New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_vch_tpiA	3423376 =	50 (1.050)	7 (0.150)	5/282	6.3	12.1%	noncoding (3423376/4641682 nt)	repeat_region	repeat region
	?	NC_000913_3_vch_tpiA	= 4213192	52 (1.110)					noncoding (4213192/4641682 nt)	repeat_region	repeat region
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

AGCGGTCTGATAAAACAGAATTTGCCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGGCCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAGTTCTGTATATCCAAATTCGTCGTAATCAAATTACTGTTCGCGATCTTGAAAGCAAACGTGAAGTGTCAG  >  NC_000913_3_vch_tpiA/4213048‑4213339                                                                                                                                                 |                                                                                                                                                    aGCGGTCGGATAACACAGAAATTGCCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCTATGGCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCGTCAAATTa                                                                                                                                                 <  2:262060/149‑1 (MQ=11)     gTCTGATAAAACAGAATTTGCCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAAATCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGaaa                                                                                                                                             >  1:117575/1‑149 (MQ=21)        tGATAAAACAGAATTTGCCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGCAGTGAAACGCCGTAGCGCCGAAGGTAGTGTGGGGCCTCCCCATCCGAAAGAAGGGAACTGCCAGGCATCAAATTAGACAAAc                                                                                                                                          >  2:361899/1‑149 (MQ=11)         gATAAAACAGAATTTGCCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAAcc                                                                                                                                         >  2:783490/1‑149 (MQ=38)           tAAAACAGAATTGGCTTGGCGGAAGTAGCGCTGTGGTCCCACCGGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAAcccc                                                                                                                                       <  2:670803/149‑1 (MQ=14)           tAAAAAAGAATGTGCGCGGGGGCAGTAGCGCGGTGGTCCCATCTGACCCCATGCTGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAAcccc                                                                                                                                       <  2:6569/149‑1 (MQ=14)            aaaaCAGAATTTGCCGGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCg                                                                                                                                      <  2:136782/149‑1 (MQ=255)              aaCAGAATTTGCCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAGTTTAGAAAAACCCCGGt                                                                                                                                    >  1:20953/1‑149 (MQ=255)               aCAGAATTTGCCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTc                                                                                                                                   <  1:660256/149‑1 (MQ=255)                  gtaTTTGCCTGGCGGAAGTGGCGCGGTGAGCCCAGCTGACTCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTCTGGGGTCTCCCCATGCGACAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCAt                                                                                                                                <  2:131687/147‑1 (MQ=14)                  gAATTTGCCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCAt                                                                                                                                <  1:783490/149‑1 (MQ=255)                    agttGCCTGGCGGCAGTAGCGCGGGGGTCCCACCTGGCCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATaa                                                                                                                              <  2:168334/147‑1 (MQ=255)                         ccTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGGCCg                                                                                                                         <  2:696502/149‑1 (MQ=255)                          cTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGTCATCAAATTAGAAAAACCCCGGTCCATAAGGCCgg                                                                                                                        <  2:219090/149‑1 (MQ=255)                          cTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGGCCgg                                                                                                                        <  2:218919/149‑1 (MQ=255)                                    taggtgggtggcCCCACCTTGCCCCATGCCGAACTTAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGGCCGGGGTTTTTTGc                                                                                                              <  1:363674/143‑1 (MQ=18)                                      gcgcGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGGCCGGGGTTTTTTGCat                                                                                                            >  1:632286/1‑149 (MQ=255)                                      gcgcGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGGCCGGGGTTTTTTGCat                                                                                                            <  2:654479/149‑1 (MQ=255)                                               tCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGGCCGGGGTTTTTTGCCTATCAattat                                                                                                   >  1:653577/1‑149 (MQ=255)                                                     cTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGGCCGGGGTTTTTTGCATATCAATTATTTGCat                                                                                             >  2:145810/1‑149 (MQ=255)                                                          cccATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGGCCGGGGTTTTTTGCATATCAATTATTTGCAtgaaga                                                                                        >  2:824788/1‑149 (MQ=255)                                                                ccGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGGCCGGGGTTTTTTGCATATCAATTATTTGCATGATGACGGGaa                                                                                  >  1:256748/1‑149 (MQ=255)                                                                      tCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTcc                                                                                                                                  <  2:256916/95‑1 (MQ=255)                                                                      tCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTcc                                                                                                                                  >  1:256916/1‑95 (MQ=255)                                                                      tCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGGCCGGGGTTTTTTGCa                                                                                                             >  1:422597/1‑116 (MQ=255)                                                                      tCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGGCCGGGGTTTTTTGCa                                                                                                             <  2:422597/116‑1 (MQ=255)                                                                        aGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGGCCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGt                                                                          <  1:317435/149‑1 (MQ=255)                                                                        aGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGACGGGAACTGCCAGACATCAAATTAGAAAAACCCCGGTCCATAACGCCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAGACTCATGt                                                                          >  2:727810/1‑149 (MQ=25)                                                                          aaGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGGCCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCa                                                                        >  1:511583/1‑149 (MQ=255)                                                                            gTGAAACGCCGTAGCGCCGATGGTACTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAAACCATGACCATAAAACAGAACCGATACGGATATCAATTATTTGCATGATGAAGTGAATCTCATGTCAGt                                                                      <  1:830336/149‑1 (MQ=17)                                                                            gTGAAACGCCGTAGCGCCGATGGCAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGGCCGGGGGTTTTTGCAGATCAATTATTTGCATAATGAAGGGAATCCCATGTCAGt                                                                      >  2:825804/1‑149 (MQ=25)                                                                             tGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGGCCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAGtt                                                                     >  1:733097/1‑149 (MQ=255)                                                                                 aCGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGGCCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAGTTCTGt                                                                 <  1:297057/149‑1 (MQ=255)                                                                                  cGCCGGAGCACGGATGGTATTGTGGGGTCCCCGCATGCGAGAGTCGTGAACTGCCAGGCATCAATTTAGAAAAACCCCGGTCCATCAGGCCGGGGTTTTTTGCATATCAATTAGTTGCATGATGAAGGTAATCTCATTTCAGTTCTGta                                                                <  2:522527/149‑1 (MQ=255)                                                                                           gcCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGGCCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAGTTCTGta                                                                <  2:378886/140‑1 (MQ=255)                                                                                           gcCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGGCCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAGTTCTGta                                                                >  1:378886/1‑140 (MQ=255)                                                                                                   tAGTGTGGGGTCTCCCCATGCGAGACTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGGCCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAGTTCTGTATATCCAAATTCGTCGTa                                               >  1:764260/1‑149 (MQ=255)                                                                                                     gtgtGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGGCCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAGTTCTGTATATCCAAATTCGTCGTAAt                                             >  1:365315/1‑149 (MQ=255)                                                                                                      tgtgGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGGCCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAGTTCTGTATATCCAAATTCGTCGTAATc                                            >  1:171055/1‑149 (MQ=255)                                                                                                      tgggaggTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAGATTGGAACAACCCCGGTCCATAAGGCCGGGGTTTTTAGCATATCAATTATTTGAATGATGAAGGAAATCTCATGTCAGTACTGTATTTCCACATTCGCCGTAATc                                            >  2:85240/6‑149 (MQ=37)                                                                                                        tgGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGGCCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAGTTCTGTATATCCAAATTCGTCGTAAGCaa                                          >  1:473583/1‑149 (MQ=255)                                                                                                          gggTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCCTAAGGCCGGGGGTTTTTGCATATCAATACTTTGCATGCTGAAGGGACTCTGGTGTTCGTTCTGTATATCCAAATTCGTCGGAATCAAAt                                        >  1:369430/1‑149 (MQ=37)                                                                                                             tctcCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGGCCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAGtt                                                                     >  1:717122/1‑117 (MQ=255)                                                                                                             tctcCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGGCCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAGtt                                                                     <  2:717122/117‑1 (MQ=255)                                                                                                                 ccccTGCGCGTGTAGCGAACTGCCATGCCTCCACGTAGAAAAACCCCCGTCCATACGACCGGGATTTCGTGCATATCAAATATTTGCATGATGAAGGGAACATCATGTCAGTTCTGGATATCCTAATTCATCGTAATAAAATTACTgct                                 >  2:198160/1‑147 (MQ=255)                                                                                                                 cccATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCAAAAGGCCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAGTTCTGTATATCCAAATTCGTCGTAATCAAATTACTGtt                                 >  1:557566/1‑149 (MQ=255)                                                                                                                  ccATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGGCCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAGTTCTGTATATCCAAATTCGTCGTAATCAAATTACTGTTc                                >  2:83277/1‑149 (MQ=255)                                                                                                                    aTGCGAGAGTAGGGAACGGCCAGGCATTAAAGTAGAAAAACCCCGGTCCATAAGGCCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAGTTCTGTATATCCAAATTCGTCGTAATCAAATTACTGTTcgc                              <  2:157889/149‑1 (MQ=255)                                                                                                                              aGGGAACTGCCAGGCATCAAATTAAAAAAACCCCGGTCCATAAGGCCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAGTTCTGTATATCCAAATTCGTCGTAATCAAATTACTGTTCGCGATCTTGaaa                    <  2:789570/149‑1 (MQ=255)                                                                                                                               gggAACTGCCAGGCATCAAATTAGAAAAACCACGGTACTTAATGTCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAGTTCTGTATATCCAAATTCGTCGTAATCAAATTACTGTTCGCGATCTTAAAAg                   <  1:786944/149‑1 (MQ=255)                                                                                                                                ggAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGGCCGGGGTTTTTTGCATATCAATAATTTGCATGATGAAGGGAATCTCATGTCAGTTCTGTATATCCAAATTCGTCGTAATCAAATTACTGTTCGCGATCTTCAAAGc                  >  2:515498/1‑149 (MQ=255)                                                                                                                                                aaaTTAGAAAAACCCCGGTCCATAAGGCCGGGGTTTTTTGCATATCAACTCACTGCTTATTGTATGGAATCTCATGGCAGTTCTGTATATCCAAATTCGTCGTAATCAAATTACTGTTCGCTATCTTGAAAGCAAACGTGAAGTGTCAg  <  1:194440/149‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                    AGCGGTCTGATAAAACAGAATTTGCCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGGCCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAGTTCTGTATATCCAAATTCGTCGTAATCAAATTACTGTTCGCGATCTTGAAAGCAAACGTGAAGTGTCAG  >  NC_000913_3_vch_tpiA/4213048‑4213339

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.