New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_pgi	3305904 =	53 (1.810)	4 (0.150)	4/264	3.5	7.3%	intergenic (‑87/+67)	mtr/deaD	tryptophan transporter of high affinity/ATP‑dependent RNA helicase
	?	NC_000913_3_pae_pgi	3305929 =	52 (1.890)					intergenic (‑112/+42)	mtr/deaD	tryptophan transporter of high affinity/ATP‑dependent RNA helicase
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

CGGTGACGTTTGGGTGGTGGTTAGTGTTGCCATGAGGGCTTCTCTCCAGTGAAAAATAGTGCGACTGCGTTGTTATGCATTGCACTGTACCAGTACACGAGTACAAAAGACAGAAAAAAAGCCCCGATGGTAAAAATCGGGGCTGTATATATTATTTTACAGATTGTGTTCGCTGTTCAGCGATGATTACGCATCACCACCGAAACGACGACGACCGGTAGAATCATCACGACGCGGAGCGCGGCCTTCACGACGTTCGCCGCTAAAACGACGACCATC  >  NC_000913_3_pae_pgi/3305785‑3306063                                                                                                                                                 |                                                                                                                                       gggggACGTTGGGGGGGTGGTTAGTGGTGCCATGAGGGCTTCTCTCCAGTGAAAAATAGTGCGACTGCGTTGTTATGCATTGCACTGTACCAGTACACGAGTACAAAAGACAGAAAAAAAGCCCCGAAGGTAAAAATCGGGGCTGtata                                                                                                                                    <  2:61751/145‑1 (MQ=255)                    gtTAGTGTTGCCATGAGGGCTTCTCTCCAGTGAAAAATAGTGCGACTGCGTTGTTATGCATTGCACTGTACCAGTACACGAGTACAAAAGACAGAAAAAAAGCCCCGATGGTAAAAATCGGGGCTGTATATATTATTTTACAGATtgtg                                                                                                                 >  1:346045/1‑149 (MQ=255)                    gtTAGTGTTGCCATGAGGGCTTCTCTCCAGTGAAAAATAGTGCGACTGCGTTGTTATGCATTGCACTGTACCAGTACACGAGTACAAAAGACAGAAAAAAAGCCCCGATGGTAAAAATCGGGGCGGTATATATTATTTTACAGATtgtg                                                                                                                 >  1:184611/1‑149 (MQ=255)                        gtgtTGCCATGAGGGCTTCTCTCCAGTGAAAAATAGTGCGACTGCGTTGTTATGCATTGCACTGTACCAGTACACGAGTACAAAAGACAGAAAAAAAGCCCCGATGGTAAAAATCGGGGCTGTATATATTATTTTACAGATTGTGTTCg                                                                                                             >  1:359374/1‑149 (MQ=255)                              ccATGAGGGCTTCTCTCCAGTGAAAAATAGTGCGACTGCGTTGTTATGCATTGCACTGTACCAGTACACGAGTACAAAAGACAGAAAAAAAGCCCCGATGGTAAAAATCGGGGCTGTATATATTATTTTACa                                                                                                                        <  1:41344/132‑1 (MQ=255)                              ccATGAGGGCTTCTCTCCAGTGAAAAATAGTGCGACTGCGTTGTTATGCATTGCACTGTACCAGTACACGAGTACAAAAGACAGAAAAAAAGCCCCGATGGTAAAAATCGGGGCTGTATATATTATTTTACa                                                                                                                        >  2:41344/1‑132 (MQ=255)                                     ggCTTCTCTCCAGAGAAAAATAGTGCGACGGCGTTATTATGCATCGCACTGTACCAGTACACGAGTACGAAGGGCAGAAAAAAAGCCCCGATGGTAAAAATCGGGGCTGTATATATTATTTTACAGATTGTGTTCGCTGTTCAGCgctg                                                                                                >  2:461121/1‑149 (MQ=255)                                      gCTTCTCTCCAGTGAAAAATAGTGCGACTGCGTTGTTATGCATTGCACTGTACCAGTACACGAGTACAAAAGACAGAAAAAAAGCCCCGATGGTAAAAATCGGGGCTGTATATATTATTTTACAGATTGTGTTCGCTGTTCAGCgatga                                                                                               >  2:492095/1‑149 (MQ=255)                                       cTTCTCTCCAGTGAAAAATAGTGCGACTGCGTTGTTATGCATTGCACTGTACCAGTACACGAGTACAAAAGACAGAAAAAAAGCCCCGATGGTAAAAATCGGGGCTGTATATATTATTTTACAGATTGTGTTCGCTGTTCAGCgatgat                                                                                              >  2:230533/1‑149 (MQ=255)                                         tctctcCAGTGAAAAATAGTGCGACTGCGTTGTTATGCATTGCACTGTACCAGTACACGAGTACAAAAGACAGAAAAAAAGCCCCGATGGTAAAAATCGGGGCTGTATATATTATTTTACAGATTGTGTTCGCTGTTCAGCGATGATTa                                                                                            <  2:70286/149‑1 (MQ=255)                                           tctcCAGTGAAAATTAGTGCGAATGCGTTGTTATGCATTGCACTGTACCAGTACACGAGTACAAAAGACAGAAAAAAAGCCCCGATGGTAAAAATCGGGGCTGTATATATTATTTTACAGATTGTGTTCGCTGTTCAGCGATGATTACg                                                                                          <  1:396632/149‑1 (MQ=255)                                              ccAGTGAAAAATAGTGCGACTGCGTTGTTATGCATTGCACTGTACCAGTACACGAGTACAAAAGACAGAAAAAAAGCCCCGATGGTAAAAATCGGGGCTGTATATATTATTTTACAGATTGTGTTCGCTGTTCAGCGATGATTACGCAt                                                                                       <  1:366000/149‑1 (MQ=255)                                                    aaaaaTAGTGCGACTGCGTTGTTATGCATTGCACTGTACCAGTACACGAGTACAAAAGACAGAAAAAAAGCCCCGATGGTAAAAATCGGGGCTGTATATATTATTTTACAGATTGTGTTCGCTGTTCAGCGATGATTACGCATcaccac                                                                                 >  1:272022/1‑149 (MQ=255)                                                     aaaaTAGTGCGACTGCGTTGTTATGCATTGCACTGTACCAGTACACGAGTACAAAAGACAGAAAAAAAGCCCCGATGGTAAAAATCGGGGCTGTATATATTATTTTACAGATTGTGTTCGCTGTTCAGCGATGATTACGCATCaccacc                                                                                >  2:353338/1‑149 (MQ=255)                                                     aaaaTAGTGCGACTGCGTTGTTATGCATTGCACTGTACCAGTACACGAGTACAAAAGACAGAAAAAAAGCCCCGATGGTAAAAATCGGGGCTGTATATATTATTTTACAGATTGTGTTCGCTGTTCAGCGATGATTACGCATCaccacc                                                                                <  1:349602/149‑1 (MQ=255)                                                      aaaTAGTGCGACTGCGTTGTTATGCATTGCGCTGTACCAGTACACGCGTACAAAAGACAGAAAAAAAGCCCCGATGGTAAAAATCGAGCCTCTACATATAATTTTACCGATTGTGTTCGCTGTTCAGCGATGATTACGCATCACGACCg                                                                               >  1:121301/1‑149 (MQ=255)                                                      aaaTAGTGCGACTGCGTTGTCACACAACAGTGGTTATCAGCACACGAGTACAAAAGACAGAAAAAAAGCCCCGATGGTAAAAATCGGGGCTGTATATATTATTTTACAGATTGTGTTCGCTGTTCAGCGATGCTTACGCATCACCACCg                                                                               >  2:113126/1‑149 (MQ=255)                                                            ggCGACTGCGTCGTTACGCATTGCACTGTACCAGTACACGAGTCCAAAAGACAGAAAAGAACCCCCGCTGGGAAAAATCGGGGCCTAACATATTATTGTACAGATAGCGGTCGCAGTTCAGCGCAGATTACGCATCACCCCCAACacga                                                                         >  2:61052/2‑149 (MQ=255)                                                                  tGCGTTGTTATGCATTGCACTGTACCAGTACACGAGTACAAAAGACAGAAAAAAAGCCCCGATGGTAAAAATCGGGGCTGTATATATTATTTTACAGATTGTGTTCGCTGTTCAGCGATGATTACGCATcaccac                                                                                 <  2:315383/135‑1 (MQ=255)                                                                  tGCGTTGTTATGCATTGCACTGTACCAGTACACGAGTACAAAAGACAGAAAAAAAGCCCCGATGGTAAAAATCGGGGCTGTATATATTATTTTACAGATTGTGTTCGCTGTTCAGCGATGATTACGCATcaccac                                                                                 >  1:315383/1‑135 (MQ=255)                                                                  tGCGTTGTTATGCATTGCACTGTACCAGTACACGAGTACAAAAGACAGAAAAAAAGCCCCGATGGTAAAAATCGGGGCTGTATATATTATTTTACAGATTGTGTTCGCTGTTCAGCGATGATTACGCATCACCACCGAAAcgacgacga                                                                   >  1:411759/1‑149 (MQ=255)                                                                         ttATGCATTGCACTGTACCAGTACACGAGTACAAAAGACAGAAAAAAAGCCCCGATGGTAAAAATCGGGGCTGTATATATTATTTTACAGATTGTGTTCGCTGTTCAGCGATGATTACGCATCACCACCGACACGACGACGACCGGTAg                                                            >  2:411464/1‑149 (MQ=255)                                                                            tGCATTGCACTGTACCAGTACACGAGTACAAAAGACAGAAAAAAAGCCCCGATGGTAAAAATCGGGGCTGTATATATTATTTTACAGATTGTGTTCGCTGTTCAGCGATGATTACGCATCACCACCGAAACGACGACGACCGGTAGAat                                                         <  2:359374/149‑1 (MQ=255)                                                                               aTTGCACTGTACCAGTACACGAGTACAAAAGACAGAAAAAAAGCCCCGATGGTAAAAATCGGGGCTGTATATATTATTTTACAGATTGTGTTCGCTGTTCAGCGATGATTACGCATCACCACCGAAACGACGACGACCGGTAGAatcat                                                      <  2:320768/149‑1 (MQ=255)                                                                               aTTGCACTGTACCAGTACACGAGTACAAAAGACAGAAAAAAAGCCCCGATGGTAAAAATCGGGGCTGTATATATTATTTTACAGATTGTGTTCGCTGTTCAGCGATGATTACGCATCACCACCGAAACGACGACGACCGGTAGAat                                                         <  2:273236/146‑1 (MQ=255)                                                                               aTTGCACTGTACCAGTACACGAGTACAAAAGACAGAAAAAAAGCCCCGATGGTAAAAATCGGGGCTGTATATATTATTTTACAGATTGTGTTCGCTGTTCAGCGATGATTACGCATCACCACCGAAACGACGACGACCGGTAGAat                                                         >  1:273236/1‑146 (MQ=255)                                                                                ttGCACTGTACCAGTACACGAGTACAAAAGACAGAAAAAAAGCCCCGATGGTAAAAATCGGGGCTGTATATATTATTTTACAGATTGTGTTCGCTGTTCAGCGATGATTACGCATCACCACCGAAACGACGACGACCGGTAGAatcatc                                                     <  1:332831/149‑1 (MQ=255)                                                                                 tGCACTGTACCAGCACACGAGTACAAAAGACAGAAAAAAAGCCCCGATGGTAAAAATCGGGGCTGTATATATTATTTTACAGATTGTGTTCGCTGTTCAGCGATGATTACGCAGCACCACCGAAACGACGACGACCGGTAGAAtcatca                                                    <  1:31181/149‑1 (MQ=255)                                                                                   cACTGTACCAGTACACGAGTACAAAAGACAGAAAAAAAGCCCCGATGGTAAAAATCGGGGCTg                                                                                                                                        >  1:415630/1‑63 (MQ=255)                                                                                   cACTGTACCAGTACACGAGTACAAAAGACAGAAAAAAAGCCCCGATGGTAAAAATCGGGGCTg                                                                                                                                        <  2:415630/63‑1 (MQ=255)                                                                                        tACCAGTACACGAGTACACAAGACAGAAAAAAAGCCCCGATGGTAAAAATCGGGGCTGTATATATTATTTTACAGAGTGTGTTCGCTGTTCAGCGATGATTACGCACCCGCACCGACAGGACGACGACCGGTGGAATCCTCGCGAcgcg                                             >  2:420037/1‑149 (MQ=255)                                                                                         aCCAGTACACGAGTACAAAAGACAGAAAAAAAGCTCCGATGGTGAAAATCGGGGCTGTATATATTATTTTACAGATTGTGTTCGCTGTTCAGCGATGTTTACGCATCACCACCGAAACGACGACGACCGGTAGAATCATTACGACGCgg                                            >  1:50374/1‑149 (MQ=255)                                                                                           cAGTACACGAGTACAAAAGACAGAAAAAAAGCCCCGATGGTAAAAATCGGGGCTGTATATATTATTTTACAGATTGTGTTCGCTGTTCAGCGATGATTACGCATCACCACCGa                                                                              <  2:102238/113‑1 (MQ=255)                                                                                           cAGTACACGAGTACAAAAGACAGAAAAAAAGCCCCGATGGTAAAAATCGGGGCTGTATATATTATTTTACAGATTGTGTTCGCTGTTCAGCGATGATTACGCATCACCACCGa                                                                              >  1:102238/1‑113 (MQ=255)                                                                                               acacGAGTACAAAAGACAGAAAAAAAGCCCCGATGGTAAAAATCGGGGCTGTATATATTATTTTACAGATTGTGTTCGCTGTTCAGCGATGATTACGCATCACCACCGAAACGACGACGACCGGTAGAATCATCACGACGCGGAGcgcg                                      <  2:55286/149‑1 (MQ=255)                                                                                                   gAGTACAAAAGACAGAAAAAAAGCCCCGATGGTAAAAATCGGGGCTGTATATATTATTTTACAGATTGTGTTCGCTGTTCAGCGATGATTACGCATCACCACCGAAACGACGACGACCGGTAGAATCATCACGACGCGGAGCGCGGCCt                                  >  1:182057/1‑149 (MQ=255)                                                                                                      ttaaaaaGACAGAAAAAAAGCCCGGATGGTAAAAATCGGGGCTGGATAAATTATTTTACAGATTGTGTTCGCTGGTCAGCGATGATTACCCTTCACCACCGAAACGACGACGACCGGTAGTATCGTCACGACGCGGAGCGCGGCCTTCa                               <  2:121301/146‑1 (MQ=255)                                                                                                         aaaaGACAGAAAAAAAGCCCCGATGGTAAAAATCGGGGCTGTATATATTATTTTACAGATTGTGTTCGCTGTTCAGCGATGATTACGCATCACCACCGAAACGACGCCGACCGGTAGAATCATCACGACGCGGAGCGCGGCCTTCacga                            >  1:82859/1‑149 (MQ=255)                                                                                                         aaaaGACAGAAAAAAAGCCCCGATGGTAAAAATCGGGGCTGTATATATTATTTTACAGATTGTGTTCGCTGTTCAGCGATGATTACGCATCACCACCGAAACGACGACGACCGGTAGAATCATCACGACGCGGAGCGCGGCCTTCacga                            >  1:204375/1‑149 (MQ=255)                                                                                                          aaaGACAGAAAAAAAGCCCCGATGGTAAAAATCGGGGCTGTATATATTATTTTACAGATTGTGTTCGCTGTTCAGCGATGATTACGCATCACCACCGAAACGACGACGACCGGTAGAATCATCACGACGCGGAGCGCGGCCTTCacgac                           <  1:492095/149‑1 (MQ=255)                                                                                                           aaGACAGAAAAAAAGCCCCGATGGTAAAAATCGGGGCTGTATATATTATTTTACAGATTGTGTTCGCTGTTCAGCGATGATTACGCATCACCACCGAAACGACGACGACCGGTAGAATCATCACGACGCGGAGCGCGGCCTTCacgacg                          <  2:277238/149‑1 (MQ=255)                                                                                                              aCAGAAAAAAAGCCCCGATGGTAAAAATCGGGGCTGTATATATTATTTTACAGATTGTGTTCGCTGTTCAGCGATGATTACGCATCACCACCGAAACGACGACGACCGGTAGAATCATCACGACGCGGAGCGCGGCCTTCACGACCTTc                       >  2:197055/1‑149 (MQ=255)                                                                                                              aCAGAAAAAAAGCCCCGATGGTAAAAATCGGGGCTGTAGATATTATTTTACAGATTGTGTTCGCTGTTCAGCGATGATTACGCATCACCACCGAAACGACGACGACCGGCAGAAACATCTCGACGCGGAACGCGGCCTCCACGACGTTc                       >  2:245847/1‑149 (MQ=255)                                                                                                                aGAAAAAATGCCCCGATGGCAAAAATCGCGGCTGTATAGCTTATTTTACAGATCGTGTTCGCTGTTCAGCGATGATTACGCACCACCACCGAAACGACGACGACCGGTAGAATCATCACGACGCGGAGCGCGGCCTTCACGACGTTcgc                     <  1:178845/149‑1 (MQ=255)                                                                                                                  aaaaaaaGCCCCGATGGTAAAAATCGGGGCTGTATATATTATTTTACAGATTGTGTTCGCTGTTCAGCGATGATTACGCATCACCACCGAAACGACGACGACCGGTAGAATCATCacgac                                                >  2:28109/1‑120 (MQ=255)                                                                                                                  aaaaaaaGCCCCGATGGTAAAAATCGGGGCTGTATATATTATTTTACAGATTGTGTTCGCTGTTCAGCGATGATTACGCATCACCACCGAAACGACGACGACCGGTAGAATCATCacgac                                                <  1:28109/120‑1 (MQ=255)                                                                                                                  aaaaaaaGCCCCGATGGTAAAAATCGGGGCTGTATATATTATTTTACAGATTGTGTTCGCTGTTCAGCGATGATTACGCATCACCACCGAAACGACGACGACCGGTAGAATCATCACGACGCGGAGCGCGGCCTTCACGACGTTcgccg                   >  1:346609/1‑149 (MQ=255)                                                                                                                    aaaaaGCCCCGATGGTAAAAATCGGGGCTGTATATATTATTTTACAGATTGTGTTCGCTGTTCAGCGATGATTACGCATCACAAGCGCGGCGACGACGACCGGTAGAATCATCACGACGCGGAGCGCGGCCTTCACGACGCTcgccgcg                 >  1:121070/1‑148 (MQ=255)                                                                                                                        aGCCCCGATGGTAAAAATCGGGGCTGTATATATTATTTTACAGATTGTGTTCGCTGTTCAGCGATGATTACGCATCACCACCGAAACGACGACGACCGGTAGAATCATCACGACGCGGAGCGCGGCCTTCACGACGTTCGCCGCTaaaa             <  1:230533/149‑1 (MQ=255)                                                                                                                              gATGGTAAAAATCGGGGCTGTATATATTATTTTACAGATTGTGTTCGCTGTTCAGCGATGATTACGCATCACCACCGAAACGACGACGACCGGTAGAATCATCACGACGCGGAGCGCGGCCTTCACGACGTTCGCCGCTAAAAcgacga       <  1:353338/149‑1 (MQ=255)                                                                                                                              gATGGTAAAAATCGGGGCTGTATATATTATTTTACAGATTGTGTTCGCTGTTCAGCGATGATTACGCATCACCACCGAAACGACGACGACCGGTAGAATCATCACGACGCGGAGCGCGGCCTTCACGACGTTCGCCGCTAAAAcgacga       <  2:272022/149‑1 (MQ=255)                                                                                                                                   tAAAAATCGGGGCTGTATATATTATTTTACAGATTGTGTTCGCTGTTCAGCGATGATTACGCATCACCACCGAAACGACGACGACCGGTAGAATCATCACGACGCGGAGCGCGGCCTTCACGACGTTCGCCGCTAAAACGACGACCATc  <  1:309357/149‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                       CGGTGACGTTTGGGTGGTGGTTAGTGTTGCCATGAGGGCTTCTCTCCAGTGAAAAATAGTGCGACTGCGTTGTTATGCATTGCACTGTACCAGTACACGAGTACAAAAGACAGAAAAAAAGCCCCGATGGTAAAAATCGGGGCTGTATATATTATTTTACAGATTGTGTTCGCTGTTCAGCGATGATTACGCATCACCACCGAAACGACGACGACCGGTAGAATCATCACGACGCGGAGCGCGGCCTTCACGACGTTCGCCGCTAAAACGACGACCATC  >  NC_000913_3_pae_pgi/3305785‑3306063

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ 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.