New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	= 3548549	24 (0.830)	11 (0.460) +TTTTTTTTTAATGATACGGCGAC	10/240	1.4	32.3%	coding (1522/2085 nt)	malQ	4‑alpha‑glucanotransferase (amylomaltase)
	?	NC_000913_3_pae_tpiA	3548573 =	31 (1.080)					coding (1498/2085 nt)	malQ	4‑alpha‑glucanotransferase (amylomaltase)

TGTCGCCGCAACCGCCATCGACTGCTCCGGATACGCTTTCGGTGCACGGAACGTCTTCTCGTGGTCGTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATCCACCGGATAGTGAACATACGCGCCCTGATCTGCCGTCTCGCCATACGGTATCCACCACAAACGCAGCATC  >  NC_000913_3_pae_tpiA/3548433‑3548715                                                                                                                                             |                                                                                                                                               tgtCGCCGCAACCGCCATCGACTGCTCCGGATACGCTTTCGGTGCACGGAACGTCTTCTCGTGGTCGTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGAt                                                                                                                                        <  1:205275/149‑1 (MQ=255)  gtCGCCGCAACCGCCATCGACTGCTCCGGATACGCTTTCGGTGCACGGAACGTCTTCTCGTGGTCGTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATc                                                                                                                                       <  1:401626/149‑1 (MQ=255)  ctccccgcAACCGCCAACCACTTCACCGGTTACCCTCTCGGTGCACGGAACGTCCTCTCGTGGTCGTTTTCGAAATAGAGCACTTTGTAAGAGCACACACCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATc                                                                                                                                       <  2:3261/145‑1 (MQ=255)   tCGCCGCAACCGCCATCGACTGCTCCGGATACGCTTTCGGTGCACGGAACGTCTTCTCGTGGTCGTGTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCt                                                                                                                                      >  2:173614/1‑149 (MQ=255)     gccgcAACCGCCATCGACTGCTCCGGATACGCTTTCGGTGCACGGAACGTCTTCTCGTGGTCGTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTc                                                                                                                                    >  1:234673/1‑149 (MQ=255)      ccgcAACCGCCATCGACTGCTCCGGATACGCTTTCGGTGCACGGAACGTCTTCTCGTGGTCGTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCa                                                                                                                                   >  2:324935/1‑149 (MQ=255)                  ttgtctgcgctggatacgctttcggtgcacggaacgtcttctcgtggtcgttttcgaaatagagtactttgtaagagtacaccccgctgctgcgcagctttttttttttaatgatacggcgacCACCGAGATCTACACCAATCACCATa                                                                                                                       <  2:148554‑M2/26‑1 (MQ=255)                    gACTGCTCCGGATACGCTTTCGGTGCACGGAACGTCTTCTCGTGGTCGTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACa                                                                                                                     <  1:324935/149‑1 (MQ=255)                     aCTGCTCCGGATACGCTTTCGGTGCACGGAACGTCTTCGCGTGGTCGTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACAg                                                                                                                    <  1:252427/149‑1 (MQ=255)                           ttggatacgcattctgtgcacggaacgtcttctcgtggtcgttttcgaaatagatcactttgtaagagtacacaccgctgctgcgcagctttttttttttaatgatacggcgacCACCGAGATCTACACCAATCACCATACAGCGATGa                                                                                                              <  2:119792‑M2/35‑1 (MQ=255)                            tggatacgctctcggtgcacggaacgtcttctcgtggtcgttttcgaaatagagcactttgtaagagtacacaccgctgctgcgcagcttttttattataactatacggacacCACCGAGATCTACACCAATCACCATACAGCGATGAc                                                                                                             <  2:152735‑M2/36‑1 (MQ=255)                            cGGATACGCTTTCGGTGCACGGAACGTCTTCTCGTGGTCGTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCCCCTTACACCGATgcc                                                                                                             >  2:31634/1‑147 (MQ=255)                                        cGGTGCATGGAACGTCTTCTCGTGGTCGTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCGa                                                                                                 <  1:504344/149‑1 (MQ=255)                                           tGCACGGAACGTCTTCTCGTGGTCGTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATGTTCACCAGTCACCATACAGCGATGACGTTTACTTTCGGGTg                                                                                              >  1:30105/1‑149 (MQ=255)                                              acgtaacttcttctcgtggtcgtttgtgaaatagagcactttgtaagagtacgcaccgctgctgcgcagttttttttttttaatgatccggcgacCACCGAGATCTACACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCa                                                                                           <  2:355105‑M2/54‑1 (MQ=255)                                                     gTCTTCTCGTGGTCGTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCga                                                                                    <  1:312609/149‑1 (MQ=255)                                                             gtggtcgttttggaaatagtggactgtgtaagagtacacaccgctgctgcgcagctttttttttttaatgatccggcgacCACCGAGATCTACACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGat                                                                            <  2:431370‑M2/69‑1 (MQ=255)                                                               ggtcgttttcgaaatagcgcactttgtaagagtacacaccgctgctgcgtagctttttttttttaatgatacggcgacCACCGAGATCTACACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGatca                                                                          <  2:369018‑M2/71‑1 (MQ=255)                                                                gTCGCTTTCGAAATAGAGCACTTTGCAAGAGGACACACCGCTGCGGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTCCACCAACCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGatcat                                                                         <  1:225422/149‑1 (MQ=255)                                                                 tCGTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGatcatc                                                                        >  2:398965/1‑149 (MQ=255)                                                                   gTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGACAGCAGCTCATCCa                                                                      >  1:196171/1‑149 (MQ=255)                                                                      ttggaaatagagcactttttacgagtacacaccgctgctgcgcagctttttttttttaatgatacggcgacCACCGAGATCTACACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATCCACCg                                                                   <  2:430582‑M2/78‑1 (MQ=255)                                                                               gagCACTTTGTAAGAGTACACACCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCAACAATCATAACACCCCTATTACCTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATCCACCGGATAGTGaa                                                          <  2:234673/149‑1 (MQ=255)                                                                                         tAAGAGTACACATCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATCCACCGGATAGTGAACATACGCGcc                                                <  1:2758/149‑1 (MQ=255)                                                                                         aagtagtacacaccggtggtgtgtagttttttttttttaatgattgggcgggCACCGAGATCTACACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATCCACCGGATAGTGAACATACGCGcc                                                <  2:74902‑M2/97‑1 (MQ=255)                                                                                              gTACACACCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATCCACCGGATAGTGAACATACGCGCCCTGAt                                           <  1:398965/149‑1 (MQ=255)                                                                                               tacacaccgctgctgcgcagcttacttactttcatgacacggacacCACCGAGATCTACACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATCCACCGGATAGTGAACATACGCGCCCTGATc                                          <  2:340384‑M2/103‑1 (MQ=255)                                                                                               tACACACCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATCCACCGGATAGTGAACATACGCGCCCTGATc                                          <  1:212767/149‑1 (MQ=255)                                                                                                acacacCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATCCACCGGATAGTGAACATACGCGCCCTGATCt                                         >  2:118891/1‑149 (MQ=255)                                                                                                   cccgctgcctacgtagctttttttttttaatgaccgggcgacCACCGAGATCTACACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATCCACCGGATAGTGAACATACGCGCCCTGATCTGcc                                      <  2:4228‑M2/107‑1 (MQ=255)                                                                                                      cGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCTAGTGCCAGAACCGAGAGCAGATCATCCACCGGATAGTGCACATACGCGCCCTGATCTGCCGtc                                   >  2:206208/1‑149 (MQ=255)                                                                                                                gcgcttatcttttttaattatcgggcggcCACCGAGATCTACACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATCCACCGGATAGTGAACATACGCGCCCTGATCTGCCGTCTCGCCATACg                         <  2:373714‑M2/120‑1 (MQ=255)                                                                                                                cAGCTTCGCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCTATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATGCTCCGGATAGTGAACATACGCGCCCTGATCTGCCGTCTCGCCATACg                         <  2:117205/149‑1 (MQ=255)                                                                                                                        cGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCCCCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATCCACCGGATAGTGAACATACGCGCCCTGATCTGCCGTCTCGCCATACGGTATccac                 <  1:178782/149‑1 (MQ=255)                                                                                                                        cGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCGAGGGCCAGAATCGAGAGCAGATCATCCACCGGGTAGTGAACATACGCGCCCTGATCTGCCGTCTCGCCATACCGTATcccc                 >  1:4220/1‑147 (MQ=255)                                                                                                                         gACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCCTACAGCGATGACGTTTACTTTCGAGTGCCCGAATCGAGAGCAGATCATCCACCGGATAGTGAACATACACGCCCTGATCTGCGGTCTCGCCATACGGTATccccc                >  1:34900/1‑149 (MQ=255)                                                                                                                            aaTCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACAGCGATGACGTGTACTTTGGAGTGCGAGAATCGAGAGCAGATCATCCACCGGAGAGTTACCATACGCGCCCTGATCTCCCGTCCCGCCCTACGGTATCCACcaca             >  2:336632/1‑149 (MQ=255)                                                                                                                               ctctACCGGTACGGTACCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATCCACCGGATAGTGAACATACGCGCCCTGATCTGCCGTCTCGCCATACGGTATCCACCacacac          >  1:502823/1‑149 (MQ=255)                                                                                                                                    ccGGTACGGTACCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATCCACCGGATAGTGAACATACGCACCCTGATCTGCCGTCTCGCCCTCCGGTATCCCCCTCAAACgaaac     >  2:350640/1‑145 (MQ=255)                                                                                                                                       gtacggtacCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATCCACCGGATAGTGaa                                                          <  1:48602/93‑1 (MQ=255)                                                                                                                                       gtacggtacCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATCCACCGGATAGTGaa                                                          >  2:48602/1‑93 (MQ=255)                                                                                                                                       gtacgctacCGAGATCTTCACCAACCACCATACAGCGATGACGTTTACTTTCGGGTGCCAGAATCGAGAGCAGATCATCCACCGGATAGTGAACATACGCGCCCTGATCTGCCGTCTCGCCATACGGTATCCACCACAAACGCAGCATc  <  2:40850/149‑1 (MQ=255)                                                                                                                                             |                                                                                                                                               TGTCGCCGCAACCGCCATCGACTGCTCCGGATACGCTTTCGGTGCACGGAACGTCTTCTCGTGGTCGTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTGCTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATCCACCGGATAGTGAACATACGCGCCCTGATCTGCCGTCTCGCCATACGGTATCCACCACAAACGCAGCATC  >  NC_000913_3_pae_tpiA/3548433‑3548715

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.