGGTCTTTTTCATGACAGTCTTAGGGAAGGT                                                                                                                                              <  2:378717/149‑1       CGTGTTCTGCATAGTCACCATGAGAGAAGTTCAGACGCATAACGTTCATGCCAGCGTCCAGCATTTTAGCTAACATCTCTTCAGATTCGGTTTTCGGTCCGATGGTGCAAACAATTTTGGTCTTTTTCATGACAGTCTTAGGGAAGGTG                                                                                                                                             <  2:628199/149‑1              tgaaaAGTCACCATCAGAGAAGTTCAGACGCATAACGTTCATGCCAGCGTCCAGCATTTTAGCTAACATCTCTTCAGATTCGGTTTTCGGTCCGATGGTGCAAACAATTTTGGTCTTTTTCATGACAGTCTTAGGGAAGGTGCGAACAA                                                                                                                                      <  2:673990/144‑1              TGCATATTCACCATAACAGAATCTCCGACGCAGAATGTTCATGCCTGCGTCCAGCATTTTAGCTATCATCTTTTCAGATTCGGTTTTCGGTCCGATGGGGCAAACAATTTTGGTCTTTTTCATGACAGTCTTAGGGAAGGTGCGAACAA                                                                                                                                      <  2:930951/149‑1              TGCATAGTCACCATGAGAGAAGTTCAGACGCATAACGTTCATGCCAGCGTCCAGCATTTTAGCTAACATCTCTTCAGATTCGGTTTTCGGTCCGATGGTGCAAACAATTTTGGTCTTTTTCATGACAGTCTTAGGGAAGGTGCGAACAA                                                                                                                                      >  2:737327/1‑149                 ATAGTCACCATGAGAGAAGTTCAGACGCATAACGTTCATGCCAGCGTCCAGCATTTTAGCTAACATCTCTTCAGATTCGGTTTTCGGTCCGATGGTGCAAACAATTTTGGTCTTTTTCATGACAGTCTTAGGGAAGGTGCGAACAAGTC                                                                                                                                   <  2:903569/149‑1                         CATGAGAGAAGTTCAGACGCATAACGTTCATGCCAGCGTCCAGCATTTTAGCTAACATCTCTTCAGATTCGGTTTTCGGTCCGATGGTGCAAACAATTTTGGTCTTTTTCATGACAGTCTTAGGGAAGGTGCGAACAAGTCCCTGATAT                                                                                                                           >  2:772207/1‑149                          ATGAGAGAAGTTCAGACGCATAACGTTCATGCCAGCGTCCAGCATTTTGGCTAACATCTCTTCAGATTCGGTTTTCGGTCCGATGGTGCACACACTTTTGGTCTTTTTCATGACAGTCTTAGGGAAGGTGCGAACAAGTCCCTGATATG                                                                                                                          >  2:743879/1‑149                           TGAGAGAAGTTCAGACGCATAACGTTCATGCCAGCGTCCAGCATTTTAGCTAACATCTCTTCAGATTCGGTTTTCGGTCCGATGGTGCAAACAATTTTGGTCTTTTTCATGACAGTCTTAGGGAAGGTGCGAACAAGTCCCTGATATGA                                                                                                                         >  1:474501/1‑149                             AGAGAATTTCTGACGCATAACGTTCATGCCAGCGGCCAGCATTTTAGCTAACATATCTTCAGATTCGGTATTCGGTCCGATGGTGCAAACAATTTTGGTCTTTTTGATGACAGTCTTAGGGAAGGTGCGAACAAGTCCCTGATAGGAGg                                                                                                                       <  2:747812/149‑2                              GAGAAGTTCAGACGCATAACGTTCATGCCAGCGTCCAGCATTTTAGCTAACATCTCTTCAGATTCGGTTTTCGGTCCGATGGTGCAAACAATTTTGGTCTTTTTCATGACAGTCTTAGGGAAGGTGCGAACAAGTCCCTGATATGAGAT                                                                                                                      <  1:148365/149‑1                               AGAAGTTCAGACGCATAACGTTCATGCCAGCGTCCAGCATTTTAGCTAACATCTCTTCAGATTCGGTTTTCGGTCCGATGGTGCAAACAATTTTGGTCTTTTTCATGACAGTCTTAGGGAAGGTGCGAACAAGTCCCTGATTTGAGATC                                                                                                                     >  2:943988/1‑149                                  AGTTCAGACGAATAACGTTCATGCCAGCGTCCAGCATTTTATTTAACATCTCTTCAGATTCGGTTTTCGGTCCGATGGTGCAAACAATTTTGGTTTTTTTCATGACAGTCTTAGGGAAGGTGCGAACAAGTCCCTGATATGAGATCATG                                                                                                                  <  2:373001/149‑1                                     TCATACGCATAACGTTCATGCCAGCGTCCAGCATTTTAGCTAACATCTCTTCAGATTCGGTTTTCGGTCCGATGGTGCAAACAATTTTGGTCTTTTTCATGACAGTCTTAGGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTT                                                                                                               <  2:448045/149‑1                                     TCAGACGCATATCGTTCATGCCATTGTCCAGCGGGGTATCTAACAGCCCTTCAGATTCGGGTTTCGGTCCGATGGTGCAAACAATTTTGGTCTTTTTCATGACAGTCTTAGGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTT                                                                                                               <  1:626020/149‑1                                     TCAGACGCATAACGTTCATGCCAGCGTCCAGCATTTTAGCTAACATCTCTTCAGATTCGGTTTTCGGTCCGATGGTGCAAACAATTTTGGTCTTTTTCATGACAGTCTTAGGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTT                                                                                                               <  1:516970/149‑1                                     TCAGACGCATAACGTTCATGCCAGCGTCCAGCATTTTAGCTAACATCTCTTCAGATTCGGTTTTCGGTCCGATGGTGCAAACAATTTTGGTCTTTTTCATGACAGTCTTAGGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTT                                                                                                               <  1:737327/149‑1                                      CAGACGCATAACGTTCATGCCAGCGTCCAGCATTTTAGCTAACATCTCTTCAGATTCGGTTTTCGGTCCGATGGTGCAAACAATTTTGGTCTTTTTCATGACAGTCTTAGGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTG                                                                                                              >  2:178020/1‑149                                                           AGCCTCCAGCATTTTAGCTAACATCTCTTCAGATTCGGTTTTCGGTCCGATGGTGCAAACAATTTTGGTCTTTTTCATGACAGTCTTAGGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAG                                                                                         <  1:533237/149‑1                                                            GCGTCCAGCATTTTAGCTAACATCTCTTCAGATTCGGTTTTCGGTCCGATGGTGCAAACAATTTTGGTCTTTTTCATGACAGTCTTAGGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGG                                                                                        <  2:203773/149‑1                                                            GCGTCCAGCATTTTAGCTAACATCTCTTCAGATTCGGTTTTCGGTCCGATGGTGCAAACAATTTTGGTCTTTTTCATGACAGTCTTAGGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGG                                                                                        <  2:57298/149‑1                                                             CGTCCAGCATTTTAGCTAACATCTCTTCAGATTCGGTTTTCGGTCCGATGGTGCAAACAATTTTGGTCTTTTTCATGACAGTCTTAGGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGG                                                                                       <  2:606283/149‑1                                                             CGTCCAGCATTTTAGCTAACATCTCTTCAGATTCGGTTTTCGGTCCGATGGTGCAAACAAGTTTGGTCTTTTTCATGACAGTCTTAGGGTAGGTGCGAACACGTCCCTGATATGAGACGTTGTTGGTCATCTGGAGCCATAGAACAGGG                                                                                       <  2:607967/149‑1                                                                  AGCATTTTAGCTAACATCTCTTCAGATTCGGTTTTCGGTCCGATGGTGCAAACAATTTTGGTCTTTTTCATGACAGTCTTAGGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGGTCAT                                                                                  >  1:314154/1‑149                                                                     ATTTTAGCTAACATCTCTTCAGATTCGGTTTTCGGTCCGATGGTGCAAACAATTTTGGTCTTTTTCATGACAGTCTTAGGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCAT                                                                               <  2:1910/149‑1                                                                      TTTTAGCTAACATCTCTTCAGATTCGGTTTTCGGTCCGATGGTGCAAACAATTTTGGTCTTTTTCATGACAGTCTTAGGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATG                                                                              >  2:621352/1‑149                                                                       tttacgTAATATCCCTTCCGATTCGGTTTCCGGTCCGGTGGTGCAAACAATTTTGGGCTTTTTCATGACAGTCTTGGGGAATGTGCGAATAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGA                                                                             <  2:387249/143‑1                                                                              aaaATCTCTTCAGATTCGGTTTTCGGTCCGATGGTGCAAACAATTTTGGTCTTTTTCATGACAGTCTTAGGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCA                                                                      >  1:240390/4‑149                                                                               ACATCTCTTCAGATTCGGTTTTCGGTCCGATGGTGCAAACAATTTTGGTCTTTTTCATGACAGTCTTAGGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAA                                                                     <  2:240390/149‑1                                                                               ACATCTCTTCAGATTCGGTTTTCGGTCCGATGGTGCAAACAATTTTGGTCTTTTTCATGACAGTCTTAGGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAA                                                                     <  1:743751/149‑1                                                                               ACATCTCTTCAGATTCGGTTTTCGGTCCGATGGTGCAAACAATTTTGGTCTTTTTCATGACAGTCTTAGGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAAGGTTCATCATGAGTCATCAA                                                                     >  2:367810/1‑149                                                                                    TCTGCAGATTCGGTTTTCGGTCCGATGGTGCAAACAATTTTGGTCTTTTTCATGACAGTCTTAGGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTAC                                                                <  1:932623/149‑1                                                                                            TTCGGTTTTCGGTCCGATGGTGCAAACAATTTTGGTCTTTTTCATGACAGTCTTAGGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTAATCTGGAGCCATAGAACAGGGGTCATCATGAGTTCTCAACTTACCTTCGCCG                                                        >  2:267576/1‑149                                                                                               GGTTTTCGGTCCGATGGTGCAAACAATTTTGGTCTTTTTCATGACAGTCTTAGGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACA                                                     <  1:772207/149‑1                                                                                                 TTTTCGGTCCGATGGTGCAAACAATTTTGGTCTTTTTCATGACAGTCTTAGGGAAGGTGCGAACAAGTCCCTGATATGCGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTGATCAACTTACCTTCGCCGAAAGT                                                   >  1:356995/1‑149                                                                                                   tcCGGTCCGATGGTGCAAACAATTTTGGTCTTTTTCATGACAGTCTTAGGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGA                                                 <  1:507179/147‑1                                                                                                     CGGTCCGATGGTGCAAACAATTTTGGTCTTTTTCATGACAGTCTTAGGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAAT                                               <  1:575368/149‑1                                                                                                           GATGGTGCAAACAATTTTGGTCTTTTTGATGACAGTCTTAGGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCA                                         <  2:833221/149‑1                                                                                                            ATGGTGCAAACAATTTTGGTCTTTTTCATGACAGTCTTAGGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAG                                        >  1:321795/1‑149                                                                                                                           TTGGTCTTTTTCATTACAGTTTTAGGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGGCATCTGGAGCCATAGAACAGGTTTCATCATGAGTCATCAACTTACCTTCGCCGGCAGTGAATTCAGCAGTAAGCGCCGTCAGAC                         <  2:285745/149‑1                                                                                                                           TTGGTCTTTTTCATGCCCGTCTTATGCAACGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGAC                         <  1:178020/149‑1                                                                                                                                 TTTTTCATGACAGTCTTAGGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGGCAGTGAATTCAGCAGTAAACGCCGTCAAACCCGAca                   >  1:247980/1‑147                                                                                                                                   TTTCATGACAGTCTTAGGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAG                 <  1:826139/149‑1                                                                                                                                             GTCTTAGGGAAGGTGCGAACAAGACCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTT       <  2:621782/149‑1                                                                                                                                                  AGGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTCCC  >  2:709345/1‑149                                                                                                                                                                                                                                                                                                        GCTGACCGTGTTCTGCATAGTCACCATGAGAGAAGTTCAGACGCATAACGTTCATGCCAGCGTCCAGCATTTTAGCTAACATCTCTTCAGATTCGGTTTTCGGTCCGATGGTGCAAACAATTTTGGTCTTTTTCATGACAGTCTTAG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_pae_tpiA/1755833‑1755687 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTCCC  <  NC_000913_3_pae_tpiA/2102943‑2102797

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.