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)	42 (1.340)	39/274	0.0	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

GGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACG  >  NC_000913_3_vch_tpiA/1300553‑1300838                                                                                                                                                  |                                                                                                                                             tcaaattacagttagttataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaataa                                                                                                                                           >  2:353308‑M2/146‑149 (MQ=255) tcaaattaaagttagttaaaaggatttccttaactgcttctcctcaccatcatgttattttcgccaaatcataatcctgggcttgctgaaaaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaataa                                                                                                                                           <  1:270006‑M2/4‑1 (MQ=255)  caaattacagttagttataaggatttccttaactgcttctcctcaccaacatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattcaactgcctttggtagaggaaagtgctgaataat                                                                                                                                          >  1:26108‑M2/145‑149 (MQ=255)   aaattacagttatttataaggatttccttaactgcttctcttgagcatcatgttattttcgccacgtcataatcctgggcttgctgaagaatacttgaaatgatattattaattccactgcctttggtgggggaaggtgttaaataata                                                                                                                                         <  2:452602‑M2/6‑1 (MQ=255)     attacagttagttataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtacaaaataataat                                                                                                                                       >  2:268918‑M2/142‑149 (MQ=255)          agttagttataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAAtt                                                                                                                                  <  1:557404‑M2/13‑1 (MQ=255)                   taaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAatta                                                                                                                         >  1:488533‑M2/128‑149 (MQ=255)                       tatttcctttactccttctcgcctccatcctgttattctcgacacatcataatccttcgcttgctgaagcataattgaactgatattattaattccactgcctttggtagaggaaagcgttaaATAATAATCAATTGTTAAATTATtgt                                                                                                                     <  2:315148‑M2/26‑1 (MQ=255)                             cttaactgcttctccttaccatcatgttattttcgccacatcataatcctgggtttgatgaagaataattgaaattatattattggtcccattacttttggtagaggtaagtggtaaATAATAATCAATTGTTAAATTATTATGAAttt                                                                                                               >  2:249941‑M2/118‑149 (MQ=255)                                     cttcttctcaccatcattttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTg                                                                                                       <  1:333893‑M2/40‑1 (MQ=255)                                        ctcttcaccatcattttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGaa                                                                                                    <  1:419074‑M2/43‑1 (MQ=255)                                        ctccccaccatcatgttattttcgcaacatcataatcctgggcttgctgaagaataattgaaattatattattaattccactgccttttgtagaggaatgtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGaa                                                                                                    <  1:227945‑M2/43‑1 (MQ=255)                                         tcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagagtaaagggcgaaATAATAATCAATTGTTAAATTAATGTGCATTTCACTAATCGAAc                                                                                                   >  1:150270‑M2/106‑149 (MQ=255)                                             caccatcatgttattttcgccacatcataatcatgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTa                                                                                               <  2:262843‑M2/48‑1 (MQ=255)                                               acatcatgttattttcgcaacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTCCATTTCACTACTGGAACTGTAAt                                                                                             <  2:305797‑M2/50‑1 (MQ=255)                                                catcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGTATTTCACTACTGGAACTGTAATc                                                                                            >  1:192982‑M2/99‑149 (MQ=255)                                                 atcatgttatcttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCa                                                                                           >  1:393966‑M2/98‑149 (MQ=255)                                                      gtgtttttcgccacatcatgatcctgggtttgctgaagaataattgaaatgatattattaattccactgcctttggtggaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGaaaa                                                                                      <  2:472201‑M2/57‑1 (MQ=255)                                                                 tacatgataacactgggcttgctgaataataattgaaatgatattatgaattcaactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAACATAGACATGc                                                                           <  2:53567‑M2/68‑1 (MQ=255)                                                                   catcataatcctgggcttgctgaagaatcattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCtt                                                                         >  1:142479‑M2/80‑149 (MQ=255)                                                                        taatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCa                                                                    >  2:526766‑M2/75‑149 (MQ=255)                                                                                  cttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTAttt                                                          <  1:353308‑M2/85‑1 (MQ=255)                                                                                      ctgaagaataattgaaatgatattattaattccactgcctttggtaaagaaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATttgatt                                                      >  1:239499‑M2/61‑149 (MQ=255)                                                                                       tgaagaataattgaaatgatattattaattccactgccttaggtagaggaaagtgctaaTTAATAATCAATTGTTAAATTATTGTGCATTTAACTACTGGAACTGTAATCAGAAAAGATAGACATGCATAGCCAATCAATATatgattg                                                     >  2:414884‑M2/60‑149 (MQ=255)                                                                                        gaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCa                                                                                           <  2:88812‑M2/52‑1 (MQ=255)                                                                                        gaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCa                                                                                           >  1:88812‑M2/59‑110 (MQ=255)                                                                                                 ttgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCACTTGTTAAATTATTATGCATTTCACTACTGGAACCGTAATCCAAAAAGAAAGAAATGCTTAGCCAATCTCTATTTGATGAAATTGAACGa                                           >  2:37471‑M2/50‑149 (MQ=255)                                                                                                     aatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGAtgtt                                       <  1:284064‑M2/104‑1 (MQ=255)                                                                                                      atgatagtattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTATTCATAAAAGATAGACATGCTTAGTCAATCTCTATTTGATTGAATTGAAAGAtgttt                                      <  1:270114‑M2/105‑1 (MQ=255)                                                                                                            ttattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAAt                                                                                             >  2:548917‑M2/39‑88 (MQ=255)                                                                                                            ttattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAAt                                                                                             <  1:548917‑M2/50‑1 (MQ=255)                                                                                                            ttattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAg                                <  1:526766‑M2/111‑1 (MQ=255)                                                                                                             tattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAgg                               >  1:99878‑M2/38‑149 (MQ=255)                                                                                                               ttaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGc                              >  2:26716‑M2/36‑148 (MQ=255)                                                                                                               ttaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGc                              <  1:26716‑M2/113‑1 (MQ=255)                                                                                                               ttaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCa                             >  1:454574‑M2/36‑149 (MQ=255)                                                                                                                taattccactgccttttgtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCCGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGCTTGTTCAGGCAt                            <  2:538847‑M2/115‑1 (MQ=255)                                                                                                                  attccactgcctttggtagaggaaagtgctaaATAATAATCAATTATTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATgg                          >  1:181843‑M2/33‑149 (MQ=255)                                                                                                                       actgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATACTTAGCCAATTTCTATTTGATTTAATTGAAGAATGTTTGTTAAGCGAGGGATgct                     >  2:223970‑M2/28‑148 (MQ=255)                                                                                                                             tttggtagaggaaatggataaATAATAATTANTTGTTAAAGTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATTCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCtat               <  2:150270‑M2/128‑1 (MQ=255)                                                                                                                                        aaagtgctaaATAATAATCTATTGTTCTATTATTGTGTATTTCATTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATa    >  1:256075‑M2/11‑149 (MQ=255)                                                                                                                                          agtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACg  <  2:488533‑M2/141‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                             GGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACG  >  NC_000913_3_vch_tpiA/1300553‑1300838

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ 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.