New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_pgi	390532 =	13 (0.800)	3 (0.190)	3/240	1.9	19.8%	pseudogene (282/1458 nt)	yaiT	pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein
	?	NC_000913_3_pae_pgi	390559 =	12 (0.780)					pseudogene (309/1458 nt)	yaiT	pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein
Rejected: Frequency below/above cutoff threshold.

AGGCACTGTAGATGGCAACTATGTAAACTATAGTGGTTTTGTCTATTACAACAACACCAATGGTGATTTCGATCAGTCCTTTAACGGCGATACCGTTAACGGCACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGTTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATGATTTTTACACTGATGCGG  >  NC_000913_3_pae_pgi/390403‑390680                                                                                                                                  |                                                                                                                                                     tcaacaaccgcatcagtgtaaaaatcatatccacccagattattaccatctgcatcaaaacgatcataataaccgccaggcagcatagaagtaatcgaaccgtgaatcactgaattactgatatcaagcTGATTa                                                                                                                                                 <  4:119248‑M1/6‑1 (MQ=255) tcaacaaccgcatcagtgtaaaaatcatatccacccagattattaccatctgcatcaaaacgatcataataaccgccaggcagcatagaagtaatcgaaccgtgaatcactgaattactgatatcaagcTGATTa                                                                                                                                                 >  3:119248‑M1/130‑135 (MQ=255) aggcaCTGTAGATGGCAACTATGTAAACTATAGTGGTTTTGTCTATTACAACAACACCCATGGTGATTTCGATCAGTCCTTTAACGGCGATACCGTTAACGGCACGATCTCAACCTATTATTTGAACCATGATTATg                                                                                                                                               <  2:137255/137‑1 (MQ=255) aggcaCTGTAGATGGCAACTATGTAAACTATAGTGGTTTTGTCTATTACAACAACACCAATGGTGATTTCGATCAGTCCTTTAACGGCGATACCGTTAACGGCACGATCTCAACCTATTATTTGAACCATGATTATg                                                                                                                                               >  1:137255/1‑137 (MQ=255)        gTAGAAGGCAACTATGTAAACTATAGAGGTTTAGTCTATAACAACAACACCAATGGTGATTTCGATCAGTCCTTTAACGACGATACCGTTAACGGCACGATCTCAACCTATTATTTGAACCATTATTATGCAGACAGTACTGCTAATCAg                                                                                                                           >  4:99571/1‑150 (MQ=255)                 aaCTATGTAAACTATAGTGGTTTTGTCTATTACAACAACACCAATGGTGATTTCGATCAGTCCTTTAACGGCGATACCGTTAACGGCACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATc                                                                                                                  >  2:143981/1‑150 (MQ=255)                  aCTATGTAAACTATAGTGGTTTTGTCTATTACAACAACACCAATGGTGATTTCGATCAGTCCTTTAACGGCGATACCGTTAACGGCACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCa                                                                                                                 <  2:20826/150‑1 (MQ=255)                            tatccacccagattattaccatctgcatcaaaacgatcataataaccgccaggcagcatagaagtaatcgaaccgtgaatcactgaattactgatatcaagcTGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAg                                                                                                                <  1:55185‑M1/39‑1 (MQ=255)                            tatccacccagattattaccatctgcatcaaaacgatcataataaccgccaggcagcatagaagtaatcgaaccgtgaatcactgaattactgatatcaagcTGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAg                                                                                                                >  2:55185‑M1/103‑141 (MQ=255)                                                     catcaaaacgatcataataaccgccaggcagcatagaagtaatcgaaccgtgaatcactgaattactgatatcaagcTGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGTTCGATTACTTCTAtg                                                                              >  3:79491‑M1/78‑150 (MQ=255)                                                                       gATCAGTCCTTTAACGGCGATACCGTTAACGGCACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGTTCGATTACTTCTATGCTGCCTGGCGGTtattat                                                            <  4:7596/150‑1 (MQ=255)                                                                          cAGTCCTTTAACGGCGATACCGTTAACGGCACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGTTCGATTACTTCTATGCTGCCTGGCGGTTATTATGAt                                                         >  4:69048/1‑150 (MQ=255)                                                                                      ggCGATACCGTTAACGGCACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGTTCGATTACTTCTATGCTGCCTGGCGGTtattat                                                            <  3:49217/135‑1 (MQ=255)                                                                                      ggCGATACCGTTAACGGCACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGTTCGATTACTTCTATGCTGCCTGGCGGTtattat                                                            >  4:49217/1‑135 (MQ=255)                                                                                                      gCACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGTTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGAt                                          <  2:103004/137‑1 (MQ=255)                                                                                                      gCACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGTTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGAt                                          >  1:103004/1‑137 (MQ=255)                                                                                                      gCACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGTTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTgg                             <  3:69048/150‑1 (MQ=255)                                                                                                                                 aTGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGTTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATGATTTTTACACTGATGCgg  <  1:187265/150‑1 (MQ=255)                                                                                                                                  |                                                                                                                                                     AGGCACTGTAGATGGCAACTATGTAAACTATAGTGGTTTTGTCTATTACAACAACACCAATGGTGATTTCGATCAGTCCTTTAACGGCGATACCGTTAACGGCACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGTTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATGATTTTTACACTGATGCGG  >  NC_000913_3_pae_pgi/390403‑390680

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