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)

AGTAACCGCGCAGCGTTGGCAGGTCATGTGTCGCCGCAACCGCCATCGACTGCTCCGGATACGCTTTCGGTGCACGGAACGTCTTCTCGTGGTCGTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTG‑CTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATCCACCGGATAGTGAACATACGCGCCCTGATCTGCCGTCTCGCCATACG  >  NC_000913_3_pae_tpiA/3548405‑3548692                                                                                                                                                  |                                                                                                                                                aGTAACCGCGCAGCGTTGGCAGGTCATGTGTCGCCGCAACCGCCATCGACTGCTCCGGATACGCTTTCGGTGCACGGAACGTCTTCTCGTGGTCGTTTTCGAAATAGCGCACTTTGTACGAGTACACACCGCTG‑CTCCGCAGGCTACCg                                                                                                                                             >  2:397291/1‑149 (MQ=255)           cAGCGTTGGCAGGTCATGTGTCGCCGCAACCGCCATCGACTGCTCCGGATACGCTTTCGGTGCACGGAACGTCTTCTCGTGGTCGTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTG‑CTGCGCAGCTTACCGACAATCTCTa                                                                                                                                   <  2:398593/149‑1 (MQ=255)                             tgtCGCCGCAACCGCCATCGACTGCTCCGGATACGCTTTCGGTGCACGGAACGTCTTCTCGTGGTCGTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTG‑CTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGAt                                                                                                                 <  1:205275/149‑1 (MQ=255)                              gtCGCCGCAACCGCCATCGACTGCTCCGGATACGCTTTCGGTGCACGGAACGTCTTCTCGTGGTCGTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTG‑CTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATc                                                                                                                <  1:401626/149‑1 (MQ=255)                              ctccccgcAACCGCCAACCACTTCACCGGTTACCCTCTCGGTGCACGGAACGTCCTCTCGTGGTCGTTTTCGAAATAGAGCACTTTGTAAGAGCACACACCGCTG‑CTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATc                                                                                                                <  2:3261/145‑1 (MQ=255)                               tCGCCGCAACCGCCATCGACTGCTCCGGATACGCTTTCGGTGCACGGAACGTCTTCTCGTGGTCGTGTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTG‑CTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCt                                                                                                               >  2:173614/1‑149 (MQ=255)                                 gccgcAACCGCCATCGACTGCTCCGGATACGCTTTCGGTGCACGGAACGTCTTCTCGTGGTCGTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTG‑CTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTc                                                                                                             >  1:234673/1‑149 (MQ=255)                                  ccgcAACCGCCATCGACTGCTCCGGATACGCTTTCGGTGCACGGAACGTCTTCTCGTGGTCGTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTG‑CTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCa                                                                                                            >  2:324935/1‑149 (MQ=255)                                              ttgtctgcgCTGGATACGCTTTCGGTGCACGGAACGTCTTCTCGTGGTCGTTTTCGAAATAGAGTACTTTGTAAGAGTACACCCCGCTG‑CTGCGCAGCTTtttttttttaatgatacggcgaccaccgagatctacaccaatcaccata                                                                                                <  2:148554‑M1/145‑50 (MQ=255)                                                gACTGCTCCGGATACGCTTTCGGTGCACGGAACGTCTTCTCGTGGTCGTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTG‑CTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACa                                                                                              <  1:324935/149‑1 (MQ=255)                                                 aCTGCTCCGGATACGCTTTCGGTGCACGGAACGTCTTCGCGTGGTCGTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTG‑CTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACAg                                                                                             <  1:252427/149‑1 (MQ=255)                                                       ttggatACGCATTCTGTGCACGGAACGTCTTCTCGTGGTCGTTTTCGAAATAGATCACTTTGTAAGAGTACACACCGCTG‑CTGCGCAGCTTtttttttttaatgatacggcgaccaccgagatctacaccaatcaccatacagcgatga                                                                                       <  2:119792‑M1/147‑59 (MQ=255)                                                        tggaTACGCTCTCGGTGCACGGAACGTCTTCTCGTGGTCGTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTG‑CTGCGCAGCTTttttattataactatacggacaccaccgagatctacaccaatcaccatacagcgatgac                                                                                      <  2:152735‑M1/148‑60 (MQ=255)                                                        cGGATACGCTTTCGGTGCACGGAACGTCTTCTCGTGGTCGTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTG‑CTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCCCCTTACACCGATgcc                                                                                      >  2:31634/1‑147 (MQ=255)                                                                    cGGTGCATGGAACGTCTTCTCGTGGTCGTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTG‑CTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCGa                                                                          <  1:504344/149‑1 (MQ=255)                                                                       tGCACGGAACGTCTTCTCGTGGTCGTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTG‑CTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATGTTCACCAGTCACCATACAGCGATGACGTTTACTTTCGGGTg                                                                       >  1:30105/1‑149 (MQ=255)                                                                          aCGTAACTTCTTCTCGTGGTCGTTTGTGAAATAGAGCACTTTGTAAGAGTACGCACCGCTG‑CTGCGCAGTTTtttttttttaatgatccggcgaccaccgagatctacaccaatcaccatacagcgatgacgtttactttcgagtgcca                                                                    <  2:355105‑M1/149‑78 (MQ=255)                                                                                 gTCTTCTCGTGGTCGTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTG‑CTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCga                                                             <  1:312609/149‑1 (MQ=255)                                                                                         gTGGTCGTTTTGGAAATAGTGGACTGTGTAAGAGTACACACCGCTG‑CTGCGCAGCTTtttttttttaatgatccggcgaccaccgagatctacaccaatcaccatacagcgatgacgtttactttcgagtgccagaatcgagagcagat                                                     <  2:431370‑M1/149‑93 (MQ=255)                                                                                           ggTCGTTTTCGAAATAGCGCACTTTGTAAGAGTACACACCGCTG‑CTGCGTAGCTTtttttttttaatgatacggcgaccaccgagatctacaccaatcaccatacagcgatgacgtttactttcgagtgccagaatcgagagcagatca                                                   <  2:369018‑M1/149‑95 (MQ=255)                                                                                            gTCGCTTTCGAAATAGAGCACTTTGCAAGAGGACACACCGCTG‑CGGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTCCACCAACCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGatcat                                                  <  1:225422/149‑1 (MQ=255)                                                                                             tCGTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTG‑CTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGatcatc                                                 >  2:398965/1‑149 (MQ=255)                                                                                               gTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTG‑CTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGACAGCAGCTCATCCa                                               >  1:196171/1‑149 (MQ=255)                                                                                                  ttggaaaTAGAGCACTTTTTACGAGTACACACCGCTG‑CTGCGCAGCTTtttttttttaatgatacggcgaccaccgagatctacaccaatcaccatacagcgatgacgtttactttcgagtgccagaatcgagagcagatcatccaccg                                            <  2:430582‑M1/146‑102 (MQ=255)                                                                                                           gagCACTTTGTAAGAGTACACACCGCTG‑CTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCAACAATCATAACACCCCTATTACCTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATCCACCGGATAGTGaa                                   <  2:234673/149‑1 (MQ=255)                                                                                                                     tAAGAGTACACATCGCTG‑CTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATCCACCGGATAGTGAACATACGCGcc                         <  1:2758/149‑1 (MQ=255)                                                                                                                     aagtagtacaCACCGGTG‑GTGTGTAGTTTtttttttttaatgattgggcgggcaccgagatctacaccaatcaccatacagcgatgacgtttactttcgagtgccagaatcgagagcagatcatccaccggatagtgaacatacgcgcc                         <  2:74902‑M1/145‑121 (MQ=255)                                                                                                                          gTACACACCGCTG‑CTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATCCACCGGATAGTGAACATACGCGCCCTGAt                    <  1:398965/149‑1 (MQ=255)                                                                                                                           tACACACCGCTG‑CTGCGCAGCTTacttactttcatgacacggacaccaccgagatctacaccaatcaccatacagcgatgacgtttactttcgagtgccagaatcgagagcagatcatccaccggatagtgaacatacgcgccctgatc                   <  2:340384‑M1/149‑127 (MQ=255)                                                                                                                           tACACACCGCTG‑CTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATCCACCGGATAGTGAACATACGCGCCCTGATc                   <  1:212767/149‑1 (MQ=255)                                                                                                                            acacacCGCTG‑CTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATCCACCGGATAGTGAACATACGCGCCCTGATCt                  >  2:118891/1‑149 (MQ=255)                                                                                                                                cccgCTGCCTACGTAGCTTtttttttttaatgaccgggcgaccaccgagatctacaccaatcaccatacagcgatgacgtttactttcgagtgccagaatcgagagcagatcatccaccggatagtgaacatacgcgccctgatctgcc               <  2:4228‑M1/148‑131 (MQ=255)                                                                                                                                  cGCTG‑CTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCTAGTGCCAGAACCGAGAGCAGATCATCCACCGGATAGTGCACATACGCGCCCTGATCTGCCGtc            >  2:206208/1‑149 (MQ=255)                                                                                                                                             gcgctTatcttttttaattatcgggcggccaccgagatctacaccaatcaccatacagcgatgacgtttactttcgagtgccagaatcgagagcagatcatccaccggatagtgaacatacgcgccctgatctgccgtctcgccatacg  <  2:373714‑M1/147‑144 (MQ=255)                                                                                                                                             cAGCTTCGCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCTATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATGCTCCGGATAGTGAACATACGCGCCCTGATCTGCCGTCTCGCCATACg  <  2:117205/149‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                AGTAACCGCGCAGCGTTGGCAGGTCATGTGTCGCCGCAACCGCCATCGACTGCTCCGGATACGCTTTCGGTGCACGGAACGTCTTCTCGTGGTCGTTTTCGAAATAGAGCACTTTGTAAGAGTACACACCGCTG‑CTGCGCAGCTTACCGACAATCTCTACCGGTACGGTACCGAGATCTTCACCAATCACCATACAGCGATGACGTTTACTTTCGAGTGCCAGAATCGAGAGCAGATCATCCACCGGATAGTGAACATACGCGCCCTGATCTGCCGTCTCGCCATACG  >  NC_000913_3_pae_tpiA/3548405‑3548692

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.