New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	AP009048	= 274373	NA (NA)	72 (0.880)	34/98	NT	100%	intergenic (‑32/‑176)	insH/mmuP	IS5 transposase and trans‑activator/predicted S‑methylmethionine transporter
	?	AP009048	576000 =	0 (0.000)					pseudogene (109/1128 nt)	nmpC	DLP12 prophage region; ECK0544:JW5078:b0553; truncated outer membrane porin

ATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTATTAAGCGCCCGGC  >  AP009048/274304‑274443                                                                      |                                                                       atgatgAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCg                                                                       >  1:2285074/1‑71 (MQ=31) atgatgAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCAACTTCCg                                                                       <  1:2995041/71‑1 (MQ=14)  tgatgaACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCgg                                                                      <  1:5835063/71‑1 (MQ=32)    atgaACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAg                                                                    <  1:3049169/71‑1 (MQ=35)     tgaACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAgg                                                                   >  1:896304/1‑71 (MQ=38)     tgaACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAgg                                                                   >  1:746556/1‑71 (MQ=38)     tgaACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAgg                                                                   >  1:4249343/1‑71 (MQ=38)       aaCCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGc                                                                  <  1:2263731/70‑1 (MQ=40)        aCCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGt                                                                <  1:3610347/71‑1 (MQ=255)         cccTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGtt                                                               <  1:4853613/71‑1 (MQ=255)         cccTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGtt                                                               <  1:340598/71‑1 (MQ=255)         cccTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGtt                                                               <  1:2646028/71‑1 (MQ=255)          ccTGTTCTATGGCTCCAGATGACAAACATGATCTCATTTCAGGGACTTGTTCGCACCTTCCGGa                                                                     >  1:1847893/1‑64 (MQ=25)          ccTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGa                                                                     >  1:7286228/1‑64 (MQ=35)          ccTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCATCCGGa                                                                     >  1:5590250/1‑64 (MQ=25)           cTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTAt                                                             <  1:4735275/71‑1 (MQ=255)             gTTCTATGGCTCCAGATGACAAACAAGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATg                                                            <  1:7367748/70‑1 (MQ=255)              ttCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGa                                                           <  1:6567904/70‑1 (MQ=255)              ttCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAg                                                          >  1:1004920/1‑71 (MQ=255)              ttCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAg                                                          >  1:4501260/1‑71 (MQ=255)              ttCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAg                                                          >  1:7346450/1‑71 (MQ=255)              ttCCATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAg                                                          >  1:6464126/1‑71 (MQ=255)               tCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGc                                                         >  1:1087466/1‑71 (MQ=255)                cTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAg                                                          >  1:1651156/1‑69 (MQ=255)                 tATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTg                                                       >  1:5381350/1‑71 (MQ=255)                  aTGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTgg                                                      >  1:2150470/1‑71 (MQ=255)                    ggCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGc                                                                  >  1:2654822/1‑57 (MQ=255)                        ccAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGccc                                                >  1:5858456/1‑71 (MQ=255)                        ccAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGccc                                                >  1:5999885/1‑71 (MQ=255)                         cAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGcc                                                 <  1:6918614/69‑1 (MQ=255)                          aGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCtt                                              <  1:4995759/71‑1 (MQ=255)                           gATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCgg                                                                      <  1:2827459/46‑1 (MQ=35)                           gATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCgg                                                                      <  1:2793940/46‑1 (MQ=35)                           gATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTgg                                                      >  1:6844845/1‑62 (MQ=255)                           gATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCttt                                             <  1:2737491/71‑1 (MQ=255)                           gATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCttt                                             >  1:2407735/1‑71 (MQ=255)                             tGACAGACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCttttt                                           <  1:5920838/71‑1 (MQ=255)                             tGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCttttt                                           <  1:1486284/71‑1 (MQ=255)                               aCAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGt                                         <  1:7477424/71‑1 (MQ=255)                                cAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGa                                                           >  1:4083574/1‑52 (MQ=255)                                cAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAg                                                          >  1:2574380/1‑53 (MQ=255)                                cAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAg                                                          >  1:1796089/1‑53 (MQ=255)                                cAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAg                                                          >  1:7424693/1‑53 (MQ=255)                                 aaaCATGATCTCATATCAGGGACTTGTTCGCACCTTCCgg                                                                      <  1:5690063/40‑1 (MQ=37)                                 aaaCATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGt                                                                <  1:6868956/46‑1 (MQ=255)                                 aaaCATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGt                                                                <  1:4169337/46‑1 (MQ=255)                                 aaaCATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTAt                                       <  1:1456073/71‑1 (MQ=255)                                   aCATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAg                                                          >  1:4083885/1‑50 (MQ=255)                                   aCATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAg                                                          >  1:2940384/1‑50 (MQ=255)                                     aTGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTgg                                                      >  1:1360696/1‑52 (MQ=255)                                      tGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGat                                  <  1:6992556/71‑1 (MQ=255)                                      tGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGat                                  <  1:6391868/71‑1 (MQ=255)                                         tctcATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTAt                                       >  1:2122526/1‑63 (MQ=255)                                          ctcATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCtttt                                            <  1:5231105/57‑1 (MQ=255)                                           tcATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGattatt                              >  1:3556167/1‑70 (MQ=255)                                            cATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTaa                            >  1:2671162/1‑71 (MQ=255)                                                tCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCttttt                                           >  1:7270388/1‑52 (MQ=255)                                                tCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCttttt                                           >  1:6630993/1‑52 (MQ=255)                                                  aGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTgg                                                      >  1:7553381/1‑39 (MQ=255)                                                  aGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATcccc                       <  1:490975/70‑1 (MQ=255)                                                    ggACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTgg                                                      <  1:2894097/37‑1 (MQ=255)                                                    ggACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTgg                                                      <  1:800143/37‑1 (MQ=255)                                                    ggACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCAcc                    >  1:2093796/1‑71 (MQ=255)                                                       cTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAAt                           >  1:5895367/1‑61 (MQ=255)                                                       cTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCGGc                 <  1:4643920/71‑1 (MQ=255)                                                         tGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGAttatta                             >  1:2272607/1‑57 (MQ=255)                                                         tGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTa               >  1:5067689/1‑71 (MQ=255)                                                         tGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTa               >  1:4958968/1‑71 (MQ=255)                                                          gTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCtttt                                            >  1:4090658/1‑41 (MQ=255)                                                          gTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTa               <  1:3171025/70‑1 (MQ=255)                                                           ttCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGa                                   >  1:7690512/1‑49 (MQ=255)                                                            tCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCt                                     <  1:3979418/46‑1 (MQ=255)                                                            tCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTAtt             <  1:4866146/70‑1 (MQ=255)                                                             cGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCt                                     <  1:6846517/45‑1 (MQ=255)                                                              gCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTATTaa           <  1:2164315/70‑1 (MQ=255)                                                               cACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGatta                                >  1:5153241/1‑48 (MQ=255)                                                               cACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAAt                           <  1:5380615/53‑1 (MQ=255)                                                               cACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTATTAAgc         <  1:6920430/71‑1 (MQ=255)                                                                aCCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTATTAAgcg        <  1:7878641/71‑1 (MQ=255)                                                                 ccTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATcc                         >  1:3942111/1‑53 (MQ=255)                                                                 ccTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATcc                         >  1:4306022/1‑53 (MQ=255)                                                                  cTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTATTAAGCGcc      <  1:2532852/71‑1 (MQ=255)                                                                    tCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCAc                     >  1:713822/1‑54 (MQ=255)                                                                      cGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTATTAAGCGCCCGgc  <  1:782646/71‑1 (MQ=255)                                                                      |                                                                       ATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTATTAAGCGCCCGGC  >  AP009048/274304‑274443

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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.