New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_pgi	381292 =	NA (NA)	6 (0.160)	6/262	4.3	NA	intergenic (‑32/‑59)	yaiX/insC1	pseudogene, interrupted by IS2A; hexapeptide transferase superfamily; putative transferase/IS2 repressor TnpA
	?	NC_000913_3_pae_pgi	381312 =	NA (NA)					intergenic (‑52/‑39)	yaiX/insC1	pseudogene, interrupted by IS2A; hexapeptide transferase superfamily; putative transferase/IS2 repressor TnpA
Rejected: Coverage evenness skew score above cutoff.

TTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGTGCCAGGACGAATAAACGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAA  >  NC_000913_3_pae_pgi/381165‑381403                                                                                                                                                    |                                                                                            ttCCTCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAAACAATTTTTACGCCATTGCTGATTATTGTGCCAGGACGTATAAACGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGt                                                                                            <  2:217096/149‑1 (MQ=255)   ccGATTCAATAACGGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGTGCCAGGACGAATAAACGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCt                                                                                          <  2:146496/149‑1 (MQ=255)            tAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGTGCCAGGACGAATAAACGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAg                                                                                 >  1:531970/1‑149 (MQ=255)               ccGCATTTTTAATCTCGGTGGCAAAACCAATATTTACGCCATTGCTGATTATTGTGCCAGGCCGAATAAACGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTTGttt                                                                              >  2:308542/1‑149 (MQ=255)                cGCATTTTTAATCTCGGTGGCACCCGCACTTTTAACGCAAAAACTGATTATTGTGCCAGGACGAATAAACGCATAATTACTAGACTGGCCCCCGGAAAATCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAAAAATAGtttt                                                                             >  2:83448/1‑149 (MQ=21)                   aTTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGTGCCAGGACGAATAAACGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAg                                                                          >  1:264087/1‑149 (MQ=255)                    tttttAATCTCGGTGGTAAAACTAATTTTTACGTCATTGCTGATTATTGTGCCAGGAAGAATAAACGCATAATTACTAGACTGGCCTCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGa                                                                         <  2:192440/149‑1 (MQ=25)                        tAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGTGCCAGGACGAATAAACGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAg                                                                     <  2:264087/149‑1 (MQ=255)                             tcGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTTTGCCAGGACGAATAAACGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCAtt                                                                <  2:399697/149‑1 (MQ=255)                              cGGTGGCAAACCCAATTTTTACTCCATTGCTGATTATTGTGCAAGGACGAATAAACGCATAATTACCAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTg                                                               <  1:57080/149‑1 (MQ=255)                                       aaCCAATTTTTGCCGTAGTGCGGGTTAGTGCGCCAGGACGAATAAACGAATAATTACTAGACTGGGCCCCTGAATTTCCAGATAACTAGTAGCACTTAAGTAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAga                                                      <  2:354391/149‑1 (MQ=17)                                           aaTTTTTACGCCATTGCTGATTATTGTGCCAGGACGAATAAACGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGa                                                                         <  2:491887/126‑1 (MQ=255)                                           aaTTTTTACGCCATTGCTGATTATTGTGCCAGGACGAATAAACGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGa                                                                         >  1:491887/1‑126 (MQ=255)                                                    gCCATTGCTGATTATTGTGCCAGGACGAATAAACGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCtt                                         <  2:675976/149‑1 (MQ=255)                                                      cATTGCTGATTATTGTGCCAGGACGAATAAACGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCACTATCACTTAAATACGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGGTTGATGtgctag                                       >  2:183666/1‑144 (MQ=255)                                                      cATTGCTGATTATTGTGCCAGGACGAATAAACGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAg                                       >  1:208043/1‑149 (MQ=255)                                                                         aGGACGAATAAACGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCAGTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACg                    >  1:205144/1‑149 (MQ=255)                                                                           gACGAATAAACGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGc                  >  1:664555/1‑149 (MQ=255)                                                                           gACGAATAAACGCATAATTACGAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGc                  >  2:632590/1‑149 (MQ=255)                                                                            aCGAATAAACGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCg                 <  2:499009/149‑1 (MQ=255)                                                                                 tAAACGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTAccg            >  1:336/1‑148 (MQ=40)                                                                                  aaaCGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACcac           >  1:550677/1‑149 (MQ=39)                                                                                     cGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAATGCAGACGGCGTAcaaacca        >  2:682180/1‑143 (MQ=255)                                                                                      gCATAATTACTAGACTGGCCCCCTGAATATCCAGAAAACCAATAACACTTAAATAAGTGGTCTAACTAACACTAGGTTTTTTACTCGCCATTGGAGACCTGATGATTGGTTTCTTAGCGCCGGAGAAACGCAGACGGCCTACCACACAg       >  2:377/1‑149 (MQ=2)                                                                                           aTTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGaaaa  <  1:98484/149‑1 (MQ=32)                                                                                           aTTACTAGACTGGCCCCCTGAATATCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATCCTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGCATCGCTGACAGCATATCACACAGCaaaa  >  1:273692/1‑149 (MQ=11)                                                                                                                                                    |                                                                                            TTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGTGCCAGGACGAATAAACGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAA  >  NC_000913_3_pae_pgi/381165‑381403

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.