New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	REL606	1409723 =	29 (0.810)	3 (0.090)	3/136	4.5	7.4%	coding (683/1236 nt)	intR	integrase
	?	REL606	1409844 =	49 (1.520)					coding (562/1236 nt)	intR	integrase
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

TTTCCATTAATGCATTGAATTCTGTTTTAGATAACGGATCAGGCTTTATTCTGTTTCGCTGTAATTTTTTTACTCCTTCAAATGGTTTAGTTGATATAAATCCCGACTGATACGCAAAACGCAACAGCGAACAGAGCAGGGCGATATA  >  REL606/1409769‑1409916                                                                            |                                                                         tttCCATTAATGCATTGAATTCTGTTTTAGATAACGGATCAGGCTTTATTCTGTTTCGCTGTAATTTTTTTACTcc                                                                          <  1:266836/76‑1 (MQ=255)  ttCCATTAATGCATTGAATTCTGTTTTAGATAACGGATCAGGCTTTATTCTGTTTCGCTGTAATTTTTTTactact                                                                         >  1:557402/1‑76 (MQ=255)   tCCCTTAATGCATTGAATTCTGTTTTAGATAACGGATCAGGCTTTATTCTGTTTCGCTGTAATTTTTTTACTCCtt                                                                        >  2:151704/1‑76 (MQ=255)     cATTAATGCATTGAATTCTGTTTTAGATAACGGATCAGGCTTTATTCTGTTTCGCAGTAATTCTTTTACTCCTTCa                                                                      >  2:972212/1‑76 (MQ=255)       ttAATGCATTGAATTCTGTTTTAGATAACGGATCAGGCTTTATTCTGTTTCGCTGTAATTTTTTTACTCCTTCaaa                                                                    <  2:615888/76‑1 (MQ=255)       ttAATGCATTGAATTCTGTTTTAGATAACGGAACAGGCTTTATTCTGTTTCGCTGTAATTTTTTTACTCCTTCaaa                                                                    >  2:913116/1‑76 (MQ=255)        tAATGCATTGAATTCTGTTTTAGATAACGGATCAGGCTTTATTCTGTTTCGCTGTAATTTTTTTACTCCTTCAAAt                                                                   <  2:356747/76‑1 (MQ=255)         naTGCATTGAATTCTGTTTTAGATAACGGATCAGGCTTTATTCTGTTTCGCTGTAATTTTTTTACTCCTTCAAATg                                                                  <  1:989313/75‑1 (MQ=255)          aTGCATTGAATTCTGTTTTAGATAACGGATCAGGCTTTATTCTGTTTCGCTGTAATTTTTTTACTCCTTCAAATgg                                                                 <  1:858922/76‑1 (MQ=255)           tGCATTGAATTCTGTTTTAGATAACGGATCAGGCTTTATTCTGTTTCGCTGTAATTTTTTTACTCCTTCAAATGGt                                                                >  2:73950/1‑76 (MQ=255)            gCATTGAATTCTGTTTTAGATAACGGATCAGGCTTTATTCTGTTTCGCTGTAATTTTTTTACTCCTTCAAATGGtt                                                               >  1:675596/1‑76 (MQ=255)            gCATTGAATTCTGTTTTAGATAACGGATCAGGCTTTATTCTGTTTCGCTGTAATTTTTTTACTCCTTCAAATGGtt                                                               <  1:44614/76‑1 (MQ=255)            gCATTGAATTCTGTTTTAGATAACGGATCAGGCTTTATTCTGTTTCGCTGTAATTTTTTTACTCCTTCAAATGGtt                                                               >  2:99365/1‑76 (MQ=255)               ttGAATTCTGTTTTAGATAACGGATCAGGCTTTATTCTGTTTCGCTGTAATTTTTTTACTCCTTCAAATAGTTTAg                                                            <  1:186418/76‑1 (MQ=255)                tGAATTCTGTTTTAGATAACGGATCAGGCTTTATTCTGTTTCGCTGTAATTTTTTTACTCCTTCAAATGGTTTAGt                                                           <  1:376946/76‑1 (MQ=255)                 gAATTCTGTTTTAGATAACGGATCAGGCTTTATTCTGTTTCGCTGTAACTTTTTAACTCCTTCAAATGGTTTAGtt                                                          >  1:482633/1‑76 (MQ=255)                  aaTTCTGTTTTAGATAACGGATCAGGCTTTATTCTGTTTCGCTGTAATTTTTTTACTCCTTCAAATGGTTTAGTTg                                                         <  2:888707/76‑1 (MQ=255)                   aTTCTGTTTTAGATAACGGATCAGGCTTTATTCTGTTTCGCTGTAATTTTTTTACTCCTTCAAATGGTTTAGTTGa                                                        <  1:662506/76‑1 (MQ=255)                     tCTGTTTTAGATAACGGATCAGGCTTTATTCTGTTTCGCTGTAATTTTTTTACTCCTTCAAATGGTTTAGTTGata                                                      >  1:377559/1‑76 (MQ=255)                       tGTTTTAGATAACGGATCAGGCTTTATTCTGTTTCGCTGTAATTTTTTTACTCCTTCAAATGGTTTAGTTGAtata                                                    <  2:675596/76‑1 (MQ=255)                        gTTTTAGATAACGGATCAGGCTTTATTCTGTTTCGCTGTAATTTTTTTACTCCTTCAAATGGTTTAGTTGATATaa                                                   >  1:38008/1‑76 (MQ=255)                         ttttAGATAACGGATCAGGCTTTATTCTGTTTCGCTGTAATTTTTTTACTCCTTCAAATGGTTTAGTTGATATaaa                                                  <  2:684687/76‑1 (MQ=255)                         ttttAGATAACGGATCAGGCTTTATTCTGTTTCGCTGTAATTTTTTTACTCCTTCAAATGGTTTAGTTGATATaaa                                                  <  1:82205/76‑1 (MQ=255)                          tttAGATAACGGATCAGGCTTTATTCTGTTTCGCTGTAATTTTTTTACTCCTTCAAATGGTTTAGTTGATATAAAt                                                 >  1:1092739/1‑76 (MQ=255)                           ttAGATAACGGATCAGGCATTATTCTGTTTCGCTGTAATTTTTTTACTCCTTCAAATGGTTTAGTTGATATAAATc                                                <  1:876316/76‑1 (MQ=255)                               aTAACGGATCAGGCTTTATTCTGTTTCGCTGTAATTTTTTTACTCCTTCAAATGGTTTAGTTGATATAAATCCCGa                                            <  1:809102/76‑1 (MQ=255)                                 aaCGGATCAGGCTTTATTCTGTTTCGCTGTAATTTTTTTACTCCTTCAAATGGTTTAGTTGATATAAATCCCGACt                                          <  2:797130/76‑1 (MQ=255)                                     gATCAGGCTTTATTCTGTTTCGCTGTACTTTTTTTACTCCTTCAAATGGTTTAGTTGATATAAATCCCGACTGATa                                      <  1:697764/76‑1 (MQ=255)                                      aTCAGGCTTTATTCTGTTTCGCTGTAATTTTTTTACTCCTTCAAATGGTTTAGTTGATATAAATCCCGACTGATAc                                     >  1:120724/1‑76 (MQ=255)                                      aTCAGGCTTTATTCTGTTTCGCTGTAATTTTTTTACTCCTTCAAATGGTTTAGTTGATATAAATCCCGACTGATAc                                     >  1:369840/1‑76 (MQ=255)                                            cTTTATTCTGTTTCGCTGTAATTTTTTTACTCCTTCAAATGGTTTAGTTGATATAAATCCCGACTGATACGCaaaa                               <  2:811955/76‑1 (MQ=255)                                             tttATTCTGTTTCGCTGTAATTTTTTTACTCCTTCAAATGGTTTAGTTGATATAAATCCCGACTGATACGCAAAAc                              <  2:422334/76‑1 (MQ=255)                                             tttATTCTGTTTCGCTGTAATCTTTTTACTCCTTCAAATGGTTTAGTTGATATAAATCCCGACTGATACGCAAAAc                              >  2:645263/1‑76 (MQ=255)                                              ttATTCTGTTTCGCTGTAATTTTTTTACTCCTTCAAATGGTTTAGTTGATATAAATCCCGACTGATACGCAAAAcn                             >  1:988738/1‑75 (MQ=255)                                               tATTCTGTTTCGCTGTAATTTTTTTACTCCTTCAAATGGTTTAGTTGATATAAATCCCGACTGATACGCAAAACGc                            >  1:303738/1‑76 (MQ=255)                                               tATTCTGGTTCGCTGTAATTTTTTTACTCCTTCAAATGGTTTAGTTGATATAAATCCCGACTGATACGCAAAACGc                            >  1:760705/1‑76 (MQ=255)                                                   cTGTTTCGCTGTAATTTTTTTACTACTTCAAATGGTTTAATTTATATAAAGCGCGACGGATACGCAAAGCGCGACa                        >  1:1060531/1‑76 (MQ=255)                                                    tGTTTCGCTGTAATTTTTTTACTCCTTCAAATGGTTTAGTTGATATAAATCCCGACTGATACGCAAAACGCAACAg                       >  1:652579/1‑76 (MQ=255)                                                     gTTTCGCTGTAATTTTTTTACTCCTTCAAATGGTTTAGTTGATATAAATCCCGACTGATACGCAAAGCNCAACacc                      <  1:1015394/76‑3 (MQ=255)                                                     gTTTCGCTGTAATTTTTTTACTCCTTCAAATGGTTTAGTTGATATAAATCCCGACTGATACGCAAAACGCAACAGc                      >  2:612948/1‑76 (MQ=255)                                                          gCTGTAATTTTTTTACTCCTTCAAATGGTTTAGTTGATATAAATCCCGACTGATACGCAAAACGCAACAGCGAACa                 <  1:73950/76‑1 (MQ=255)                                                          gCTGTAAGTTTTTTACTCCTTCAAATGGTTTAGTTGATATAAATCCCGACTGATACGCAAAACGCAACAGCGAACa                 <  2:237665/76‑1 (MQ=255)                                                            tGTAATTTTTTTACTCCTTCAAATGGTTTAGTTGATATAAATCCCGACTGATACGCAAAACGCAACAGCGAACaga               <  2:377559/76‑1 (MQ=255)                                                            tGTAATTTTTTTACTCCTTCAAATGGTTTAGTTGATATAAATCCCGACTGATACGCAAAACGCAACAGCGAACaga               <  1:332341/76‑1 (MQ=255)                                                            tGTAATTTTTTTACTCCTTCAAATGGTTTAGTTGATATAAATCCCGACTGATACGCAAAACGCAACAGCGAACaga               <  1:795739/76‑1 (MQ=255)                                                                aTTTTTTTACTCCTTCAAATGGTTTAGTTGATATAAATCCCGACTGATACGCAAAACGCAACAGCGAACAGAGCAg           <  2:760705/76‑1 (MQ=255)                                                                aTTTTTTGACTCCTTCAAATGGTTTAGTTGATATAAATCCCGACTGATACGCAAAACGCAACAGCGagcagagcag           <  1:581090/76‑1 (MQ=255)                                                                 tttttttACTCCTTCAAATGGTTTAGTTGATATAAATCCCGACTGATACGCAAAACGCAACAGCGAACAGAGCAgg          >  2:126670/1‑76 (MQ=255)                                                                  ttttttACTCCTTCAAATGGTTTAGTTGATATAAATCCCGACTGATACGCAAAACGCAACAGCGAACAGAGCAggg         >  1:427668/1‑76 (MQ=255)                                                                        aCTCCTTCAAATGGTTTAGTTGATATAAATCCCGACTGATACGCAAAACGCAACAGCGAACAGAGCAGGGCGatat   <  2:1092737/76‑1 (MQ=255)                                                                         cgccTTCAAATGGTTTAGTTGANATAAATCCCGNCTGATACGNAAAACGCAACCGCGAACAGAGCNGGGCGAtata  <  2:1010163/74‑1 (MQ=255)                                                                         cTCCTTCAAATGGTTTAGTTGATATAAATCCCGACTGATACGCAAAACGCAACAGCGAACAGAGCAGGGCGAtata  <  1:12874/76‑1 (MQ=255)                                                                         atCCTTCATATGGTTTAGTTGATATAGATGCCGACTGAGACGCANAACGCAACAGNGAACAGAGCAGGGCGAtata  <  1:126670/75‑1 (MQ=255)                                                                            |                                                                         TTTCCATTAATGCATTGAATTCTGTTTTAGATAACGGATCAGGCTTTATTCTGTTTCGCTGTAATTTTTTTACTCCTTCAAATGGTTTAGTTGATATAAATCCCGACTGATACGCAAAACGCAACAGCGAACAGAGCAGGGCGATATA  >  REL606/1409769‑1409916

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ 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.