New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_vch_tpiA	= 1299498	0 (0.000)	40 (1.080)	33/276	0.2	100%	noncoding (1299498/4641682 nt)	repeat_region	repeat region
	?	NC_000913_3_vch_tpiA	1300698 =	0 (0.000)					noncoding (1300698/4641682 nt)	repeat_region	repeat region

CAAATTACAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTCCCG  >  NC_000913_3_vch_tpiA/1299355‑1299646                                                                                                                                                |                                                                                                                                                     tgaattACAGTTAGTTATAAGGATTTCCTTAACTGCTTATCCTTACCATCATGTTATTTTCGCCACCTCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataat                                                                                                                                                 <  2:580262‑M1/147‑6 (MQ=255)   aaTTACAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGTTAAataataa                                                                                                                                               <  1:656214‑M1/149‑8 (MQ=255)     ttACAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatc                                                                                                                                             <  1:331352‑M1/149‑10 (MQ=255)                          tCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcat                                                                                                                        >  1:592130‑M1/1‑119 (MQ=255)                             tcaatgtcttctcctCTCCATGATGTTATTTTCGCCACATCATAATTCTGGGCTTTCTGAAGAATAATTGAAATGATATTCTTAATCCCTCTGTCTTTTGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttc                                                                                                                     <  2:378032‑M1/142‑34 (MQ=255)                               aaCTGCGTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcac                                                                                                                   <  1:670293‑M1/149‑36 (MQ=255)                                 cTGTTTCTCCTTAGCCTCATGTTATTTTCGCTCCATCATAATCCGTGGCTTGCTGATGTATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAttaataatccattgttaaattattgtgcatttcacta                                                                                                                 <  2:16940‑M1/149‑38 (MQ=255)                                    cTTCTCCTCTCCAGCATGTTATTCTCGCCACATCATAATCCTGGTCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGTGAGAGGAAAGTGCTAAacaataatcgattgttaaattattgtgcatttcactactg                                                                                                              <  2:9992‑M1/149‑41 (MQ=255)                                    cTTCTCCTCACCATCATGTTATTTTCGCCAGATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactg                                                                                                              <  2:307251‑M1/149‑41 (MQ=255)                                       ctcctcACCGGCAGGTGAGTTGCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAAGTCCACTGCCTTTGGGAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaa                                                                                                           <  2:536670‑M1/149‑44 (MQ=255)                                               catcatGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattttgcatttcaccactggaactgtaatc                                                                                                   >  2:355190‑M1/1‑98 (MQ=255)                                                 tcatGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcag                                                                                                 >  2:667204‑M1/1‑96 (MQ=255)                                                    tGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaa                                                                                              <  1:173918‑M1/149‑57 (MQ=255)                                                         ttttCGCCACATCATAAGTCTTGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagata                                                                                         <  2:52548‑M1/149‑62 (MQ=255)                                                             cGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagaca                                                                                     <  1:143527‑M1/149‑66 (MQ=255)                                                                cacaTCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgc                                                                                  >  1:395449‑M1/1‑81 (MQ=255)                                                                 acaTCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgct                                                                                 >  1:216725‑M1/1‑80 (MQ=255)                                                                   atcatGATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattattaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgctta                                                                               >  1:639146‑M1/1‑78 (MQ=255)                                                                   atcatAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagataaacgtgctta                                                                               >  2:476522‑M1/1‑78 (MQ=255)                                                                   atcatAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactataatcagaaaagatagacatgcttc                                                                               >  2:644465‑M1/1‑78 (MQ=255)                                                                                      tGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagataagatagacatgcttagccaatctctatttgattg                                                            >  1:587820‑M1/1‑59 (MQ=255)                                                                                          gaaTAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaatt                                                        <  1:674019‑M1/149‑95 (MQ=255)                                                                                                ttGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagc                                                  >  2:652379‑M1/1‑49 (MQ=255)                                                                                                ttGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaaga                                                  >  1:399077‑M1/1‑49 (MQ=255)                                                                                                ttGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaaga                                                  >  1:29790‑M1/1‑49 (MQ=255)                                                                                                     attatattatTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgttt                                             <  1:196082‑M1/146‑106 (MQ=255)                                                                                                        atatTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaa                                                                                                           >  1:452093‑M1/1‑41 (MQ=255)                                                                                                        atatTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaa                                                                                                           <  2:452093‑M1/84‑44 (MQ=255)                                                                                                           ttagtaATTCCACTGCCTGTGGTTAAGTAAATTTCTTAataataatcaattgttaaattattgtgcatttcactattttaactgtaatcagaaaacatagacatgctcagccaatctctatttgagtgaattgaaagatgtttgttaag                                       <  2:186678‑M1/149‑112 (MQ=255)                                                                                                                      aCTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgca                            <  1:465760‑M1/149‑123 (MQ=255)                                                                                                                        tGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaag                          >  2:125138‑M1/1‑25 (MQ=255)                                                                                                                         gCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagc                         <  1:125138‑M1/149‑126 (MQ=255)                                                                                                                           cTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgctta                                                                               <  2:531510‑M1/93‑72 (MQ=255)                                                                                                                           cTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgctta                                                                               >  1:531510‑M1/1‑22 (MQ=255)                                                                                                                            tttGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgttt                                             >  2:58739‑M1/1‑21 (MQ=255)                                                                                                                            tttGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgttt                                             <  1:58739‑M1/126‑106 (MQ=255)                                                                                                                                   gagGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagattct               <  2:196983‑M1/149‑136 (MQ=255)                                                                                                                                        aaGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagattctgatac          >  2:358125‑M1/1‑9 (MQ=255)                                                                                                                                          gTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagattctgatacgg        <  2:206320‑M1/149‑143 (MQ=255)                                                                                                                                           tGCTAAataataatcaattgttaaattatggtgcatttcactactggaactgtaatcagaaaagatcgacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatatattctgatacggt       >  1:251861‑M1/1‑6 (MQ=255)                                                                                                                                             cTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgaatgaattgaaagatgtttgttaaggcatggatgcaagctatagattctgatacggtca     >  2:243919‑M1/1‑4 (MQ=255)                                                                                                                                                aataataatcaattgttaagttattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagacaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagatatagattctgatacggtcaata  >  2:569793‑M1/1‑1 (MQ=255)                                                                                                                                                |                                                                                                                                                     CAAATTACAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTCCCG  >  NC_000913_3_vch_tpiA/1299355‑1299646

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.