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.

ACATTGCGGACCAATCGTTGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGTGCCAGGACGAATAAACGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAA  >  NC_000913_3_pae_pgi/381144‑381403                                                                                                                                                     |                                                                                                                aCATTGCGGACCAATCGTTGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGTGCCAGGACGAATAAACGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAat                                                                                                                 <  2:250702/149‑1 (MQ=255)     tGCGGACCAATCGTTGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGTGCCAGGACGAATAAACGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCa                                                                                                             <  1:678774/149‑1 (MQ=255)     tGCGGACCAATCGTTGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGTGCCAGGACGAATAAACGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCa                                                                                                             <  1:505366/149‑1 (MQ=255)            cAATCGTTGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACTAATTTTTACGCCATTGCTGATTATTGTGCCAGGACGAATAAACGCATAATTACTAGACTGGCCCCTTGAATCTCCAGAAAACCACTATCACTTAAAt                                                                                                      >  2:98484/1‑149 (MQ=255)                  ttGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGTGCCAGGACGAATAAACGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAg                                                                                                   >  2:282520/1‑146 (MQ=255)                  ttGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGTGCCAGGACGAATAAACGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAg                                                                                                   <  1:282520/146‑1 (MQ=255)                  ttGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGTGCCAGGACGAATAAACGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGa                                                                                                <  2:12149/149‑1 (MQ=255)                     cTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGTGCCAGGACGAATAAACGCATAATTACTAGACTGGCCCCCCGAATCTCCAGACAACCAATATCACTTAAATAAGt                                                                                                  >  2:464601/1‑144 (MQ=255)                     cTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGTGCCAGGACGAATAAACGCATAATTACTAGACTGGCCCCCCGAATCTCCAGACAACCAATATCACTTAAATAAGt                                                                                                  <  1:464601/144‑1 (MQ=255)                      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                                                                         >  1:491887/1‑126 (MQ=255)                                                                aaTTTTTACGCCATTGCTGATTATTGTGCCAGGACGAATAAACGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGa                                                                         <  2:491887/126‑1 (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)                                                                                                                                                     |                                                                                                                ACATTGCGGACCAATCGTTGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGTGCCAGGACGAATAAACGCATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAA  >  NC_000913_3_pae_pgi/381144‑381403

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.