New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	= 349876	59 (1.110)	6 (0.190) +CTACAGTTCAGTTCACCCCGTAGGCCTGATAAGTCGCGTCAGCGGCGCATCAGGCATCG	4/166	4.8	14.8%	noncoding (272/365 nt)	REP25 (repetitive extragenic palindromic) element; contains 8 REP sequences	REP25 (repetitive extragenic palindromic) element; contains 8 REP sequences
	?	NC_000913_3_pae_tpiA	= 349972	NA (NA)					intergenic (+400/‑40)	prpB/prpC	2‑methylisocitrate lyase/2‑methylcitrate synthase
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

GTGCACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAG‑ACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGAGCGACACAACGATCCTGCAAAACAGTACCCATGTCATTAAACCGAAAAAATCTGTGGCACTTTCTGGCGTTCCGGCGGGCAATACGGCGCTCTGCACCGT  >  NC_000913_3_pae_tpiA/349830‑350115                                                                                                                                                |                                                                                                                                                ttGCACGGAACTGTAGGTCGGACAAGACGCATAGCGTCGCATCCGACAACCGATGACTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAG‑ACGCATAGCGTCGCATCCGACAACAAtctc                                                                                                                                           <  1:8494/148‑1 (MQ=255) gTGCACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAG‑ACGCATAGCGTCGCATCCGACAACAAtctc                                                                                                                                           <  2:723614/149‑1 (MQ=38)   gCACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAG‑ACGCATAGCGTTGCATCCGACAACAATCTCGa                                                                                                                                         >  2:25282/1‑149 (MQ=255)    cattggaCTGTAGGGGCGATAAGACGGATGGCCACGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAG‑ACGCATAGCGTCGCATCCGACAACAATCTCGAc                                                                                                                                        <  2:32174/143‑1 (MQ=11)    cACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAG‑ACGCATAGCGTCGCATCCGACAACAATCTCGAc                                                                                                                                        >  1:531970/1‑149 (MQ=39)      cTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAG‑ACGCATAGCGTCGCATCCGACAACAATCTCGAccc                                                                                                                                      <  2:929236/149‑1 (MQ=255)            cgTAGGCCGGATGAGACGCATAGCGTCGCATCCGACAACCGATGCCGGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAG‑ACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACaaa                                                                                                                                <  1:247412/148‑1 (MQ=255)               agttCGGACAAGACGCCTAGCGTCCCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAG‑ACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGa                                                                                                                             <  1:287392/146‑1 (MQ=255)                  tCGGATAAGACGCATAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAG‑ACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATaa                                                                                                                          <  1:880833/149‑1 (MQ=255)                      aTAAGACGCATAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACCGAACTGTAGGTCGGATAAG‑ACGCATAGCGTTGCATCCGACAACAATCTCGACCCTACAAATGATAACAAt                                                                                                                      <  1:25282/149‑1 (MQ=255)                        aaGACGCATAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAG‑ACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGa                                                                                                                    <  1:632729/149‑1 (MQ=255)                           aCGCATAGCGTCGCATCCGACAACCGATGCCTGATGTGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGAACGC‑TACTGGCATGTCCGCCAACAATCCCTACCCTACAAATGGTAACAATGACGa                                                                                                                 >  1:685219/1‑149 (MQ=14)                           aCGCAACGCGCCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAG‑ACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGa                                                                                                                 <  2:881291/149‑1 (MQ=255)                             gctatgCGTCTTATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAG‑ACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAgg                                                                                                               >  2:678738/6‑149 (MQ=255)                                 ggCGTCGCATCCGACAACCGATGCCTGATGCGCCACTGACGCGACTTATCAGGCCTACGGGGTCAACTGAACTGTAGGTCGGATAAG‑ACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGacaa                                                                                                           <  1:833519/148‑1 (MQ=255)                                 aGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAG‑ACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATg                                                                                                                              <  1:526875/130‑1 (MQ=255)                                 aGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAG‑ACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATg                                                                                                                              >  2:526875/1‑130 (MQ=255)                                     tCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGCTAAG‑ACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGa                                                                                                                    <  2:753735/136‑1 (MQ=255)                                     tCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGCTAAG‑ACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGa                                                                                                                    >  1:753735/1‑136 (MQ=255)                                        cATCCGACAACCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAG‑ACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGAGc                                                                                                    <  1:752638/149‑1 (MQ=255)                                        cATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAG‑ACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGAGc                                                                                                    >  2:746611/1‑149 (MQ=255)                                          tCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAG‑ACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGAGCGa                                                                                                  <  2:602727/149‑1 (MQ=255)                                           ccgcgaaCCGATGCCTGATGCGCCGCTGACCCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGCTCGGATAAG‑ACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGAGCGac                                                                                                 <  2:808914/144‑1 (MQ=255)                                            cGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAG‑ACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGAGCGaca                                                                                                <  1:933519/149‑1 (MQ=255)                                                   cGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAG‑ACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGAGCGACACAACGAt                                                                                         <  1:678738/149‑1 (MQ=255)                                                          tGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGGTAAG‑ACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACaa                                                                                                                       >  1:504580/1‑112 (MQ=255)                                                          tGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAG‑ACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACaa                                                                                                                       <  2:504580/112‑1 (MQ=255)                                                                gccgcTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAG‑ACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGAGCGACAAAACGATCCTGCAAAACAGt                                                                            >  2:568935/1‑149 (MQ=255)                                                                 gcgcTGACGCGACTTATCAGGCGTACGGGGTGAACTGAACTGTAGGTCGGATAAG‑ACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGAGCGACACAACGATCCTGCAAAACAGTa                                                                           <  2:126027/148‑1 (MQ=255)                                                                   gcTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAG‑ACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGAGCGACACAACGATCCTGCAAAACAGTAcc                                                                         <  1:931129/149‑1 (MQ=255)                                                                          cgACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAG‑ACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGAGCGACACAACGATcc                                                                                       <  2:903548/128‑1 (MQ=255)                                                                          cgACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAG‑ACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGAGCGACACAACGATcc                                                                                       >  1:903548/1‑128 (MQ=255)                                                                            aCTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAG‑ACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACGTGGCCGACACAACGATCCTGCAAAACAGTACCCATGTCAtt                                                                <  2:630486/149‑1 (MQ=255)                                                                              ttATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAG‑ACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGAGCGACACAACGATCCTGCAAAACAGTACCCATGTCATTaa                                                              >  2:492661/1‑149 (MQ=255)                                                                                aTCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAG‑ACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGAGCGACACAACGATCCTGCAAAACAGTACCCATGTCATTAAAc                                                            <  2:278916/149‑1 (MQ=255)                                                                                       cTACGGGGTGAACTGAACTGTAGGTCGGCTAAG‑ACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGGGGGCCACACCGATCCTGCAGAAGATTCCCCATGCCATTAAAACCaaaca                                                     >  2:204961/1‑147 (MQ=25)                                                                                             gctgaactgaacTGTAAGCCGGATAAG‑ACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGAGCGACACAACGATCCTGCAAAACAGTACCCATGTCATTAAACCGAAAAAATCtgt                                               <  1:447442/147‑1 (MQ=255)                                                                                               tgaactgaacTGTAGGTCGGATAAG‑ACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGAGCGACACAACGATCCTGCAAAACAGTACCCATGTCATTAAACCGAAAAAATCTGTgg                                             <  2:22688/149‑1 (MQ=255)                                                                                                        gcgTAGGTCGGATAAG‑ACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGAGCGACACAACGATCCTGCAAAACAGTACCCATGTCATTAAACCGAAAAAATCTGTGGCACTTTCTg                                    <  1:448352/147‑1 (MQ=255)                                                                                                        ctgTAGGTCGGATAAG‑ACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGAGCGACACAACGATCCTGCAAAACAGTACCCATGTCATTAAACCGAAAAAATCTGTGGCACTTTCTg                                    <  2:491275/149‑1 (MQ=255)                                                                                                        ctgTAGGTCGGATAAG‑ACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGAGCGACACAACGATCCTGCAAAACAGTACCCATGTCATTAAACCGAAAAAATCTGTGGCACTTTCTg                                    >  1:491275/1‑149 (MQ=255)                                                                                                        ctgGAGGGCGGATAAG‑ACGCAGAGCGACGCACCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGAGCGACACAACGATCCTGCAAAACAGTACCCATGTCATTAAACCGAAAAAATCTGTGGCACTTTCTg                                    <  2:919231/149‑1 (MQ=255)                                                                                                          gTAGGTCGGATAAG‑ACGCATCGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGAGCGACACAACGATCCTGCAAAACAGTACCCATGTCATTAAACCGAAAAAATCTGTGGCACTTTCTGGc                                  <  1:303489/149‑1 (MQ=255)                                                                                                          gTAGGTCGGATAAG‑ACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGAGCGACACAACGATCCTGCAAAACAGTACCCATGTCATTAAACCGAAAAAATCTGTGGCACTTTCTGGc                                  <  2:295763/149‑1 (MQ=255)                                                                                                            aGGTCGGATAAG‑ACGCATAGCGTCGCAGCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGAGCGACACAACGATCCTGCAAAACAGTACCCATGTCATTAAACCGAAACAATCTGTGGCACTTTCTGGCGt                                <  2:932142/149‑1 (MQ=255)                                                                                                                   aTAAC‑ACGCATAGCGTCGCATCCGACAACAATCTCGACCCCACAAATGAGAAAAATGACGCGGACAACATGAGCGACACAACGATCCTGCAAAACAGTACCCATCGCATTAAACCGAAAGAATCTGTGACACTTTCTGTCGCTcctacg                         >  2:376583/1‑145 (MQ=255)                                                                                                                         aCGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGAGCGACACAACGATCCTGCAAAACAGTACCCATGTCATTAAACCGAAAAAATCTGTGGCCCTTTCTGGCGTTCCGGCGGGCaa                    >  2:49542/1‑149 (MQ=255)                                                                                                                         aCGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGAGCGACACAACGATCCTGCAAAACAGTACCCATGTCATTAAACCGAAAAAATCTGTGGCACTTTCTGGCGTTCCGGCGGGCaa                    >  1:383137/1‑149 (MQ=255)                                                                                                                           gCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGAGCGACACAACGATCCTGCAAAACAGTACCCATGTCATTAAACCGAAAAAATCTGTGGCACTTTCTGGCGTTCCGGCGGGCAATa                  <  1:65792/149‑1 (MQ=255)                                                                                                                             tgaGCGTCGGAGCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGAGCGACACAACGATCCTGCAAAACAGTACCCATGTCATTAAACCGAAAAAATCTGTGGCACTTTCTGGCGTTCCGGCGGGCAATACg                <  2:134390/147‑1 (MQ=255)                                                                                                                                gCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGAGCGACACAACAATCCTGCAAAACAGAACCCATGTCATTAAACCAAAAAAATCTGTGGCACTTTCTGGCGTTCCCGCGGGCAATACGgcg             >  2:200978/1‑149 (MQ=255)                                                                                                                                 cGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGAGCGACACAACGATCCTGCAAAACAGTACCCATGTCATTAAACCGAAAAAATCTGTGGCACTTTCTGGCGTTCCGGCGGGCAATACGgcgc            <  2:531970/149‑1 (MQ=255)                                                                                                                                           gACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGAGCAACACAACGATCCTGCAAAACAGTACCCATGTCATTAAACCGAAAAAATCTGTGGCACTTTCTGGCGTTCCGGCGGGCAATACGGCGCTCTGCACCGt  >  2:329326/1‑149 (MQ=255)                                                                                                                                                |                                                                                                                                                GTGCACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAG‑ACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGAGCGACACAACGATCCTGCAAAACAGTACCCATGTCATTAAACCGAAAAAATCTGTGGCACTTTCTGGCGTTCCGGCGGGCAATACGGCGCTCTGCACCGT  >  NC_000913_3_pae_tpiA/349830‑350115

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.