New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	2725829 =	19 (1.220)	5 (0.340)	5/232	1.2	24.5%	intergenic (‑83/+240)	kgtP/rrfG	alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon
	?	NC_000913_3_pae_tpiA	2725849 =	13 (0.890)					intergenic (‑103/+220)	kgtP/rrfG	alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon

TACTTGTCAGTTTGCTGTCTGCCGTTACAGTACTTTCAGCCATGCCATTATGTCTCCTGCCGTAATCCGATGCTTTTGTCGGTCGCTTTTGTTTATTTTTTTTGTAAAGGAAATATTATACATTTGTTGCATATCATTATGCAACCTTAACCATGAATTTAGTTAGCAGGAAAATGGTTATTGAGGAGCTTAAGGATAAATTTCTGGTAAGGAGGACACGTATGGAAGTGGGCAAGTTGGGGAAGCCGTATCCGTTGCTGAATCTGGCATATGTGGGAGTATAAGACGC  >  NC_000913_3_pae_tpiA/2725704‑2725992                                                                                                                                                  |                                                                                                                                                atgccagattcagcaacggatacggcttccccaacttgcccacttccatacgtgtcctccttaccagaaatttatccttaagctcctcaataaccattttcctgctaactaaattcatggttaaggttgcataatgatatgcaacCTTaa                                                                                                                                             <  3:64965‑M2/5‑1 (MQ=255)            ttGCTGTCTGCCGTTACAGCCCTTTCAGCCATGCCATTATGTCGTCTGCCGTAATCCGATGCTTTTGTCGGTCGCTTTTGTTTATTTTTTTTGTAAAGGAAATATTATACATTTGTTGCATATCATTATGCAACCTTAACCATGAATtta                                                                                                                                  <  1:1923/150‑1 (MQ=255)                             aGTACTTTCAGCCATGCCATTATGTCTCCTGCCGTAATCCGATGCTTTTGTCGGTCGCTTTTGTTTATTTTTTTTGTAAAGGAAATATTATACATTTGTTGCATATCATTATGCAACCTTAACCATGAATTTAGTTAGCAGGAAAATGGt                                                                                                                 >  1:73161/1‑150 (MQ=255)                                                   tGTCTCCTGCCGTAATCCGATGCTTTTGTCGGTCGCTTTTGTTTATTTTTTTTGTAAAGGAAATATTATACATTTGTTGCATATCATTATGCAACCTTAACCATGAATTTAGTTAGCAGGAAAATGGTTATTgag                                                                                                          <  4:34048/135‑1 (MQ=255)                                                   tGTCTCCTGCCGTAATCCGATGCTTTTGTCGGTCGCTTTTGTTTATTTTTTTTGTAAAGGAAATATTATACATTTGTTGCATATCATTATGCAACCTTAACCATGAATTTAGTTAGCAGGAAAATGGTTATTgag                                                                                                          >  3:34048/1‑135 (MQ=255)                                                     tctcCTGCCGTAATCCGATGCTTTTGTCGGTCGCTTTTGTTTATTTTTTTTGTAAAGGAAATATTATACATTTGTTGCATATCATTATGCAACCTTAACCATGAATTTAGTTAGCAGGAAAATGGTTATTGAGGAGCTTAAGGATAAAtt                                                                                         >  2:190674/1‑150 (MQ=255)                                                       tcCTGCCGTAATCCGATGCTTTTGTCGGTCGCTTTTGTTTATTTTTTTTGTAAAGGAAATATTATACATTTGTTGCATATCATTATGCAACCTTAACCATGAATTTAGTTAGCAGGAAAATGGTTATTGAGGAGCTTAAGGATAAATTTc                                                                                       >  3:5269/1‑150 (MQ=255)                                                            ccGTAATCCGATGCTTTTGTCGGTCGCTTTTGTTTATTTTTTTTGTAAAGGAAATATTATACATTTGTTGCATATCATTATGCAACCTTAACCATGAATTTAGTTAGCAGGAAAATGGTTATTGAGGAGCTTAAGGATAAATTTCTGGTa                                                                                  >  2:162230/1‑150 (MQ=255)                                                                 cagaaatttatccttaagctcctcaataaccattttcctgctaactaaattcatggttaagGTTGCATATCATTATGCAACCTTAACCATGa                                                                                                                                       <  3:30726‑M1/31‑1 (MQ=255)                                                                 cagaaatttatccttaagctcctcaataaccattttcctgctaactaaattcatggttaagGTTGCATATCATTATGCAACCTTAACCATGa                                                                                                                                       >  4:30726‑M1/62‑92 (MQ=255)                                                                    cGATGCTTTTGTCGGTCGCTTTTGTTTATTTTTTTTGTAAAGGAAATATTATACATTTGTTGCATATCATTATGCAACCTTAACCATGAATTTAGTTAGCAGGAAAATGGTTATTGAGGAGCTTAAGGATAAATTTCTGGTAAGGAGGac                                                                          <  2:73161/150‑1 (MQ=255)                                                                          ttttGTCGGTCGCTTTTGTTTATTTTTTTTGTAAAGGAAATATTATACATTTGTTGCATATCATTATGCAACCTTAACCATGAATTTAGTTAGCAGGAAAATGGTTATTgag                                                                                                          >  1:170164/1‑112 (MQ=255)                                                                          ttttGTCGGTCGCTTTTGTTTATTTTTTTTGTAAAGGAAATATTATACATTTGTTGCATATCATTATGCAACCTTAACCATGAATTTAGTTAGCAGGAAAATGGTTATTgag                                                                                                          <  2:170164/112‑1 (MQ=255)                                                                              gtcggtcgCTTTTGTTTATTTTTTTTGTAAAGGAAATATTATACATTTGTTGCATATCATTATGCAACCTTAACCATGAATTTAGTTAGCAGGAAAATGGTTATTGAGGAGCTTAAGGATAAATTTCTGGTAAGGAGGACACGTATGGaa                                                                <  4:5269/150‑1 (MQ=255)                                                                                   ctcctcaataaccattttcctgctaactaaattcatggttaaggttgcataatgatatgcaacCTTAACCATGAATTTAGTTAGCAGGAAAATGGTTATTgaggag                                                                                                       >  1:13577‑M2/64‑106 (MQ=255)                                                                                   ctcctcaataaccattttcctgctaactaaattcatggttaaggttgcataatgatatgcaacCTTAACCATGAATTTAGTTAGCAGGAAAATGGTTATTgaggag                                                                                                       <  2:13577‑M2/43‑1 (MQ=255)                                                                                   ctcctcaataaccattttcctgctaactaaattcatggttaagGTTGCATATCATTATGCAACCTTAACCATGAATTTAGTTAGCAGGAAAATGGTTATTgaggag                                                                                                       >  1:13577‑M1/44‑106 (MQ=255)                                                                                   ctcctcaataaccattttcctgctaactaaattcatggttaagGTTGCATATCATTATGCAACCTTAACCATGAATTTAGTTAGCAGGAAAATGGTTATTgaggag                                                                                                       <  2:13577‑M1/63‑1 (MQ=255)                                                                                                                   tcatggttaaggttgcataatgatatgcaacCTTAACCATGAATTTAGTTAGCAGGAAAATGGTTATTGAGGAGCTTAAGGATAAATTTCTg                                                                                     <  3:30726‑M2/61‑1 (MQ=255)                                                                                                                   tcatggttaaggttgcataatgatatgcaacCTTAACCATGAATTTAGTTAGCAGGAAAATGGTTATTGAGGAGCTTAAGGATAAATTTCTg                                                                                     >  4:30726‑M2/32‑92 (MQ=255)                                                                                                                         ttaagGTTGCATATCATTATGCAACCTTAACCATGAATTTAGTTAGCAGGAAAATGGTTATTGAGGAGCTTAAGGATAAATTTCTGGTAAGGAGGACACGTATGGAAGTGGGCAAGTTGGGGAAGCCGTATCCGTTGCTGAATCTGGCat                     <  3:64965‑M1/145‑1 (MQ=255)                                                                                                                          aTTTGTTGCATATCATTATGCAACCTTAACCATGAATTTAGTTAGCAGGAAAATGGTTATTGAGGAGCTTAAGGATAAATTTCTGGTAAGGAGGACACGTATGGAAGTGGGCAAGTTGGGGAAGCCGTATCCGTTGCTGAATCTgg                        >  2:95486/1‑146 (MQ=255)                                                                                                                          aTTTGTTGCATATCATTATGCAACCTTAACCATGAATTTAGTTAGCAGGAAAATGGTTATTGAGGAGCTTAAGGATAAATTTCTGGTAAGGAGGACACGTATGGAAGTGGGCAAGTTGGGGAAGCCGTATCCGTTGCTGAATCTgg                        <  1:95486/146‑1 (MQ=255)                                                                                                                                    TATCATTATGCAACCTTAACCATGAATTTAGTTAGCAGGAAAATGGTTATTGAGGAGCTTAAGGATAAATTTCTGGTAAGGAGGACACGTATGGAAGTGGGCAAGTTGGGGAAGCCGTATCCGTTGCt                                >  2:174058‑M1/1‑128 (MQ=255)                                                                                                                                    TATCATTATGCAACCTTAACCATGAATTTAGTTAGCAGGAAAATGGTTATTGAGGAGCTTAAGGATAAATTTCTGGTAAGGAGGACACGTATGGAAGTGGGCAAGTTGGGGAAGCCGTATCCGTTGCt                                <  1:174058‑M1/128‑1 (MQ=255)                                                                                                                                            tgcaacCTTAACCATGAATTTAGTTAGCAGGAAAATGGTTATTGAGGAGCTTAAGGATAAATTTCTGGTAAGGAGGACACGTATGGAAGTGGGCAAGTTGGGGAAGCCGTATCCGTTGCTGAATCTGGCATATGTGGGAGTATAAGAcgc  >  1:63792‑M2/7‑150 (MQ=255)                                                                                                                                               aacCTTAACCATGAATTTAGTTAGCAGGAAAATGGTTATTGAGGAGCTTAAGGATAAATTTCTGGTAAGGAGGACACGTATGGAAGTGGGCAAGTTggg                                                  <  3:56972‑M2/96‑1 (MQ=255)                                                                                                                                               aacCTTAACCATGAATTTAGTTAGCAGGAAAATGGTTATTGAGGAGCTTAAGGATAAATTTCTGGTAAGGAGGACACGTATGGAAGTGGGCAAGTTggg                                                  >  4:56972‑M2/4‑99 (MQ=255)                                                                                                                                                  cTTAACCATGAATTTAGTTAGCAGGAAAATGGTTATTGAGGAGCTTAAGGATAAATTTCTGGTAAGGAGGACACGTATGGAAGTGGGCAAGTTGGGGAAGCCGTATCCGTTGCTGAATCTGGCATATGTGGGa             <  3:52120/133‑1 (MQ=255)                                                                                                                                                  cTTAACCATGAATTTAGTTAGCAGGAAAATGGTTATTGAGGAGCTTAAGGATAAATTTCTGGTAAGGAGGACACGTATGGAAGTGGGCAAGTTGGGGAAGCCGTATCCGTTGCTGAATCTGGCATATGTGGGa             >  4:52120/1‑133 (MQ=255)                                                                                                                                                  |                                                                                                                                                TACTTGTCAGTTTGCTGTCTGCCGTTACAGTACTTTCAGCCATGCCATTATGTCTCCTGCCGTAATCCGATGCTTTTGTCGGTCGCTTTTGTTTATTTTTTTTGTAAAGGAAATATTATACATTTGTTGCATATCATTATGCAACCTTAACCATGAATTTAGTTAGCAGGAAAATGGTTATTGAGGAGCTTAAGGATAAATTTCTGGTAAGGAGGACACGTATGGAAGTGGGCAAGTTGGGGAAGCCGTATCCGTTGCTGAATCTGGCATATGTGGGAGTATAAGACGC  >  NC_000913_3_pae_tpiA/2725704‑2725992

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