New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_vch_tpiA	59280 =	35 (1.080)	9 (0.320)	5/248	3.3	24.1%	noncoding (59280/4641682 nt)	repeat_region	repeat region
	?	NC_000913_3_vch_tpiA	59320 =	26 (0.920)					noncoding (59320/4641682 nt)	repeat_region	repeat region
Rejected: Coverage evenness skew score above cutoff.

TACCTCCTTATATGATGAGGTAATTATTATTAATAAAATCCCCCCCAAAAAAATTGATACTAAAGGAGTTGCTACTGAAGAAGTTGCTACTAAAAAAGTACTGCTGAACAAATTACTGACAACGCAATTATTGAATGAGCCAGAATAAGCTAAGGTTGAAGGGGCTGGAACGCCCCTTCAACCTTAGCAGTAGCGTGGGATGATTTCACAATTAGAAAGACCTGCATGATGAGCTAGAGAAGAGGCTAGTGACGCAAGGCGTCGTGCAGGACACGGATCACCGAGATGGGCAT  >  NC_000913_3_vch_tpiA/59132‑59424                                                                                                                                                     |                                                                                                                                                 tACCTCCTTATATGATGAGGTAATTATTATTAATAAAATCCCCCCCAAAAAAATTGATACTAAAGGAGTTGCTACTGAAGAAGTTGCTACTAAAAAAGCACTGCTGAACAAATTACTGACAACGCAATTATTGAATGAGCCAGAATAAg                                                                                                                                                  <  2:2578/149‑1 (MQ=255)       ctTATATGATGAGGTAATTATTATTAATAAAATCCCCCCCAAAAAAATTGATACTAAAGGAGTTGCTACTGAAGAAGTTGCTACTAAAAAAGTACTGCTGAACAAATTACTGACAACGCAATTATTGAATGAGCCAGAATAAGCTAAgg                                                                                                                                            >  2:193798/1‑149 (MQ=255)            atgatgAGGTAATTATTATTAATAAAATCCCCCCGAAAAAAATTGATACTAAAGGCGTTGCTATTGAAGAACTTGCTAATTAAAAAGTACTGCTGAACAAATTACTGACAACGCAATTATTGAATGAGCCAGAATAAGCTAAGGTTGaa                                                                                                                                       <  1:512737/149‑1 (MQ=255)              gatgaGGTAATTATTATTAATAAAATCCCCCCCAAAAAAATTGATACTAAAGGAGTTGCTACTGAAGAAGTTGCTACTAAAAAAGTACTGCTGAACAAATTACTGACAACGCAATTATTGAATGAGCCAGAATAAg                                                                                                                                                  <  1:236756/136‑1 (MQ=255)              gatgaGGTAATTATTATTAATAAAATCCCCCCCAAAAAAATTGATACTAAAGGAGTTGCTACTGAAGAAGTTGCTACTAAAAAAGTACTGCTGAACAAATTACTGACAACGCAATTATTGAATGAGCCACAATAAg                                                                                                                                                  >  2:236756/1‑136 (MQ=255)                 gatgTAATTATTATTAATAAAATCCCCCCCAAAAAAATTGATACTAAAGTAGTTGCTACTGAAGAAGTTGCTACTAAAAAAGTACTGCTGAACAAATTACTGACAACGCAATTATTGAATGCGCCAGCCCTACCTGAGGTTGAAGGGGc                                                                                                                                  <  2:500206/146‑1 (MQ=255)                  aGGTAATTATTATTAATAAAATCCCCCCCAAAAAAATTGATACTAAAGGAGTTGCTACTGAAGAAGTTGCTACTAAAAAAGTACTGCTGAACAAATTACTGACAACGCAATTATTGAATGAGCCAGAATAAGCTAAGGTTGAAGGGGCt                                                                                                                                 >  1:457498/1‑149 (MQ=255)                       attattattAATAAAATCCCCCCCAAAAACACTGATACTAAAGGAGTTGCTACTGAAGAACGTGCTACTAAAAAAGTACTACTGAACAAACTACTGACTACGCAATTATAGAATGAGCCAGACTAAGCTAAGGTTGAAGGGGCTGGAAc                                                                                                                            <  1:470748/149‑1 (MQ=255)                           ttattaATAAAATCCCCCCCAAAAAAATTGATACGAAAGGAGTTGCTACTGAAGAAGTTGCTACTAAAAAAGTACTGCTGAACAAATTACTGACAACGCAATTATTGAATGAGCCAGAATAAGCTAAGGTTGAAGGGGCTGGAACGccc                                                                                                                        <  2:457498/149‑1 (MQ=255)                                aataaAATCCCCCCCAAAAAAATTGATACTAAAGGAGTTGCTACTGAAGAAGTTGCTACTAAAAAAGTACTGCTGAACAAATTACTGACAACGCAATTATTGAATGAGCCAGAATAAGCTAAGGt                                                                                                                                           >  2:303071/1‑125 (MQ=255)                                aataaAATCCCCCCCAAAAAAATTGATACTAAAGGAGTTGCTACTGAAGAAGTTGCTACTAAAAAAGTACTGCTGAACAAATTACTGACAACGCAATTATTGAATGAGCCAGAATAAGCTAAGGt                                                                                                                                           <  1:303071/125‑1 (MQ=255)                                                    aaTTGATACTAAAGGAGTTGCTACTGAAGAAGTTGCTACTAAAAAAGTACTGCTGAACAAATTACTGACAACGCAATTATTGAATGAGTCAGAATAAGCTAAGGTTGAAGGGGCTGGAACGCCCCTTCAACCTTAGCAGTAGCGTGGga                                                                                               <  1:102076/149‑1 (MQ=255)                                                                    gTTGCTACTGAAGAAGTTGCTACTAAAAAAGTACTGCTGAACAAATTACTGACAACGCAATTATTGAATGAGCCAGAATAAGCTAAGGTTGAAGGGGCAGGAACGCCCCTTCAACCTTAGCAGTAGCGTGGGATGATTTCACAATTAGa                                                                               >  2:350239/1‑149 (MQ=255)                                                                        cTACTGAAGAAGTTGCTACTAAAAAAGTACTGCTGAACAAATTACTGACAACGCAATTATTGAATGAGCCAGAATAAGCTaa                                                                                                                                              >  2:205636/1‑82 (MQ=255)                                                                        cTACTGAAGAAGTTGCTACTAAAAAAGTACTGCTGAACAAATTACTGACAACGCAATTATTGAATGAGCCAGAATAAGCTaa                                                                                                                                              <  1:205636/82‑1 (MQ=255)                                                                                    ttGCTACTAAAAAAGTACTGCTGAACAAATTACTGACAACGCAATTATTGAATGAGCCAGAATAAGCTAAGGTTGAAGGGGCTGGAACGCCCCTTCAACCTTAGCAGTAGCGTGGGATGATTTCACAATTAGAAAGACCTGCAtgatga                                                               >  1:489120/1‑149 (MQ=255)                                                                                      gCTACTAAAAAAGTACTGCTGAACAAATTACTGACAACGCAATTATTGAATGAGCCAGAATAAGCTAAGGTTGAAGGGGCTGGAACGCCCCTTCAACCTTAGCAGTAGCGTGGGATGATTTCACAATTAGAAAGACCTGCATGATGAGc                                                             <  1:193798/149‑1 (MQ=255)                                                                                         actaAAAAAGTACTGCTGAACAAATTACTGACAACGAAAATATTGAATGAGCCAGAATAAGATAAGGATGAAGGGGCTGGAACGCCGCTTCAACCTTAGCAGCAGCGAGGGATGATTTCACAATTAGAAAGATCTGCATGATGAGATat                                                          >  2:67114/1‑148 (MQ=255)                                                                                          ctaAAAAAGGACTGCCGAACAAATTACTTAGAACGCAATTATTGAATGAGCCAGAATAAGCTAAGGTTGAAGGTGCTTGAACGCCCCTTCAACCTTAGCAGTAGCGTGGGATGATTTCACAATTAGAAAGACCTGCAGGATGAGCTaga                                                         <  1:248325/149‑1 (MQ=255)                                                                                            aaaaaaGTACTGCTGAACAAATTACTGACAACGCAATTATAGAATGAGCAAAAATAAGCTAAGATTGAAGAGGCTGGAACGCCCATTCAACCTTAGCAGTAGCGAGAGATGATTTCACAATTGGAAAGACACGAACGATGAGCTAgaga                                                       >  2:222786/1‑149 (MQ=255)                                                                                             aaaaaGTACTGCTGAACAAATTACTGACAACGCAATTATTGAATGAGCCAGAATAAGCTAAGGTTGAAGGGGCTGGAACGCCCCTTCAACCTTAGCAGTAGCGTGGTATGATTTCACAATTAGAAAGACCTGCATGATGAGCTAGagaa                                                      <  1:292099/149‑1 (MQ=255)                                                                                             aaaaaGTACTGCTGAACAAATTACTGACAACGCAATTATTGAATGAGCCAGAATAAGATAAGGTAGAAGGGGCTGGAACGCCCCTTCAACCTTAGCAGTAGCGTGGGATGATTTCACAATTAGAAAGACCTGCATGATGAGCTAGagaa                                                      >  1:394442/1‑149 (MQ=255)                                                                                              aaaaGTACTGCTGAACAAATTACTGACAACGTAATTATTGAATGAGCCAGAATAAGCTAAGGTTGAAGGGGCTGGAACGCCCCTTCAACTTTAGCAGTAGCGTGGGATTATTTCACAATTAGAAAGACCTGCATGATGAGCTAGagaag                                                     <  1:551443/149‑1 (MQ=255)                                                                                                        ctgAACAAATTACTGACAACGCAATTATTGAATGAGCCAGAATAAGCTAAGGTTGAAGGGGCTGGAACGcccc                                                                                                                       <  2:183144/73‑1 (MQ=255)                                                                                                        ctgAACAAATTACTGACAACGCAATTATTGAATGAGCCAGAATAAGCTAAGGTTGAAGGGGCTGGAACGcccc                                                                                                                       >  1:183144/1‑73 (MQ=255)                                                                                                                         accGCAAGAATGGAATGAGCCAGAATAAGATAAATATGAAGGGGCTAGAACGCCCCTGCAAACATAGAAGTAGCGTGGGATGATTACACAATTAGAAAAACGTGCATGATCAGCTAGAGAAGAGGCTAGTGATGCAAAACGTCGTGCAg                          >  2:522266/3‑149 (MQ=255)                                                                                                                             taaggattGAATGAGCCAGAATAAGCTAAGGTTGAAGGGGCTGGAACGCCCCTTCAACCTTAGCAGTAGCGTGGGATGATTTCACAAGTAGAAAGACCTGCATGATGAGCTAGAGAAGAGGCTAGTGACGCAAGGCGTCGTGCAGGaca                      <  2:489120/144‑1 (MQ=255)                                                                                                                              aaTTATTGAATGAGCCAGAATAAGCTAAGGTTGAAGGGGCTGGAACGCCCCTTCAAc                                                                                                                 >  1:477982/1‑57 (MQ=255)                                                                                                                              aaTTATTGAATGAGCCAGAATAAGCTAAGGTTGAAGGGGCTGGAACGCCCCTTCAAc                                                                                                                 <  2:477982/57‑1 (MQ=255)                                                                                                                                       aTGAGCCAGAATAAGCTAAGGTTGAAGGGGCTGGAACGCCCCTTCAATCTTAGCAGTAGCGTGGGATGATTTCACAATTAGAAAGACCTGCATGATGAGCTagag                                                        >  2:185670/1‑105 (MQ=255)                                                                                                                                       aTGAGCCAGAATAAGCTAAGGTTGAAGGGGCTGGAACGCCCCTTCAATCTTAGCAGTAGCGTGGGATGATTTCACAATTAGAAAGACCTGCATGATGAGCTagag                                                        <  1:185670/105‑1 (MQ=255)                                                                                                                                            ccAGAATAAGCTAAGGTTGAAGGGGCTGGAACGCCCCTTCAACCTTAGCAGTAGCGTGGGATGATTTCACAATTAGAAAGACCTGCatg                                                                   >  1:113814/1‑89 (MQ=255)                                                                                                                                            ccAGAATAAGCTAAGGTTGAAGGGGCTGGAACGCCCCTTCAACCTTAGCAGTAGCGTGGGATGATTTCACAATTAGAAAGACCTGCatg                                                                   <  2:113814/89‑1 (MQ=255)                                                                                                                                              agaagaAGCTAAGGTTGAAGGGGCTGGAACGCCCCTTCAACCTTAGCAGTAGCGTGGGATGATTTCACAATTAGAAAGACCTGCATGATGAGCTAGTTATGTGGTTATTGACGCAAGGCGTCGTGCAGGACACGGATCACCGAGATggg     <  1:77578/149‑1 (MQ=255)                                                                                                                                                 aTAAGTTAAGGTTGAAGGGGTTGGAACGCCCCTTCAACCTTAGCAGTAGCGTGGGATGATTTCACAATTAGAAAGACCTGCATGATGAGCTAGAGAAGAGGCTAGTGACGCAAGGCGTCGTGCAGGACACGGATCACCGAGATGGGCAt  <  2:525614/149‑1 (MQ=255)                                                                                                                                                     gCTAAGGTTGAAGGGGCTGGAACGCCCCTTCAACCTTAGCAGTAGCGTGGGATGATTTCACAATTAGAAAGACCTGCATGATGAGCTAGAGAAGAGGCTAGTGACGCAAGGcgtcg                               <  2:197612/116‑1 (MQ=255)                                                                                                                                                     gCTAAGGTTGAAGGGGCTGGAACGCCCCTTCAACCTTAGCAGTAGCGTGGGATGATTTCACAATTAGAAAGACCTGCATGATGAGCTAGAGAAGAGGCTAGTGACGCAAGGcgtcg                               >  1:197612/1‑116 (MQ=255)                                                                                                                                                     |                                                                                                                                                 TACCTCCTTATATGATGAGGTAATTATTATTAATAAAATCCCCCCCAAAAAAATTGATACTAAAGGAGTTGCTACTGAAGAAGTTGCTACTAAAAAAGTACTGCTGAACAAATTACTGACAACGCAATTATTGAATGAGCCAGAATAAGCTAAGGTTGAAGGGGCTGGAACGCCCCTTCAACCTTAGCAGTAGCGTGGGATGATTTCACAATTAGAAAGACCTGCATGATGAGCTAGAGAAGAGGCTAGTGACGCAAGGCGTCGTGCAGGACACGGATCACCGAGATGGGCAT  >  NC_000913_3_vch_tpiA/59132‑59424

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.