New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	4322620 =	32 (0.890)	5 (0.140)	5/276	4.3	12.8%	pseudogene (111/372 nt)	phnE	defective phosphonate ABC transporter permease;transport; Transport of small molecules: Anions; membrane channel protein component of Pn transporter; membrane component of ABC superfamily
	?	NC_000913_3_pae_tpiA	4322653 =	37 (1.050)					pseudogene (78/372 nt)	phnE	defective phosphonate ABC transporter permease;transport; Transport of small molecules: Anions; membrane channel protein component of Pn transporter; membrane component of ABC superfamily
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

CCGAGCGGACGTTGGATTCGAAGCGATAGAGGGAGTAGGAGATCAGCAGTGGCATCACCTGTGGCAGCACGCCGTAGAGGATCTCTTCGAGCTTGTTGGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGCCGGTGGTGTGGATAAACAGCGCCAGCACGCCAGCACGCCAGCGAACGGGCCGAGGCCGACGGCGACCACGAACAGCATGGCGAAGACCATTTCGTTAATGGC  >  NC_000913_3_pae_tpiA/4322523‑4322801                                                                                                                                   |                                                                                                                                                     ccGAGCGGACGTTGGATTCGAAGCGATAGAGGGAGTAGGAGATCAGCAGTGGCATCACCTGTGGCAGCACGCCGTAGAGGATCTCTTCGAGCTTGTTGGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTCAATCGCTTCCAcc                                                                                                                                    >  2:366368/1‑149 (MQ=255)           gTTGGATTGGATGCGATAGAGGGGTTGGCGGATCCGCAGTGCCATCGCCTGTGGCGGTTCGCCGTAGACGATCTCTCCGAGCTTGTCGGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTCAAGCGCTTCCACCGCTTCGGaaa                                                                                                                          <  2:324971/149‑1 (MQ=255)                    gAAGCGATAGAGGGAGTAGGAGATCAGCAGTGGCATCACCTGTGGCAGCACGCCGTAGAGGATCTCTTCGAGCTTGTTGGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTgg                                                                                                                 >  1:289742/1‑149 (MQ=255)                     aaGCGATAGAGGGAGTAGGAGATCAGCAGTGGCATCACCTGTGGCAGCACGCCGTAGAGGATCGCTTCGAGCTTGTTGGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGga                                                                                                                >  1:341060/1‑149 (MQ=255)                             ggtggAGTAGGAGATCAGCAGTGGCATCACCTGTGGCAGCACGCCGTAGAGGATCTCTTCGAGCTTGTTGGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGc                                                                                                        <  2:307447/146‑1 (MQ=255)                                      ggAGATCAGCAGTGGCATCACCTGTGGCAGCACGCCGTAGAGGATCTCTTCGAGCTTGTTGGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGCCGGTGgtgt                                                                                               <  1:366368/149‑1 (MQ=255)                                      ggAGATCAGCAGTGGCATCACCTGTGGCAGCACGCCGTAGAGGATCTCTTCGAGCTTGTTGGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTAGACGCCACGCCGgtcgtgc                                                                                               >  2:565191/1‑148 (MQ=255)                                         gaTCAGCAGTGGCATCACCTGTGGCAGCACGCCGTAGAGGATCTCTTCGAGCTTGTTGGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAACAGCTGGGCGACCACGCCGGTGGTGTGGa                                                                                            >  2:373247/1‑149 (MQ=255)                                          aTCAGCAGTGCCACCACCTGTGGCAGCACGCCGTAGAGGATCTCTTCGAGCTTGTTGGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGCCGGTGGTGTGGAt                                                                                           >  2:77151/1‑149 (MQ=255)                                              gcagGGGCATCACCTGTGGCAGCAGGCCGTAGAGGATCTCTTCGAGCTTGTTGGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGCCGGTGGTGTGGATAAAc                                                                                       <  2:605056/149‑1 (MQ=255)                                               cagTGGCATCACCTGTGGCAGCACGCCGTAGAGGATCTCTTCGAGCTTGTTGGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGCCGGTGGTGTGGATAAACa                                                                                      <  1:361234/149‑1 (MQ=255)                                                   ggCATCACCTGGGGCAGCACGCCGTAGAGGATCTCTTCGAGCTTGTTGGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGCCGGTGGTGTGGATAAACAgcgc                                                                                  <  2:467047/149‑1 (MQ=255)                                                       tCACCTGTGGCAGCACGCCGTAGAGGATCTCTTCGAGCTTGTTGGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGCCGGTGGTGTGGATAAACAGcgccagc                                                                              >  1:340498/1‑149 (MQ=255)                                                         ccctgcagcagcaCGCCGTAGAGGATCTCTCCGAGCTTGTTGGTACCGGTGGCGAGAATGCCTTCCACCGGGCCGGGCTCAATCGCTTCCACCGCGTCGGAAAGTAGCTTGGAGAGCACGCCGGTGGTGTGGATAAACAGcgccagcac                                                                            <  1:416039/142‑1 (MQ=255)                                                         cccTGTGGCAGCACGCCGGAGAGGATCTCTTCGAGCTTGTTGGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGCCGGTGGTGTGGATAAACAGcgccagcac                                                                            <  2:341060/148‑1 (MQ=255)                                                           cTGTGGCAGCACGCCGTAGAGGATCTCTTCGAGCTTGTTGGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTCAATCGCTTCCACCCCTTCGGCAAGCAGCTTGGGGAGCACGCCGGTGGTGCGGATCAACAGccccagcacgc                                                                          >  2:248428/1‑149 (MQ=255)                                                           cTGTGGCAGCACGCCGTAGAGGATCTCTTCGAGCTTGTTGGCACCGGTGGCGCGAATGCCTCCCATCTGGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGGGCACGCCGGGGGTGTGGATAAACAGcgccagcacgc                                                                          >  1:91047/1‑149 (MQ=255)                                                              tgGCAGCACGCCGTAGAGGATCTCTGCGAGCGTGGTGGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGCCGGTGGTGTGGATAAACAGcgccagcacgccag                                                                       <  2:145192/149‑1 (MQ=255)                                                                     ccGCCGTAGAGGACCTCTTCGAGCTTGTTGGCACCGGGGGCGCGAATGCCTTCCACCGGGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGCCGGTGGTGTGGATAAACAGCGCCAgcacgccagcacgcca                                                                <  1:136887/148‑1 (MQ=255)                                                                             gagGATCCTTGCGAGCGTGTTGGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTCAATCGCTTCCACCGCTTCGGCAAGCAGCTTGGAGAGCACGCCGGTGGTGTGGATAAACAGCGCCAGCACGCCAGCACGCCAGCGAACgg                                                        <  2:265886/149‑1 (MQ=255)                                                                                    tctTCGAGCTTGTTGGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGCCGGTGGTGTGGATAAACAGCGCCAGCACGCCAGCACGCCAGCGAACGggccgagg                                                 >  1:81647/1‑149 (MQ=255)                                                                                      ttCGAGCTTGTTGGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGCCGGTGGTGTGGATAAACAGCGCCAGCACGCCAGCACGCCAGCGACCGggccgaggcc                                               >  2:374888/1‑149 (MQ=255)                                                                                      ttCGAGCTTGTTGGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTCAACCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGCCGGTGGTGTGGATAAACAGCGCCAGCACGCCAGCACGCCAGCGAACGggccgaggcc                                               >  1:419659/1‑149 (MQ=255)                                                                                         gAGCTTGTTGGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGCCGGTGGTGTGGATAAACAGCGCCAGCACGCCAGCACGCCAGCGAACGGGCCGAGGCCGAc                                            >  1:412832/1‑149 (MQ=255)                                                                                            cTTGTTGGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTCAATCGCTTCCAACGCTTAGGAAAGCAGCTTGGAGAGCACGCCGGTGGTGTGGATAAACAGCGCCGGCACGCCAGCACGCCAGCGAAGGGGCCGAGGCCGACGGc                                         >  1:374804/1‑149 (MQ=255)                                                                                               gttgGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGCCGGTGGTGTGGATAAACAGCGCCAGCACGCCAGCACGCCAGCGAACGGGCCGAGGCCGACGGCGAc                                      <  2:412832/149‑1 (MQ=255)                                                                                                ttgGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTAAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGCCGGTGGTGTGGATAAACAGCGCCAGCACGCCAGCACGCCAGCGAACGGGCCGAGGCCGACGGCGAcc                                     <  1:176204/149‑1 (MQ=255)                                                                                                       cGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGCCGGTGGTGTGGATAAACAGCGCCAGCACGCCAGCACGCCAGCGAACGGGCCGAGGCCGACGGCGACCACGAACa                              >  1:92895/1‑149 (MQ=255)                                                                                                          tGGCGCGAATGCCTTCCACCGGGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGCCGGTGGTGTGGATAAACAGCGCCAGCACGCCAGCACGCCAGCGAACGGGCCGAGGCCGACGGCGACCACGAACAGCa                           <  2:340498/149‑1 (MQ=255)                                                                                                             cgcgAATGCCTTCCACCGGGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGCCGGTGGTGTGGATAAACAGCGCCAGCACGCCAGCACGCCAGCGAACGGGCCGAGGCCGACGGCGACCACGAACAGCATgg                        <  1:522317/149‑1 (MQ=255)                                                                                                               gaaaTGCTTGCCACCGGGCCGGGCTCAATCGCTTCCACCGGTTCGGAAAGCAGCTTGGAGAGCACGCCGGTGGTGTGGATAAACAGCGCCAGCACGCCAGCACGCCAGCGAACGGGCCGAGGCCGACGGCGACCACGAACAGCATGGCg                      <  2:124380/147‑1 (MQ=255)                                                                                                                  aggCCTTCACCCGGGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGCCGGTGGTGTGGATAAACAGCGCCAGCACGCCAGCACGCCAGCGAACGGGCCGAGGCCGACGGCGACCACGAACAGCATGGCGAAg                   <  2:89553/147‑1 (MQ=255)                                                                                                                      cTTCCACCGGGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGCCGGTGGTGTGGATAAACAGCGCCAGCACGCCAGCACGCCAGCGAACGGGCCGAGGCCGACGGCGACCACGAACAGCATGGGGACGGCCa               >  2:197435/1‑149 (MQ=255)                                                                                                                       ttCCACCGGGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGCCGGTGGTGTGGa                                                                                            <  2:566578/71‑1 (MQ=255)                                                                                                                       ttCCACCGGGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGCCGGTGGTGTGGa                                                                                            <  2:566587/71‑1 (MQ=255)                                                                                                                       ttCCACCGGGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGCCGGTGGTGTGGa                                                                                            >  1:566587/1‑71 (MQ=255)                                                                                                                       ttCCACCGGGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGCCGGTGGTGTGGa                                                                                            >  1:566578/1‑71 (MQ=255)                                                                                                                                gccgggcTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGCCGGTGGTGTGGATAAACAGCGCCAGCACGCCAGCACGCCAGCGAACGGGCCGAGGCCGACGGCGACCACGAACAGCATGGCGAAGACCATTTCGTTAAt     <  2:417999/149‑1 (MQ=255)                                                                                                                                  cgggcTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGCCGGTGGTGTGGATAAACAGCGCCAGCACGCCAGCACGCCAGCGAACGGGCCGAGGCCGACGGCGACCACGAACAGCATGGCGAAGACCATTTCGTTAATgg   >  1:409553/1‑149 (MQ=255)                                                                                                                                   gggcTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGCCGGTGGTGTGGATAAACAGCGCCAGCACGCCAGCACGCCAGCGAACGGGCCGAGGCCGACGGCGACCACGAACCGCATGGGGAAGACCCGTTCGTTAATGgc  >  2:334976/1‑149 (MQ=255)                                                                                                                                   |                                                                                                                                                     CCGAGCGGACGTTGGATTCGAAGCGATAGAGGGAGTAGGAGATCAGCAGTGGCATCACCTGTGGCAGCACGCCGTAGAGGATCTCTTCGAGCTTGTTGGCACCGGTGGCGCGAATGCCTTCCACCGGGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGCCGGTGGTGTGGATAAACAGCGCCAGCACGCCAGCACGCCAGCGAACGGGCCGAGGCCGACGGCGACCACGAACAGCATGGCGAAGACCATTTCGTTAATGGC  >  NC_000913_3_pae_tpiA/4322523‑4322801

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ 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.