New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	= 254374	0 (0.000)	44 (1.430)	21/166	0.3	100%	coding (59/402 nt)	crl	sigma factor‑binding protein Crl
	?	NZ_CP009273	269667 =	NA (NA)					intergenic (+3/+145)	ykfC/BW25113_RS01325	reverse transcriptase domain‑containing protein/IS5‑like element IS5 family transposase

AACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NZ_CP009273/254288‑254374 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGC  >  NZ_CP009273/269667‑269755                                                                                                                                                                                  AACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCAGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGGAA                                                                                        <  2:145997/90‑1       TGCATCACAACAGGAGATAGCAATGACGTTACGGAGTGGACACCCGAAGAGCAGATTGATCAAAAAAGTTACCGCACTAGGGAAGGTGCG                                                                                  >  1:32450/1‑90         CATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGGAAGGTGCGAA                                                                                <  1:710210/90‑1          ATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGGAAGGTGCGAAT                                                                               >  2:567713/1‑90             ACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGGAAGGTGCGAATAAG                                                                            <  1:567713/90‑1              CAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGGAAGGTGCGAATAAGC                                                                           <  1:68138/90‑1                     AGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGGAAGGTGCGAATAAGCGGGGAAA                                                                    >  2:284791/1‑90                        TAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGGAAGGTGCGAATAAGC                                                                           <  2:892813/80‑1                        TAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGGAAGGTGCGAATAAGC                                                                           >  1:892813/1‑80                        TAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGGAA                                                                                        <  2:547504/67‑1                        TAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGGAA                                                                                        >  1:547504/1‑67                                ACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGC                                                         <  2:19389/90‑1                                  GTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTG                                                       >  1:790453/1‑90                                    TACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGAC                                                     >  2:602/1‑90                                    TACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGAC                                                     >  2:374427/1‑90                                    TACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGAC                                                     <  2:830930/90‑1                                      CCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTC                                                   <  2:486038/90‑1                                          GTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTC                                               >  1:631546/1‑90                                          GTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTC                                               >  2:695704/1‑90                                             GACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATT                                            <  2:238147/90‑1                                                  CCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATT                                       <  1:269635/90‑1                                                    GAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTC                                     >  2:729108/1‑90                                                           AGATTGATCAAAAAATTTACCGCACTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGT                              >  2:722730/1‑90                                                               TGATCAAAAAATTTACCGCACTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCA                                                  <  1:123305/66‑1                                                               TGATCAAAAAATTTACCGCACTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCA                                                  >  2:123305/1‑66                                                                                   CTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAA      >  2:40307/1‑90                                                                                    TAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAA     <  1:364261/90‑1                                                                                    TAGGGAAGGTGCGAATAAG‑GGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAAT    <  2:390999/90‑1                                                                                     AGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAAT    <  1:805306/90‑1                                                                                     AGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAAT    <  2:805973/90‑1                                                                                     AGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAAT    <  2:847659/90‑1                                                                                     AGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAAT    <  2:311365/90‑1                                                                                     AGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAAT    <  1:47015/90‑1                                                                                     AGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAAT    <  1:622645/90‑1                                                                                     AGGGAAGGTGCGAATAAGCGGAGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAAT    <  1:625978/90‑1                                                                                      GGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATG   >  2:688201/1‑90                                                                                      GGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATG   >  1:21456/1‑90                                                                                      GGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATG   >  2:215779/1‑90                                                                                      GGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATG   >  1:794647/1‑90                                                                                      GGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATG   >  1:789912/1‑90                                                                                      GGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATG   >  1:736831/1‑90                                                                                      GGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATG   >  1:388324/1‑90                                                                                      GGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAA     >  2:593310/1‑88                                                                                      GGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAA     <  1:593310/88‑1                                                                                       GGAAGGTGCGAATAAGCGGGGGAATTCTTCTCGGCTGGCTCAGCCATTTCATTTCTTCATGTTTGAGCCGTTTTTTTCTCCCGTAAATGC  >  1:713411/1‑90                                                                                       GGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGC  >  1:125804/1‑90                                                                                       GGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGC  >  2:57361/1‑90                                                                                       GGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGC  >  2:488650/1‑90                                                                                       GGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGC  >  2:611142/1‑90                                                                                       GGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGC  >  1:786890/1‑90                                                                                                                                                                                  AACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NZ_CP009273/254288‑254374 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGC  >  NZ_CP009273/269667‑269755

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ 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.