New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	= 253532	32 (0.950)	3 (0.120) +AAGGGACGAATATATTTGCCCATGTACCATTCCAT	3/212	3.7	9.1%	pseudogene (54/207 nt)	ykfJ	pseudogene
	?	NC_000913_3_pae_tpiA	3071270 =	48 (1.430)					intergenic (‑26/+189)	fbaA/pgk	fructose‑bisphosphate aldolase, class II/phosphoglycerate kinase
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

CAGTACCGACGCAGTTTACTGCTGGCAGTGCGAAGTTGTTTTCTTTTGCTACCTGGAAAACTTTCTGTACGTCATCACCAGTGATTACGCCAGGTTTTACGAAATCAAAAATCTTAGACATGTCTCTTGTCCTGTATCGTCGGGCCTTATACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCTCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGAAAAATTGCGTGCTCTAAAAGC  >  NC_000913_3_pae_tpiA/3071124‑3071419                                                                                                                                                   |                                                                                                                                                      cAGTACCGACGCAGTTTACTGCTGGCAGTGCGAAGTTGTTTTCTTTTGCTACCTGGAAAACTTTCTGTACGTCATCACCAGTGATTACGCCAGGTTTTACGAAATCAAAAATCTTAGACATGTCTCTTGTCCTGTATCGTCGGGCCTtat                                                                                                                                                    <  2:546358/150‑1 (MQ=255)       cGACGCAGTTTACTGCTGGCAGTGCGAAGTTGTTTTCTTTTGCTACCTGGCCATCCGTTTGGACGTCATCACCAGTGATTACGCCAGGTTTTACGAAATCAAAAATCTTAGACATGTCTCTTGTCCTGTATCGTCGGGCCTTATACTCGt                                                                                                                                              <  1:437189/150‑1 (MQ=255)        gACGCAGTTTACTGCTGGCAGTGCGAAGTTGTTTTCTTTTGCTACCTGGAAAACTTTCTGTACGTCATCACCAGTGATTACGCCAGGTTTTACGAAATCAAAAATCTTAGACATGTCTCTTGTCCTGTATCGTCGGGCCTTATACTCGTc                                                                                                                                             >  1:569669/1‑150 (MQ=255)         aCGCAGTTTACTGCTGGCAGTGCGAAGTTGTTTTCTTTTGCTACCTGGAAAACTTTCTGTACGTCATCACCAGTGATTACGCCAGGTTTTACGAAATCAAAAATCTTAGACATGTCTCTTGTCCTGTATCGTCGGGCCTTATACTCGTCa                                                                                                                                            >  1:397695/1‑150 (MQ=255)           gctgTTTACTGCTGGCAGTGCGAAGTTGTTTTCTTTTGCTACCTGGAAAACTTTCTGTACGTCATCACCAGTGATTACGCCAGGTTTTACGAAATCAAAAATCTTAGACATGTCTCTTGTCCTGTATCGTCGGGCCTTATACTCGTCATa                                                                                                                                          <  1:215941/147‑1 (MQ=255)           gCAGTTTACTGCTGGCAGTGCGAAGTTGTTTTCTTTTGCTACCTGGAAACCTTTCTGTACGTCATCACCAGTGATTACGACAGGTTTTACGAAATCAAAAATCTTAGACATGTCTCTTGTCCTTTATCGTCGCGCCTTATACTCGttcta                                                                                                                                          >  2:192432/1‑146 (MQ=255)                                       ttttCTTTTGCTACCTGGAAAACTTTCTGTACGTCATGACCAGTGATTACGCCAGGTTTTACGAAATCAAAAATCTTAGACATGTCTCTTGTCCTGTATCGTCAGGCCTTATACTCGTCATAc                                                                                                                                         <  1:145168/123‑1 (MQ=255)                                       ttttCTTTTGCTACCTGGAAAACTTTCTGTACGTCATGACCAGTGATTACGCCAGGTTTTACGAAATCAAAAATCTTAGACATGTCTCTTGTCCTGTATCGTCAGGCCTTATACTCGTCATAc                                                                                                                                         >  2:145168/1‑123 (MQ=255)                                        tttCTTTTGCTACCTGGAAAACTTTCTGTACGTCATCACCAGTGATTACGCCAGGTTTTACGAAATCAAAAATCTTAGACATGTCTCTTGTCCTGTATCGTCGGGCCTTATACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTCCGtt                                                                                                             >  2:44481/1‑150 (MQ=255)                                         ttCTTTTGCTACCTGGCAACCTTTCTGTACGTCATCACCAGTGAATACGCCAAGATTTACGAAATAAAACACCTTAGACTTTTTTCTTGTCCTGTATCGTCGGGCCTTATACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTc                                                                                                            <  1:265699/150‑1 (MQ=37)                                           tttttGCTACCTTGAAACTGTTCTGGACGTCAGCACCAGTGATTAAGCCAGGTTTTAGTAAATCAAAAATCTTAGACATGTCTATTGTCATGTATCGGCGGGCCTTATACTCGTCATACTTCAAGTTGCATGTGCAGCGTCTGCGTTCGc                                                                                                          <  2:469006/149‑1 (MQ=25)                                                   aCCTGGAAAACTTTCTGTACGTCATCACCAGTGATTACGCCAGGTTTTACGAAATCAAAAATCTTAGACATGTCTCTTGTCCTGTATCGTCGGGCCTTATACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCa                                                                                                  <  1:281260/150‑1 (MQ=255)                                                      tGGAAAACTTTCTGTACGTCATCACCAGTGATAACGCCAGGTTTTACGAAATCAAAAATCTTAGACATGTCTCTTGTCCTGTATCATCGGGCCTTATACTCGTCATACTTCAAGTTGTCAGTGCCGCGTGTGCGTTCGCTCACCCGAGTc                                                                                               >  2:7640/1‑150 (MQ=38)                                                        gAAAACTTTCTGTACGTCATCACCAGTGATTACGCCAGGTTTTACGAAATCAAAAATCTTAGACATGTCTCTTGTCCTGTATCGTCGGGCCTTATACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCac                                                                                             <  1:330129/150‑1 (MQ=255)                                                                       gTCATCACCAGTGATTACGCCAGGTTTTACGAAATCAAAAATCTTAGACATGTCTCTTGTCCTGTATCGTCGGGCCTTATACTCGTCATACTTCAAGTTGCATTTGCTTCGTCTGCGTTCGCTCACCCCAGTCCCTTACTTCTGTaaacc                                                                              >  2:375461/1‑147 (MQ=37)                                                                         catcaCCAGTGATTACGCCAGGTTTTACGAAATCAAAAATCTTAGACATGTCTCTTGTCCTGTATCGTCGGGCCTTATACTCGTCATa                                                                                                                                          >  1:247583/1‑88 (MQ=255)                                                                         catcaCCAGTGATTACGCCAGGTTTTACGAAATCAAAAATCTTAGACATGTCTCTTGTCCTGTATCGTCGGGCCTTATACTCGTCATa                                                                                                                                          <  2:247583/88‑1 (MQ=255)                                                                          atcaCCAGTGATTACGCCAGGTTTTACGAAATCAAAAATCTTAGACATGTCTCTTGTCCTGTATCGTCGGGCCTTATACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCt                                                                           >  1:312236/1‑150 (MQ=255)                                                                           tcaCCAGTGATTACGCCAGGTTTTACGAAATCAAAAATCTTAGACATTTCTCTTGTCCTGTATCGTCGGGCCTTATACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTg                                                                          <  1:566772/150‑1 (MQ=255)                                                                             aCCAGTGATTACGCCAGGTTTTACGAAATCAAAAATCTTAGACATGTCTCTTGTCCTGTATCGTCGGGCCTTATACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTggg                                                                        >  2:553552/1‑150 (MQ=255)                                                                              ccAGTGATTACGCCAGGTTTTACGAAATCAAAAATCTTAGACATGTCTCTTGTCCTGTATCGTCGGGCCTTATACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTgggg                                                                       >  2:508213/1‑150 (MQ=255)                                                                                    aTTACGCCAGGTTTTACGAAATCAAAAATCTTAGACATGTCTCTTGTCCTGTATCGTCGGGCCTTATACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGCTTCAc                                                                 >  1:353430/1‑150 (MQ=255)                                                                                    aTTACGCCAGGTTTTACGAAATCAAAAATCTTAGACATGTCTCTTGTCCTGTATCGTCGGGCCTTATACTCGTCATACTTCAAGTTGCATGTGATCCGTTTTCTTTTTTGCACCCCAGTCACTTATTTATGTAAGCTCCTGGGGATTCAc                                                                 >  1:288711/1‑150 (MQ=25)                                                                                        gtggaGGTTTTACGAAATCAAAAAGTTTAGAGATGTCGCTTGTCCTGTATCGTCGTGCCTTATCCTCGTCATACTTCAAGTTGCATGTGCTGCGCTTGCGTTCTCTCACCCCATTCACTTACTTATGTAAGCTCCTGGGGCTTCActctc                                                             <  2:109231/146‑1 (MQ=18)                                                                                           cAGGTTTTACGAAATCAAAAATCTTAGACATGTCTCTTGTCCTGTATCGTCGGGCCTTATACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTaa                                                                                 >  1:28761/1‑127 (MQ=255)                                                                                           cAGGTTTTACGAAATCAAAAATCTTAGACATGTCTCTTGTCCTGTATCGTCGGGCCTTATACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTaa                                                                                 <  2:28761/127‑1 (MQ=255)                                                                                           cAGGTTTTACGAAATCAAAAATCTTAGACATGTCTCTTGTCCTGTATCGTCGGGCCTTATACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCTCTTg                                                          >  2:244156/1‑150 (MQ=255)                                                                                             ggTTTTACGAAATCAAAAATCTTAGACATGTCTCTTGTCCTGTATCGTCGGGCCTTATACTCGTCATACTTCAAGTTGCATGTGCTGCGTGTGCGTTCCCTCACCACTGCCTCGTACTTATGTAAGCTCCTGGGGATTCACTCTCTTGTc                                                        <  2:219914/150‑1 (MQ=25)                                                                                               ttttACGAAATCAAAAATCTTAGACATGTCTCTTGTCCTGTATCGTCGGGCCTTATACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCTCTTGTCGc                                                      >  1:551498/1‑150 (MQ=255)                                                                                                                tCTTAGACATGTCTCTTGTCCTGTATCGTCGGGCCTTATACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCTCTTGTCGCCTTCCTGCAACTCGAat                                     >  1:217819/1‑150 (MQ=255)                                                                                                                  ttAGACATGTCTCTTGTCCTGTATCGTCGGGCCTTATACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAGGATCCTGGGGCTTCACTCTCTTGTCGCCTTCCTGCAACTCGActtt                                   >  2:198522/1‑149 (MQ=255)                                                                                                                  ttAGACATGTCTCTTGTCCTGTATCGTCGGGCCTTATACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCTCTTGTCGCCTTCCTGCAACTCGAatta                                   >  1:172619/1‑150 (MQ=255)                                                                                                                  ttAGACATGTCTCTTGTCCTGTATCGTCGGGCCTTATACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCTCTTGTCGCCTTCCTGCAACTCGAatta                                   <  2:217819/150‑1 (MQ=255)                                                                                                                      aCATGTCTCTTGTCCTGTACCGTCGCGCCTTATACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCTCTTGTCGCCTTCCTGCAACTCGAATTATTTa                               <  2:456413/150‑1 (MQ=255)                                                                                                                        aTGTCTCTTGTCCTGTATCGTCGGGCCTTATACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCTCTTGTCGCCTTCCTGCAACTCGAATTATTTagg                             >  2:383420/1‑149 (MQ=255)                                                                                                                        aTGTCTCTTGTCCTGTATCGTCGGGCCTTATACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCTCTTGTCGCCTTCCTGCAACTCGAATTATTTaga                             >  2:340205/1‑150 (MQ=255)                                                                                                                        aTGTCTCTTGTCCTGTATCGTCGGGCCTTATACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCTCTTGTCGCCTTCCTGCAACTCGAATTATTTaga                             <  1:508213/150‑1 (MQ=255)                                                                                                                                tGTCCTGTATCGTCGGGCCTTATACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCTCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGaaa                     >  2:521130/1‑150 (MQ=255)                                                                                                                                     tGTATCGTCGGGCCTTATACTCGTCATACTTCAAATTGCCTGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCTCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGAAAAATTg                >  2:514223/1‑150 (MQ=255)                                                                                                                                         tcgtcgGGCCTTATACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCTCTTGTCGCCTTCCTGCAACTCGaa                                      <  1:283995/124‑1 (MQ=255)                                                                                                                                         tcgtcgGGCCTTATACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCTCTTGTCGCCTTCCTGCAACTCGaa                                      >  2:283995/1‑124 (MQ=255)                                                                                                                                            tcgGGCCTTATACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCTCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGAAAAATTGCGTGctc         <  1:203109/150‑1 (MQ=255)                                                                                                                                               ggCCTTATACTCGTCATACTTTAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCTCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGAAAAATTGCGTGCTCTaa      >  1:148714/1‑150 (MQ=255)                                                                                                                                               ggCCTTATACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCa                                                                  <  1:556616/90‑1 (MQ=37)                                                                                                                                               ggCCTTATACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCa                                                                  >  2:556616/1‑90 (MQ=37)                                                                                                                                               ggCCTTATACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTACGTAAGCTCCTGGGGATTCACTCTCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGAAAAATTGCGTGCTCTaa      >  1:256830/1‑150 (MQ=255)                                                                                                                                                gCCTTATACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCGGTCAGTTACTTATGTAAGCTCCTGGGGATTCACTCTCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGAAAAATTGCGTGCGCTaaa     >  1:352473/1‑150 (MQ=255)                                                                                                                                                 ccTTATACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCTCTTGTCGCCTTCCTGCCACTCGAATTATTTAGAGTATGAAAACTTGCGTGCTCTacaa    >  2:352104/1‑150 (MQ=255)                                                                                                                                                   ttATACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCTCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGAAAAATTGCGTGCTCTAAAAgc  >  1:517725/1‑150 (MQ=255)                                                                                                                                                   ttATACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCTCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGAAAAATTGCGTGCTCTAAAAgc  >  1:518427/1‑150 (MQ=255)                                                                                                                                                   ttATACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTATATTCGGGCCGGCCTGCAACTCGAATTATTTAGAGTATGAAAAATTGCGTGCTCTAAAAgc  >  1:437174/1‑150 (MQ=17)                                                                                                                                                   ttATACTCGTCATACTTCAAGGTGCATGTGCTGCGTCTGGGTTAGCTCTCCCTAGTCACTTTCTTATGTAAGCTCATGGGGATTCACTCTCTTGTCGCCTTCCTGCAACTCGAATTATTTAGACTATGAAAACGGCCGTCCTCTCAAAgc  >  2:139037/1‑150 (MQ=11)                                                                                                                                                   |                                                                                                                                                      CAGTACCGACGCAGTTTACTGCTGGCAGTGCGAAGTTGTTTTCTTTTGCTACCTGGAAAACTTTCTGTACGTCATCACCAGTGATTACGCCAGGTTTTACGAAATCAAAAATCTTAGACATGTCTCTTGTCCTGTATCGTCGGGCCTTATACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCTCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGAAAAATTGCGTGCTCTAAAAGC  >  NC_000913_3_pae_tpiA/3071124‑3071419

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.