New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_hsa_tpiA	3216668 =	45 (1.390)	3 (0.100)	3/262	NT	7.1%	noncoding (68/78 nt)	REP228 (repetitive extragenic palindromic) element; contains 2 REP sequences	REP228 (repetitive extragenic palindromic) element; contains 2 REP sequences
	?	NC_000913_3_hsa_tpiA	= 4614265	36 (1.170)					noncoding (27/388 nt)	REP352 (repetitive extragenic palindromic) element; contains 8 REP sequences	REP352 (repetitive extragenic palindromic) element; contains 8 REP sequences

TATATCTAAATAAAACTCGCAAATGATAATGATTGTTAATCATGATAAATGCAAGCGATTTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATGAGCCATCATCACGAAGGGTGTTGTAAACATGAAG  >  NC_000913_3_hsa_tpiA/3216520‑3216815                                                                                                                                                     |                                                                                                                                                    agcctaaccgcccggagcaggctgcccgtgtgttcgccgtgctttgcgagttgcgccgggaaccggcggatgagattgcgcaagcgttgcttaataacacgtatacgttgtttaccgtgccgtaggccggataaggcgttcccgccgca                                                                                                                                                     <  2:589413‑M1/1‑1 (MQ=255)    acttaaataacACTCGCACATGTTAGTGCGTTTTCATGATGATAAACGCAAGTGACTTGTAGATCTGATATGTCTATAGTCTATTAAGATGAACCGCCTCTTCTCAGCCATCATTACTCAACGTCGGATGCGGCGTGAACGCCTTATcc                                                                                                                                                  <  2:1149/146‑1 (MQ=255)     taaccgcccggagcaggctgcccgtgtgttcgccgtgctttgcgcgttgcgccgggaaccggcgggagagattgcgcaagcgttgcttaataaaacgtataagttgtttaacgtgtcgtaggccggataatgcgttcacgccgcATCCg                                                                                                                                                 <  2:375158‑M1/5‑1 (MQ=255)     taaccgcccggagcaggctgcccgtgtgttcgccgtgctttgcgagttgcgccgggaaccggcggatgagattgcgcaagcgttgcttaataacacgtatacgttgtttaacgtgccgtaggccggataaggcgttcacgccgcATCCg                                                                                                                                                 <  2:528314‑M1/5‑1 (MQ=255)     tCTAAATAAAACTCGCAAATGATAATGATTGTTAATCATGATAAATGCAAGCGATTTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCGGATGCGGCGTGACCCCCTTATCCg                                                                                                                                                 >  2:28261/1‑149 (MQ=255)      cTAAATAAAACTCGCAAATGATAATGATTGTTAATCATGATAAATGCAAGCGATTTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCGGATGCGGCGTGAACGCCTTATCCgg                                                                                                                                                <  1:40414/149‑1 (MQ=255)        ccgcccggagcaggctgcccgtgtgttcgccgtgctttgcgagttgcgccgggaaccggcggatgagattgcgcaagcgttgcttaataacacgtatacgttgtttaacgtgccgtaggccggataaggcgttcccgccgcATCCGGcc                                                                                                                                              <  2:485972‑M1/8‑1 (MQ=255)         aataaaACTCGCAAATGATAATGATTGTTAATCATGATAAATGCAAGCGATTTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCGGATGCGGCGTGACCGCCTTATCCGGcca                                                                                                                                             >  1:133787/1‑148 (MQ=255)         aataaaACTCGCAAATGATAATGATTGTTAATCATGATAAATGCAAGCGATTTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCGGATGCGGCGTGAACGCCTTATCCAGCCt                                                                                                                                             >  1:515753/1‑149 (MQ=255)                cTCGCAAATGATAATGATTGTTAATCATGATAAATGCAAGCGATTTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGtgtg                                                                                                                                      >  1:303860/1‑149 (MQ=255)                 tCGCAAATGATAATGCTTGTTAATCATGATAAATGCAAGCGATTTGTAGAACTGAAATGTCCATAATCTAATAAGACGAAAAACCTCTTCTCCGGCCTCATTACTAAACGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTGTga                                                                                                                                     >  2:428612/1‑149 (MQ=37)                 tCGCAAATGATAATGATTGTTAATCATGATAAATGCAAGCGATTTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCGGATGCGGCGTGACCGCCTTATCCGGCCTCCGTGTga                                                                                                                                     >  2:168715/1‑149 (MQ=255)                  cGCAAATGATAATGATTGTTAATCATGATAAATGCAAGCGATTTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCGGATGCGGCGTGAACGCCTTATCCGGCCTActcgagag                                                                                                                                    >  1:263866/1‑142 (MQ=255)                  cGCAAATGATAATGATTGTTAATCATGATAAATGCAAGCGATTTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGtgtgcg                                                                                                                                    >  1:437372/1‑147 (MQ=255)                  cGCAAAGGATAATGATTGTTAATCATGATAAATGCAAGCGATTTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCGCCCCTTCTCAGGCATCATTACTCAACGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTGTgag                                                                                                                                    <  2:394390/149‑1 (MQ=255)                   gCAAATGATAATGATTGTTAATCATGATAAATGCAAGCGATTTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCGCCGCTTTTCAGGCATCATTACGTAACGCCGGATGCGGCGTGAACGCCTTATACGGCCTACATGTggga                                                                                                                                   >  2:281797/1‑149 (MQ=39)                      aatgataattatTGTTAATCATGATAAATGCAAGCGATTTGTAGAACTGATATGTCGATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTGTGAGATGa                                                                                                                                <  1:579059/149‑1 (MQ=255)                         gataatgatTGTTAATCATGATAAATGCAAGCGATTTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTGTGAGGTGAGTc                                                                                                                             >  1:382706/1‑149 (MQ=255)                               gatTGTTAATCATGATAAATGCAAGCGATTTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTGTGAAATGAGTCCACGtt                                                                                                                       >  2:145008/1‑149 (MQ=255)                                     tAATCATGATAAATGCAAGCGATTTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTGTGAGATGAGTCCACGTTTaaaaa                                                                                                                 <  1:613437/149‑1 (MQ=255)                                          aTGATAAATGCAAGCGATTTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTGTGAGATGAGTCCACGTTTAAAAATCAtt                                                                                                            <  1:21483/149‑1 (MQ=255)                                                aaTGCAAGCGATGTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTaca                                                                                                      <  2:462216/149‑1 (MQ=255)                                                                 gAACTGATATGTCTTTAGTCTGATGAGACGAACCGACTCTTCTCAGGCATCATTACTCAACGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTGTGAGATGAGTCCAAGTATAAAAATAATTTTTACACTTGCGAGAACGCTcct                                                                                     >  1:533267/1‑147 (MQ=38)                                                                 gAACTGATATGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCat                                                                                     >  1:308314/1‑149 (MQ=255)                                                                 cgaCTGGTAGGTCTGTGGTCGGGTAAGACGAACCGCCTTTGCTCAGGCATCATTACTCAACGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCat                                                                                     <  1:378362/147‑1 (MQ=38)                                                                     tGATATGTCTATAGTCTGATAAGGCGAACCGCCTCTTCTCCGGCTTCATTACTCAACGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCa                                                                                 <  1:478746/149‑1 (MQ=255)                                                                       atatGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGa                                                                               <  1:219749/149‑1 (MQ=255)                                                                        tatGGCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGat                                                                              <  2:222094/149‑1 (MQ=255)                                                                              tataGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAAt                                                                        <  1:357351/149‑1 (MQ=255)                                                                                  gTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTGTGAGATGAGTCCACGTTTAAACATCATTTTTACACCTGCAAGAACGCTCATATCCGCGATaaactgga                                                                    >  2:272099/1‑144 (MQ=39)                                                                                  gTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGa                                                                    <  1:440212/149‑1 (MQ=255)                                                                                       aTAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGatatat                                                               >  2:462138/1‑149 (MQ=255)                                                                                       aTAAAACGAACCGCCTCGTCTCAGAGATCACTACTCAACGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTGTGAGATAAAAAAAAAAAAAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGatatat                                                               <  2:112817/149‑1 (MQ=25)                                                                                           gACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTaa                                                           >  2:508430/1‑149 (MQ=255)                                                                                               aaCCGCCTCTTCTCATGCATCAGTACTCAACGCCGTATGCGGCGTCAACGCCTTAGCCTGCCTACGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTaa                                                       <  1:278944/149‑1 (MQ=255)                                                                                                aCCGCCTCTTCTCAGGCATCATTACTCAACGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTGTGAGATGAGTCCACGTTTAAAAATCATGTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAg                                                      >  1:591940/1‑149 (MQ=255)                                                                                                 ccGCCTCTTCTCAAGCATCATTACTCAACGCCGGATGCGACGTGAACGCCTTATCCGGCCTACGTGTGAGATAAGTCCACGTTGAAAAATCATTTTTACACTTGCAAGAACGCACAAATCAGATATAAATTGCATATATCTCAtcaggc                                                     >  2:274460/1‑144 (MQ=255)                                                                                                        ttctCAGGCATCATTACTCAACGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAagga                                              <  2:66188/149‑1 (MQ=255)                                                                                                         tcgcAGGCAGCATTACTCAACGGCGGATGCGGCGGGAACGCCTTATCCGGCCTACGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCCCATATCAGATATAAATTAGATATATCTAATTAAGCAAAaggag                                             <  2:378298/146‑1 (MQ=255)                                                                                                                   catTACTCAACGCCGGATGCGGCGTGCATTATTTATCCTTCCTACGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATGa                                   <  2:590350/149‑1 (MQ=255)                                                                                                                   catTACTCAACGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATGa                                   <  1:117959/149‑1 (MQ=255)                                                                                                                   catCACTCAACGCCGGATGAGGCGTGAACGTCCTATCCGGCCAACGTGTGAGATGAGACCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAAGTAAGCAAAAGGAGGCTGATATGa                                   <  1:180409/149‑1 (MQ=255)                                                                                                                    atTACTCAACGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATGAg                                  <  1:360953/149‑1 (MQ=255)                                                                                                                         tCAACGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATGAGCcatc                             >  1:27285/1‑149 (MQ=255)                                                                                                                         tCAACGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTGTGAGATGAGTCAACGTTTAAGAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAAAGAGACTGATATGAGCcatc                             >  1:359946/1‑149 (MQ=255)                                                                                                                            aCGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATGAGCCatcatc                          <  1:314727/149‑1 (MQ=255)                                                                                                                              gccggataaggcgttcacgccgcATCCGGCCTACGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAACAGGAGGCTGATATAAACAAACATCAc                        <  2:581929‑M1/126‑1 (MQ=255)                                                                                                                              gCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATGAGCCATCATCAc                        <  1:420910/149‑1 (MQ=255)                                                                                                                                 ggataaggcgttcacgccgcATCCGGCCTACGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAAtt                                                                       >  2:132614‑M1/21‑99 (MQ=255)                                                                                                                                 ggataaggcgttcacgccgcATCCGGCCTACGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAAtt                                                                       <  1:132614‑M1/79‑1 (MQ=255)                                                                                                                                 ggATGCGGCGTGAACGCCTTATCCGGCCTACGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATGAGCCATCATCACGaa                     <  1:285910/149‑1 (MQ=255)                                                                                                                                        gggTGAACGCCTTATCCGGCCTAAGTGTGAGATGAGTCAACTTTTAAAAACTATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATGAGCCATCATCACGAAGGGtgtt              <  1:113781/147‑1 (MQ=255)                                                                                                                                        ccgTGAACGCTTTACACGGCTTACGTGTGAGATGAGTCCACGTTTAAAGATCATTTTTACACTTGCACGAACGCGCATAACAGGTATAGATTAGATATATCTAATTAAGCAAAAGTAGGCTGATATGCGCCACCAGGACGAACGgcgta              <  2:161860/148‑2 (MQ=255)                                                                                                                                         cgTGAACGCCTTATCCGGCCTACGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTACCCTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTCAGCAAAAGGAGGCTGATATGAGCCATCATCACGAAGGGtgttg             >  2:40076/1‑149 (MQ=255)                                                                                                                                                 ccTTATCCGGCCTACGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATGAGCCATCATCACGAAGGGTGTTGTAAACATg     >  2:310429/1‑149 (MQ=255)                                                                                                                                                 ccTCATCCTGCACACGTGAGAAAATAGTCCACGATTAAAAATCATTTTTACACTTGCAAGAACGCTCATAACAGATATAAACTAGACAAAACCAAATAAGCAAAAGGACGCTAATATGAGCCATCATCACCAAGTGTGTTGTAAACATg     <  2:34016/149‑1 (MQ=255)                                                                                                                                                   ttATCCGAGCTACGTGTGAGATGAGACCATGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATGAGCCATCATCACGAAGGGTGTTGTAAACATGaa   <  2:426967/149‑1 (MQ=255)                                                                                                                                                    tATCCGGCCTACGTGTGAGATGAGTCCACGTTTAATAATCATTTTGACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATGAGCCATCATCACGAAGGGTGTTGTAAACATGAAg  <  1:15512/149‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                    TATATCTAAATAAAACTCGCAAATGATAATGATTGTTAATCATGATAAATGCAAGCGATTTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTGTGAGATGAGTCCACGTTTAAAAATCATTTTTACACTTGCAAGAACGCTCATATCAGATATAAATTAGATATATCTAATTAAGCAAAAGGAGGCTGATATGAGCCATCATCACGAAGGGTGTTGTAAACATGAAG  >  NC_000913_3_hsa_tpiA/3216520‑3216815

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ 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.