New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	3950444 =	18 (0.720)	4 (0.170)	4/270	2.7	17.3%	intergenic (+24/‑63)	ilvL/ilvX	ilvG operon leader peptide/uncharacterized protein
	?	NC_000913_3_pae_tpiA	3950470 =	21 (0.890)					intergenic (+50/‑37)	ilvL/ilvX	ilvG operon leader peptide/uncharacterized protein
Rejected: Frequency below/above cutoff threshold.

TACGAGTGATTAGCCTGGTCGTGATTAGCGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACAT‑AACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACGGGGAACTAACTATGAATGGCGCACAGTGGGTGGTACATGCGTTGCGGGCACAGGGTGTGAACACCGTTT  >  NC_000913_3_pae_tpiA/3950335‑3950617                                                                                                                                        |                                                                                                                                                     tACGAGTGATTAGCCTGGTCGTGATTAGCGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTa                                                                                                                                         >  2:291651/1‑149 (MQ=255)         aTTAGCCTGGTCGTGATTAGCGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACAT‑a                                                                                                                                >  1:367413/1‑149 (MQ=255)                  gtggTGATTAGCGGGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACCAACTAAGACCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACAT‑AACCgaggag                                                                                                                       <  2:177174/146‑1 (MQ=255)                    agttagttccccgtcctgaatcttgagaaacagaattttgtgctgttattcattgtctgctcctcggttatgtttttaaggtcaaaaaaaACCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACAT‑AACCGAGGAGCa                                                                                                                     >  1:206263‑M1/91‑149 (MQ=255)                     gTGATTAGCGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAAAAT‑AAACAAGGAGAAg                                                                                                                    >  1:63901/1‑149 (MQ=255)                                  tggtgATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACAT‑AACCGAGGAGCAGACAATGAATAACa                                                                                                       <  2:38468/149‑1 (MQ=255)                                  tggtgATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACAT‑AACCGAGGAGCAGACAATGAATAACa                                                                                                       <  2:260130/149‑1 (MQ=255)                                    gtgATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACAT‑AGCCGGGGAGCAGACAATGAATaagatc                                                                                                     >  1:391592/1‑145 (MQ=255)                                    gtgATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACAT‑AACCGAGGAGCAGACAATGAATAACAGc                                                                                                     >  1:15221/1‑149 (MQ=255)                                     gaatcttgagaaacagaattttgtgctgttattcattgtctgctcctcggttatgtttttaaggtcaaaaaaaACCCCCGCACCGAAAGGTCCGGGGGtttttt                                                                                                                                                  >  1:110187‑M1/74‑104 (MQ=255)                                     gaatcttgagaaacagaattttgtgctgttattcattgtctgctcctcggttatgtttttaaggtcaaaaaaaACCCCCGCACCGAAAGGTCCGGGGGtttttt                                                                                                                                                  <  2:110187‑M1/31‑1 (MQ=255)                                      gATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACACCTGCACCGAAAGGTCCGGGGGAAAGCGCGGAGGTTAAAAACATAAACCGAAG‑GGAGACAATGAATAACAGcac                                                                                                   >  1:308569/1‑149 (MQ=255)                                                             cTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACAT‑AACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCa                                                                            <  2:367413/149‑1 (MQ=255)                                                                             tgctcctcggttatgtttttaaggtcaaaaaaaacccccggacctttcggtgcgggggtTTTTTTTGACCTTAAAAACAT‑AACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACGGGGaactaact                                                            >  1:206263‑M2/60‑149 (MQ=255)                                                                             aaaGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACAT‑AACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACGGGGaactaact                                                            >  1:291967/1‑149 (MQ=255)                                                                               aGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACAT‑AACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACGGGGAACTAACTAt                                                          <  1:307465/149‑1 (MQ=255)                                                                                       agaTCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACAT‑AACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACGGGGAACTAACTATGAATGgcg                                                  >  1:255469/1‑149 (MQ=255)                                                                                        gaTCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTg                                                                                                                                               >  1:356084/1‑56 (MQ=255)                                                                                        gaTCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTg                                                                                                                                               <  2:356084/56‑1 (MQ=255)                                                                                            aaGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACAT‑AACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACGGGGAACTAACTATGAATAGCGcacac                                             >  2:248867/1‑148 (MQ=255)                                                                                               ccTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACAT‑AACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACGGGGAACTAACTATGAATGGCGCACAgtgg                                          <  1:291651/149‑1 (MQ=255)                                                                                                         aaaaaacccccggacctttcggtgcgggggtTTTTTTTGACCTTAAAAACAT‑AACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTc                                                                             >  1:110187‑M2/32‑104 (MQ=255)                                                                                                         aaaaaacccccggacctttcggtgcgggggtTTTTTTTGACCTTAAAAACAT‑AACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTc                                                                             <  2:110187‑M2/73‑1 (MQ=255)                                                                                                                CCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACAT‑AACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACGGTGAACTAACTATGAATGGCGCACAGTGGGTGGTACATGCGTTGCg                         <  1:320201‑M1/149‑1 (MQ=255)                                                                                                                 CCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACAT‑AACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACGGTGAACTAACTATGAATGGCGCACAGTGGGTGGTACATGCGTTGcgc                        >  2:320201‑M1/1‑148 (MQ=255)                                                                                                                      aCCGAAAGGGCCGGGGGTTTTTTTTGACCTTAAAAACAT‑AACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACGGGGAACTAACTATGAATGGCGCACAGTGGGTGGTACATGCGTTGCGGGcaca                   <  2:156943/149‑1 (MQ=255)                                                                                                                         gAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACAT‑AACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACGGGGAACTAACTATGAATGGCGCACAGTGGGTGGTACATGCGTTGCGGGCACAggg                >  1:342871/1‑149 (MQ=255)                                                                                                                           aaGGTCCGGGGGTTTTTTTTGACCTTAAAAACAT‑AACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACGGGGAACTAACTATGAATGGCGCACAGTGGGTGGTACATGCGTTGCGGGCACAGGgtg              <  2:255469/149‑1 (MQ=255)                                                                                                                             cgTCCTGGAGTTTTTATTTACCTTAAAAACAT‑AACCGAACAACAAACAATTAATAACATCACAAAAGTCTGTTTCTCAAGATTCAGGACGTGTAACTAACTATGAATGTCGCACAGTGGTTGGTACATGCGTTGCGGGCACAGGGtgtg            <  2:329906/148‑1 (MQ=255)                                                                                                                               tgcgggggtTTTTTTTGACCTTAAAAACAT‑AACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACGGGGAACTAACTATGAATGGCGCACAGTGGGTGGTACATGCGTTGCGGGCACAGGGTGTGaa          <  2:206263‑M2/140‑1 (MQ=255)                                                                                                                                     ggtTTTTTTTGACCTTAAAAACAT‑AACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACGGGGAACTAACTATGAATGGCGCACAGTGGGTGGTACATGCGTTGCGGGCACAGGGTGTGAACACCGt    >  2:374054‑M2/4‑149 (MQ=255)                                                                                                                                       tTTTTTTTGACCTTAAAAACAT‑AACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACGGGGAACTAACTATGAATGGCGCACAGTGGGTGGTACATGCGTTGCGGGCACAGGGTGTGAACACCGttt  >  1:112493‑M2/2‑149 (MQ=255)                                                                                                                                        |                                                                                                                                                     TACGAGTGATTAGCCTGGTCGTGATTAGCGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACAT‑AACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACGGGGAACTAACTATGAATGGCGCACAGTGGGTGGTACATGCGTTGCGGGCACAGGGTGTGAACACCGTTT  >  NC_000913_3_pae_tpiA/3950335‑3950617

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.