New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	AP009048	= 2018583	2 (0.040)	46 (0.960)	33/98	NT	96.0%	coding (579/687 nt)	fliH	flagellar biosynthesis protein
	?	AP009048	= 2521059	NA (NA)					intergenic (+170/+30)	insL/yfeA	predicted transposase/predicted diguanylate cyclase

GCAACGTGTGGATGATATGCTCGGCGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  AP009048/2018514‑2018583 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ccATAAGCGCTAACTTAAGGGTTGAACCATCTGAAGAATGCGACGCCTCGGTGCCTCGTTAAGACGATGCCT  <  AP009048/2521059‑2520990                                                                                                                                              GCAACGTGTGGATGATATGCTCGGCGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCA                                                                       >  1:525462/1‑71  CAACGTGTGGATGATATGCTCGGCGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCAT                                                                      <  1:1459252/71‑1               ATATGCTCGGCGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCATAAGCGCTAACTT                                                          <  1:2358714/70‑1               ATATGCTCGGCGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCATAAGCGCTAACTT                                                          <  1:188802/70‑1               ATATGCTCGGCGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCATAAGCGCTAACTT                                                          <  1:183520/70‑1                TATGCTCGGCGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCATAAGCGCTAACTTAA                                                        <  1:3495075/71‑1                TATGCTCGGCGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCATAAGCGCTAACTT                                                          >  1:4160391/1‑69                TATGCTCGGCGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCA                                                                       >  1:1766993/1‑56                    CTCGGCGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCATAAGCGCTAACTTAAGGG                                                     <  1:2484562/70‑1                       GGCGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCATAAGCGCTAACTTAAGGGTT                                                   <  1:2317249/69‑1                         CGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCATAAGCGCTAACTTAAGGGTTGAAC                                               >  1:2704502/1‑71                           CTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCATAAGCGCTAACTTAAGGGTTGAACCA                                             <  1:2755164/71‑1                            TACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCATAAGCGCTAACTTAAGGGTTGAACCAT                                            >  1:3174497/1‑71                              CCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCATAAGCGCTAACTTAAGGGTTGAACCATCT                                          >  1:2937150/1‑71                              CCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCATAAGCGCTAACTTAAGGGTTGAACCATC                                           <  1:2704351/70‑1                              CCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCATAAGCGCTAACTTAAGGGTTGAACCAT                                            <  1:1733948/69‑1                              CCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCATAAGCGCTAACTTAAGGGTTGAACCAT                                            <  1:2190065/69‑1                              CCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCATAAGCG                                                                 <  1:1345827/48‑1                               CTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCATAAGCGCTAACTTAAGGGTTGAACCATCT                                          >  1:643069/1‑70                                 TAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCATAAGCGCTAACTTAAGGGTTGAACCATCTG                                         >  1:1412594/1‑69                                  AAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCATAAGCGCTAACTTAAGGGTTGAACCATCTGAA                                       <  1:4011993/70‑1                                    GTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCATAAGCGCTAACTTAAGGGTTGAACCATCTGA                                        <  1:4167445/67‑1                                     TTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCATAAGCGCTAACTTAAGGGTTGAACCA                                             <  1:1385265/61‑1                                     TTTGCATGGCTGGCGCTTGCGGGGCGATCCCACCATAAGCGCTA                                                              <  1:4062644/44‑1                                       TGCATGGCTGGCGCTTGCGGGGCGATCCCACCATAAGCGCTAACTTAAGGGTTGAACCATCTGAAG                                      <  1:1893034/66‑1                                       TGCATGGCTGGCGCTTGCGGGGCGATCCCACCATAAGCGCTAACTTAAGG                                                      >  1:1938852/1‑50                                        GCATGGCTGGCGCTTGCGGGGCGATCCCACCATAAGCGCTAACTTAAGGGTTGAACCATCTGAAGAATGC                                 <  1:1935312/70‑1                                        GCATGGCTGGCGCTTGCGGGGCGATCCCACCATAAGCGCTAACTTAAGGGTTGAACCATCTGAAGAATGC                                 <  1:936696/70‑1                                          ATGGCTGGCGCTTGCGGGGCGATCCCACCATAAGCGCTAACTTAAGGGTTGAACCATCTGAAGAATGC                                 <  1:402743/68‑1                                          ATGGCTGGCGCTTGCGGGGCGATCCCACCATAAGCGCTAACTTAAGGGTTGAACCATCTGAAGAA                                    <  1:2102901/65‑1                                           TGGCTGGCGCTTGCGGGGCGATCCCACCATAAGCGCTAACTTAAGGGTTG                                                  <  1:3722892/50‑1                                            GGCTGGCGCTTGCGGGGCGATCCCACCATAAGCGCTAACTTAAGGGTTGAACCATCTGAAGAATGCGACGC                            >  1:3262766/1‑71                                            GGCTGGCGCTTGCGGGGCGATCCCACCATAAGCGCTAACTTAAGGGTTGAACCATCTGAAGAATGCGACGC                            >  1:1584200/1‑71                                            GGCTGGCGCTTGCGGGGCGATCCCACCATAAGCGCTAACTTAAGGGTTGAACCATCTGAAGAATGCGACGC                            >  1:999238/1‑71                                             GCTGGCGCTTGCGGGGCGATCCCACCATAAGCGCTAACTTAAGGGTTGAACCATCTGAAGAATGCGACGC                            <  1:2462806/70‑1                                                  CGCTTGCGGGGCGATCCCACCATAAGCGCTAACTTAAGGGTTGAACCATCTGAAGAATGCGACGCCTCGGT                      <  1:3441668/71‑1                                                    CTTGCGGGGCGATCCCACCATAAGCGCTAACTTAAGGGTTGAACCATCTG                                         <  1:1413568/50‑1                                                       GCGGGGCGATCCCACCATAAGCGCTAACTTAAGGGTTGAACCATC                                           >  1:258682/1‑45                                                       GCGGGGCGATCCCACCATAAGCGCTAACTTAAGGGTTGAA                                                >  1:4374856/1‑40                                                        CGGGGCGATCCCACCATAAGCGCTAACTTAAGGGTTGAACCATCTGAAGAATGCGACGCCTCGGTGCCTCG                <  1:2516824/71‑1                                                        CGGGGCGATCCCACCATAAGCGCTAACTTAAGGGTTGAACCATCTGAAGAATGCGACGCCTCGGTGCCTCG                <  1:2503619/71‑1                                                          GGGCGATCCCACCATAAGCGCTAACTTAAGGGTTGAACCATCTGAAGAATGCGACGCCTCGGTGCCTCGT               <  1:3118129/70‑1                                                           GGCGATCCCACCATAAGCGCTAACTTAAGGGTTGAACCATCTGAAGAATGCGACGCCTCGGTGCCTCGTTA             <  1:1081709/71‑1                                                           GGCGATCCCACCATAAGCGCTAACTTAAGGGTTGAACCATCTGAAGAATGCGACGCCTCGGTGCCTCG                <  1:2654351/68‑1                                                           GGCGATCCCACCATAAGCGCTAACTTAAGGGTTGAACCATCTGAAGAA                                    >  1:1148031/1‑48                                                             CGATCCCACCATAAGCGCTAACTTAAGGGTTGAACCATCTGAAGAATGCGACGCCTCGGTGCCTCGTTAAG           <  1:817077/71‑1                                                              GATCCCACCATAAGCGCTAACTTAAGGGTTGAACCATCTGAAGAATGCGACGCCTCGGTGCCTCGTTAAGA          >  1:3593741/1‑71                                                              GATCCCACCATAAGCGCTAACTTAAGGGTTGAACCATCTGAAGAATGCGACGCCTCGGTGCCTCGTTAAGA          >  1:2123884/1‑71                                                               ATCCCACCATAAGCGCTAACTTAAGGGTTGAACCATCTGAA                                       <  1:1090457/41‑1                                                                TCCCACCATAAGCGCTAACTTAAGGGTTGAACCATCTGAAGAATGCGACGCCTCGGTGCCTCGTTAAGAC         <  1:1142550/70‑1                                                                 CCCACCATAAGCGCTAACTTAAGGGTTGAACCATCTGAAGAATGCGACGCCTCGGTGCCTCGTTAAGACGA       >  1:1055574/1‑71                                                                 CCCACCATAAGCGCTAACTTAAGGGTTGAACCATCTGAA                                       <  1:3618423/39‑1                                                                  CCACCATAAGCGCTAACTTAAGGGTTGAACCATCTGAAGAATGCGACGCCTCGGTGCCTCGTTAAGACGAT      <  1:4055795/71‑1                                                                  CCACCATAAGCGCTAACTTAAGGGTTGAACCATCTGAAGAATGCGACGCCTCGGTGCCTCGTTAAGACGA       <  1:2218004/70‑1                                                                  CCACCATAAGCGCTAACTTAAGGGTTGAACCATCTGAAGAATGCGACGCCTCGGTGCCTCGTTAAGACGA       <  1:4309274/70‑1                                                                   CACCATAAGCGCTAACTTAAGGGTTGAACCATCTGAAGAATG                                  >  1:127880/1‑42                                                                    ACCATAAGCGCTAACTTAAGGGTTGAACCATCTGAAGAATGCGACGCCTCGGTGCCTCGTTAAGACGATGC    >  1:3351832/1‑71                                                                     CCATAAGCGCTAACTTAAGGGTTGAACCATCTGAAGAATGCGACGCCTCGGTGCCTCGTTAAGACGATGCC   >  1:1705146/1‑71                                                                     CCATAAGCGCTAACTTAAGGGTTGAACCATCTGAAGAATGCGACGCCTCGGTGCCTCGTTAAGACGATGCC   <  1:617370/71‑1                                                                     CCATAAGCGCTAACTTAAGGGTTGAACCATCTGAAGAATGCGACGCCTCGGTGCCTCGTTAAGACGAT      >  1:3401231/1‑68                                                                     CCATAAGCGCTAACTTAAGGGTTGAACCATCTGAAGAATGCGACGCCTCGGTGCCTCGTTAAGACGA       >  1:3980142/1‑67                                                                     CCATAAGCGCTAACTTAAGGGTTGAACCATCTGAAGAATGCGACGCCTCGGTGCCTCGTTAAGACGA       >  1:795137/1‑67                                                                     CCATAAGCGCTAACTTAAGGGTTGAACCATCTGAAGAATGCGACGCCTCGGTGCCTCGTTAAGACGA       >  1:2213723/1‑67                                                                     CCATAAGCGCTAACTTAAGGGTTGAACCATCTGAA                                       <  1:1595106/35‑1                                                                      CATAAGCGCTAACTTAAGGGTTGAACCATCTGAAGAATGCGACGCCTCGGTGCCTCGTTAAGACGATGCCT  <  1:162502/71‑1                                                                      CATAAGCGCTAACTTAAGGGTTGAACCATCTGAAGAATGCGACGCCTCGGTGCCTCGTTAAGACGATGCCT  <  1:374264/71‑1                                                                      CATAAGCGCTAACTTAAGGGTTGAACCATCTGAAG                                      <  1:192465/35‑1                                                                                                                                              GCAACGTGTGGATGATATGCTCGGCGCTACCTTAAGTTTGCATGGCTGGCGCTTGCGGGGCGATCCCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  AP009048/2018514‑2018583 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ccATAAGCGCTAACTTAAGGGTTGAACCATCTGAAGAATGCGACGCCTCGGTGCCTCGTTAAGACGATGCCT  <  AP009048/2521059‑2520990

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ 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.