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)	35 (1.110)	35/276	0.1	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

ACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATT  >  NC_000913_3_vch_tpiA/1300560‑1300830                                                                                                                                           |                                                                                                                                     tcagttagttataagtatttccttatctgcttctcctcactatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCaa                                                                                                                            <  2:130360‑M2/11‑1 (MQ=255)  cagttagttataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAAt                                                                                                                           <  1:314156‑M2/12‑1 (MQ=255)       agttataaggatttccttaactgcttctcctcaccatcatgttattttctccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTa                                                                                                                      <  2:162098‑M2/17‑1 (MQ=255)               ggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATtg                                                                                                              >  1:477122‑M2/125‑149 (MQ=255)                gatttccttaactgcttttcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATtgt                                                                                                             <  1:158829‑M2/26‑1 (MQ=255)                   ttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCa                                                                                                          <  2:27567‑M2/29‑1 (MQ=255)                                   cctcacctgtatgttagtttcgctacatcataagcctgggcgtgctgaaggataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACt                                                                                          <  2:211224‑M2/45‑1 (MQ=255)                                     tcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGt                                                                                        >  2:91025‑M2/103‑149 (MQ=255)                                         catcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCCCTACTTGAACTGTAATc                                                                                    >  2:399602‑M2/99‑149 (MQ=255)                                                   ttttcgccatatcatattccttggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATa                                                                          <  2:42791‑M2/61‑1 (MQ=255)                                                     ttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGa                                                                        <  1:493162‑M2/63‑1 (MQ=255)                                                         ccacatcatacgcctgggctttctgaagagtaattgcaatgatattattaattccactgcctttgtgagaggaaagtgcgaaATAATAATCAATTGTTAAATTATTGTTCATTTCACGACTGGAACTGTAATCAGAAAAGATAGACATg                                                                    <  2:389554‑M2/67‑1 (MQ=255)                                                          cacatcacaatcctgggcttgctgaagaataattgaaatgatattgttaattgcgctgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGc                                                                   <  1:444159‑M2/68‑1 (MQ=255)                                                                 taatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaata                                                                                                                                    >  1:540523‑M2/75‑77 (MQ=255)                                                                 taatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaata                                                                                                                                    <  2:540523‑M2/3‑1 (MQ=255)                                                                            ttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATttg                                                 >  2:385200‑M2/64‑149 (MQ=255)                                                                             tgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATttga                                                <  1:272164‑M2/87‑1 (MQ=255)                                                                                 gaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATttgattga                                            >  1:150967‑M2/59‑149 (MQ=255)                                                                                    gaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGattgaatt                                         <  2:150967‑M2/94‑1 (MQ=255)                                                                                     aataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGattgaattg                                        <  2:477122‑M2/95‑1 (MQ=255)                                                                                            gaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGAtg                                 >  2:245872‑M2/48‑149 (MQ=255)                                                                                              aatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATATCTATTTGATTGAATTGAAAGAtgtt                               >  2:324956‑M2/46‑149 (MQ=255)                                                                                               atgagattagtaattccaatgcctgtgggagaggaaagtgctaaAGTATAAGCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACCGGCTTAGCCAATCTCTATTTGATTGAATTGAAAGAtggtt                              <  2:202707‑M2/105‑1 (MQ=255)                                                                                                tgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCAAATCTCTATTTGATTGAATTAAAAGCggtttg                             >  2:355286‑M2/44‑149 (MQ=255)                                                                                                  atattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTTAAAGAtttttgtt                           >  2:22096‑M2/42‑149 (MQ=255)                                                                                                   tattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTa                          >  1:224852‑M2/41‑149 (MQ=255)                                                                                                        ttaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCa                     >  2:473339‑M2/36‑149 (MQ=255)                                                                                                         taattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCAt                    >  1:260919‑M2/35‑149 (MQ=255)                                                                                                          aattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATg                   <  2:260919‑M2/116‑1 (MQ=255)                                                                                                                 ctgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCaa            <  1:91025‑M2/123‑1 (MQ=255)                                                                                                                      tttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCtat       >  1:237936‑M2/22‑149 (MQ=255)                                                                                                                         ggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGACCTGTAATCCGAAAAGAGAGACACGCTTTGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTACGGCATGGATGCAAGCTATAGa    <  2:291675‑M2/131‑1 (MQ=255)                                                                                                                           tagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGAtt  >  1:13815‑M2/17‑149 (MQ=255)                                                                                                                            agaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAAt                                                                                     >  2:395497‑M2/16‑65 (MQ=255)                                                                                                                            agaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAAt                                                                                     <  1:395497‑M2/50‑1 (MQ=255)                                                                                                                                          aATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGAtt  <  1:363530‑M2/133‑1 (MQ=255)                                                                                                                                          aATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGAtt  >  2:363530‑M2/2‑134 (MQ=255)                                                                                                                                           |                                                                                                                                     ACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATT  >  NC_000913_3_vch_tpiA/1300560‑1300830

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ 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.