New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_pgi	786795 =	21 (1.300)	4 (0.270)	4/232	1.5	16.9%	intergenic (+110/+48)	aroG/gpmA	3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, phenylalanine repressible/phosphoglyceromutase 1
	?	NC_000913_3_pae_pgi	786822 =	20 (1.340)					intergenic (+137/+21)	aroG/gpmA	3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, phenylalanine repressible/phosphoglyceromutase 1
Rejected: Frequency below/above cutoff threshold.

ACTGGCGAATGCAGTAAAAGCGCGTCGCGGGTAAGGTTTAATTGTCGGATGCGCCGTCAGAGTGGCGTATCCGATGAATCACCACAGGCCTGATAAGTCGCGCAGCGTCGCATCAGGCAATGTGCTCCATTGTTAGCAACAAAAAAGCCGACTCACTTGCAGTCGGCTTTCTCATTTTAAACGAATGACGTTTACTTCGCTTTACCCTGGTTTGCAACCGCCGCTGCTTTCGCTGCGATCTCGTCAGCATTACCCAGATAATAGCGTTTCAGCGGTTTGAAATTCT  >  NC_000913_3_pae_pgi/786652‑786937                                                                                                                                                |                                                                                                                                               gcgtgccgctggtgtatgagttcgacgagaatttcaaaccgctgaaacgctattatctgggtaatgctgacgagatcgcagcgaacgcatcggcggttgcaaaccagggtaaagcgaagtaaacgtcattcgtgtaagatgagAAAGCCg                                                                                                                                          <  1:196328‑M1/7‑1 (MQ=255)    tgccgctggtgtatgagttcgacgagaatttcaaaccgctgaaacgctattatctgggtaatgctgacgagatcgcagcgaaagcagcggcggttgcaaaccagggtaaagcgaagtaaacgtcattcgtttaaaatgagAAAGCCGACt                                                                                                                                       <  2:7942‑M1/10‑1 (MQ=255)          tGCAGTAAAAGCGCGTCGCGGGTAAGGTTTAATTGTCGGATGCGCCGTCAGAGTGGCGTATCCGATGAATCACCACAGGCCTGATAAGTCGCGCAGCGTCGCATCAGGCAATGTGCTCCATTGTTAGCAACAAAAAAGCCGACTCACTTg                                                                                                                                 <  2:35914/150‑1 (MQ=255)               tAAAAGCGCGTCGGGGGTAAGGATTAATTGTCGGATCCGCCGACAGAGTGGCGTATCCGACGAATCCCCACAGGCCTGATAAGTCGCGAAGCGTAGCATCAGGCGAAGGGCTACATTGTTAGCAACAAAAAAGCCGACTGACTTGCAGTc                                                                                                                            >  2:196328/1‑150 (MQ=255)                     cgcgTCGCGGGTAAGGTTTAATTGTCGGATGCGCCGTCAGAGTGGCGTATCCGATGAATCACCACAGGCCTGATAAGTCGCGCAGCGTCGCATCAGGCAATGTGCTCCATTGTTAGCAACAAAAAAGCCGACTCACTTGCAGTCGGCttt                                                                                                                      <  1:49023/150‑1 (MQ=255)                             gaatttcaaaccgctgaaacgctattatctgggtaatgctgacgagatcgcagcgaaagcagcggcggttgcaaaccagggtaaagcgaagtaaacgtcattcgtttaaaatgagAAAGCCGACTCACTTGCAGTCGGCTTTCTCAtttt                                                                                                              <  4:99860‑M1/35‑1 (MQ=255)                                  aGGTTTAATTGTCGGATGCGCCGTCAGAGTGGCGTATCCGATGAATCACCACAGGCCTGATAAGTCGCGCAGCGTCGCATCAGGCAATGTGCTCCATTGTTAGCAACAAAAAAGCCGACTCACTTGCAGTCGGCTTTCTCATTTTAAACg                                                                                                         >  4:64531/1‑150 (MQ=255)                                                    attatctgggtaatgctgacgagatcgcagcgaaagcagcggcggttgcaaaccagggtaaagcgaagtaaacgtcattcgtttaaaatgagAAAGCCGACTCACTTGCAGTCGGCTTTCTCATTTTAAACGAATGACGTTTACTTCGCt                                                                                       >  3:99860‑M1/93‑150 (MQ=255)                                                                  cGTATCCGATGAATCACCACAGGCCTGATAAGTCGCGCAGCGTCGCATCAGGCAATGTGCTCCATTGTTAGCAACAAAAAAGCCGACTCACTTGCAGTCGGCTTTCTCATTTTAAACGAATGACGTTTACTTCGCTTTACCCTGGTTTGc                                                                         >  2:77777/1‑150 (MQ=255)                                                                        cGATGAATCACCACAGGCCTGATAAGTCGCGCAGCGTCGCATCAGGCAATGTGCTCCATTGTTAGCAACAAAAAAGCCGACTCACTTGCAGTCGGCTTTCTCATTTTAAACGAATGACGTTTACTTCGCTTTACCCTGGTTTGCAAccgc                                                                   >  1:35871/1‑150 (MQ=255)                                                                                agcgaaagcagcggcggttgcaaaccagggtaaagcgaagtaaacgtcattcgtttaaaatgagAAAGCCGACTCACTTGCAGTCGGCTTtctc                                                                                                                   <  4:35411‑M1/30‑1 (MQ=255)                                                                                agcgaaagcagcggcggttgcaaaccagggtaaagcgaagtaaacgtcattcgtttaaaatgagAAAGCCGACTCACTTGCAGTCGGCTTtctc                                                                                                                   >  3:35411‑M1/65‑94 (MQ=255)                                                                                    acaGGCCTGATAAGTCGCGCAGCGTCGCATCAGGCAATGTGCTCCATTGTTAGCAACAAAAAAGCCGACTCACTTGCAGTCGGCTTTCTCATTTTAAACGAATGACGTTTACTTCGCTTTACCCTGGTTTGCAACCGCCGCTGCTTTCGc                                                       >  1:7942/1‑150 (MQ=255)                                                                                    acaGGCCTGATAAGTCGCGCAGCGTCGCATCAGGCAATGTGCTCCATTGTTAGCAACAAAAAAGCCGACTCACTTGCAGTCGGCTTTCTCATTTTAAACGAATGACGTTTACTTCGCTTTACCCTGGTTTGCAACCGCCGCTGCTTTCGc                                                       >  4:74346/1‑150 (MQ=255)                                                                                       ggCCTGATAAGTCGCGCAGCGTCGCATCAGGCAATGTGCTCCATTGTTAGCAACAAAAAAGCCGACTCACTTGCAGTCGGCTTTCTCATTTTAAACGAATGACGTTTACTTCGCTTTACCCTGGTTTGCAACCGCCGCTGCTTTCGCTGc                                                    <  3:64531/150‑1 (MQ=255)                                                                                         ccTGATAAGTCGCGCAGCGTCGCATCAGGCAATGTGCTCCATTGTTAGCAACAAAAAAGCCGACTCACTTGCAGTCGGCTTTCTCATTTTAAACGAATGACGTTTACTTCGCTTTACCCTGGTTTGCAACCGCCGCTGCTTTCGCTGCGa                                                  <  4:120299/150‑1 (MQ=255)                                                                                              tAAGTCGCGCAGCGTCGCATCAGGCAATGTGCTCCATTGTTAGCAACAAAAAAGCCGACTCACTTGCAGTCGGCTTTCTCATTTTAAACGAATGACGTTTACTTCGCTTTACCCTGGTTTGCAACCGCCGCTGCTTTCGCTGCGATCTCg                                             >  1:98176/1‑150 (MQ=255)                                                                                               aaGTCGCGCAGCGTCGCATCAGGCAATGTGCTCCATTGTTAGCAACAAAAAAGCCGACTCACTTGCAGTCGGCTTTCTCATTTTAAACGAATGACGTTTACTTCGCTTTACCCTGGTTTGCAACCGCCGCTGCTTTCGCTGCGATCTCGt                                            >  2:4950/1‑150 (MQ=255)                                                                                                  tCGCGCAGCGTCGCATCAGGCAATGTGCTCCATTGTTAGCAACAAAAAAGCCGACTCACTTGCAGTCGGCTTTCTCATTTTAAACGAATGACGTTTACTTCGCTTTACCCTGGTTTGCAACCGCCGCTGCTTTCGCTGCGATCTCGTCAg                                         >  1:101977/1‑150 (MQ=255)                                                                                                               cATCAGGCAATGTGCTCCATTGTTAGCAACAAAAAAGCCGACTCACTTGCAGTCGGCTTTCTCATTTTAAACGAATGACGTTTACTTCGCTTTACCCTGGTTTGCAACCGCCGCTGCTTTCGCTGCGATCTCGTCAGCATTACCCAGata                            >  4:103606/1‑150 (MQ=255)                                                                                                                    ggCAATGTGCTCCATTGTTAGCAACAAAAAAGCCGACTCACTTGCAGTCGGCTTTCTCATTTTAAACGAATGACGTTTACTTCGCTTTACCCTGGTTTGCAACCGCCGCTGCTTTCGCTGCGATCTCGTCAGCATTACCCAGATAATAGc                       >  2:139533/1‑150 (MQ=255)                                                                                                                         tgtgCTCCATTGTTAGCAACAAAAAAGCCGACTCACTTGCAGTCGGCTTTCTCATTTTAAACGAATGACGTTTACTTCGCTTTACCCTGGTTTGCAACCGCCGCTGCTTTCGCTGCGATCTCGTCAGCATTACCCAGATAATAGCGTTTc                  >  3:105132/1‑150 (MQ=255)                                                                                                                           tgCTCCATTGTTAGCAACAAAAAAGCCGACTCACTTGCAGTCGGCTTTCTCATTTTAAACGAATGACGTTTACTTCGCTTTACCCTGGTTTGCAACCGCCGCTGCTTTCGCTGCGATCTCGTCAGCATTACCCAGATAATAGCGTTTCAg                <  1:77777/150‑1 (MQ=255)                                                                                                                            gCTCCATTGTTAGCAACAAAAAAGCCGACTCACTTGCAGTCGGCTTTCTCATTTTAAACGAATGACGTTTACTTCGCTTTACCCTGGTTTGCAACCGCCGCTGCTTTCGCTGCGATCTCGTCAGCATTACCCAGATAATAGCGTTTCAGc               >  2:6212/1‑150 (MQ=255)                                                                                                                                    gTTAGCAACAAAAAAGCCGACTCACTTGCAGTCGGCTTTCTCATTTTAAACGAATGACGTTTACTTCGCTTTACCCTGGTTTGCAACCGCCGCTGCTTTCGCTGCGATCTCGTCAGCATTACCCAGATAATAGCGTTTCAGCGGTTTGaa       <  1:6212/150‑1 (MQ=255)                                                                                                                                     ttAGCAACAAAAAAGCCGACTCACTTGCAGTCGGCTTTCTCATTTTAAACGAATGACGTTTACTTCGCTTTACCCTGGTTTGCAACCGCCGCTGCTTTCGCTGCGATCTCGTCAGCATTACCCAGATAATAGCGTTTCAGCGGTTTGaaa      <  3:74346/150‑1 (MQ=255)                                                                                                                                         caacaaAAAAGCCGACTCACTTGCAGTCGGCTTTCTCATTTTAAACGAATGACGTTTACTTCGCTTTACCCTGGTTTGCAACCGCCGCTGCTTTCGCTGCGATCTCGTCAGCATTACCCAGATAATAGCGTTTCAGCGGTTTGAAATtct  <  2:35871/150‑1 (MQ=255)                                                                                                                                                |                                                                                                                                               ACTGGCGAATGCAGTAAAAGCGCGTCGCGGGTAAGGTTTAATTGTCGGATGCGCCGTCAGAGTGGCGTATCCGATGAATCACCACAGGCCTGATAAGTCGCGCAGCGTCGCATCAGGCAATGTGCTCCATTGTTAGCAACAAAAAAGCCGACTCACTTGCAGTCGGCTTTCTCATTTTAAACGAATGACGTTTACTTCGCTTTACCCTGGTTTGCAACCGCCGCTGCTTTCGCTGCGATCTCGTCAGCATTACCCAGATAATAGCGTTTCAGCGGTTTGAAATTCT  >  NC_000913_3_pae_pgi/786652‑786937

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.