New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	AP009048	3748797 =	2 (0.040)	55 (0.980)	41/102	NT	96.5%	coding (184/984 nt)	tnaB	tryptophan transporter of low affinity
	?	AP009048	4056220 =	NA (NA)					intergenic (‑564/+15)	yrhB/insB	hypothetical protein/IS1 transposase InsAB'

TTTCTGGGGTGCCTTTATCCTTATCATTGCCTGGTTTTCAATGCTTCATTCCGGGTTATTGTTATTAG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  AP009048/3748864‑3748797 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCC  >  AP009048/4056220‑4056289                                                                                                                                            TTTCTGGGGTGCCTTTATCCTTATCATTGCCTGGTTTTCAATGCTTCATTCCGGGTTATTGTTATTAGGG                                                                      >  1:4848430/1‑70   TCTGGGGTGCCTTTATCCTTATCATTGCCTGGTTTTCAATGCTTCATTCCGGGTTATTGTTATTAGGGTA                                                                    <  1:517885/70‑1   TCTGGGGTGCCTTTATCCTTATCATTGCCTGGTTTTCAATGCTTCATTCCGGGTTATTGTTATTAGGGTA                                                                    <  1:4094102/70‑1       GGGTGCCTTTATCCTTATCATTGCCTGGTTTTCAATGCTTCATTCCGGGTTATTGTTATTAGGGTAAT                                                                  <  1:4616149/68‑1        GGTGCCTTTATCCTTATCATTGCCTGGTTTTCAATGCTTCATTCCGGGTTATTGTTATTAGGGTAATGACT                                                              >  1:3648114/1‑71         GTGCCTTTATCCTTATCATTGCCTGGTTTTCAATGCTTCATTCCGGGTTATTGTTATTAGGGTAATGACTC                                                             >  1:342665/1‑71            CCTTTATCCTTATCATTGCCTGGTTTTCAATGCTTCATTCCGGGTTATTGTTATTAGGGTAATGACTCCA                                                           <  1:3279374/70‑1               TTATCCTTATCATTGCCTGGTTTTCAATGCTTCATTCCGGGTTATTGTTATTAGGGTAATGACTCCAACT                                                        >  1:2281142/1‑70               TTATCCTTATCATTGCCTGGTTTTCAATGCTTCATTCCGGGTTATTGTTATTAGGGTAATGAC                                                               >  1:1989477/1‑63               TTATCCTTATCATTGCCTGGTTTTCAATGCTTCATTCCGGGTTATTGTTATTAGGGTAATGAC                                                               >  1:5189289/1‑63               TTATCCTTATCATTGCCTGGTTTTCAATGCTTCATTCCGGGTTATTGTTATTAGGGTAATGAC                                                               >  1:3816591/1‑63                TATCCTTATCATTGCCTGGTTTTCAATGCTTCATTCCGGGTTATTGTTATTAGGGTAAT                                                                  >  1:4395355/1‑59                TATCCTTATCATTGCCTGGTTTTCAATGCTTCATTCCGGGTTATTGTTATTAGGGTA                                                                    >  1:1336787/1‑57                 ATCCTTATCATTGCCTGGTTTTCAATGCTTCATTCCGGGTTATTGTTATTAGGGTAATGACTCCAACTTA                                                      <  1:1245103/70‑1                 ATCCTTATCATTGCCTGGTTTTCAATGCTTCATTCCGGGTTATTGTTATTAGGGTAATGACTCCAACTTA                                                      <  1:998831/70‑1                     TTATCATTGCCTGGTTTTCAATGCTTCATTCCGGGTTATTGTTATTAGGGTAATGACTCCAACTTATT                                                    <  1:1026620/68‑1                     TTATCATTGCCTGGTTTTCAATGCTTCATTCCGGGTTATTGTTATTAGGGTA                                                                    <  1:4729164/52‑1                      TATCATTGCCTGGTTTTCAATGCTTCATTCCGGGTTATTGTTATTAGGGTAATGACTCCAACTTATTGA                                                  >  1:3127843/1‑69                       ATCATTGCCTGGTTTTCAATGCTTCATTCCGGGTTATTGTTATTAGGGTAATGACTCCAACTTATTGATAG                                               >  1:3316078/1‑71                        TCATTGCCTGGTTTTCAATGCTTCATTCCGGGTTATTGTTATTAGGGTAATGACTCCAACTTATTGA                                                  >  1:775271/1‑67                            TGCCTGGTTTTCAATGCTTCATTCCGGGTTATTGTTATTAGGGTAATGACTCCAACTTATTGATAGTGTTT                                          >  1:1410487/1‑71                            TGCCTGGTTTTCAATGCTTCATTCCGGGTTATTGTTATTAGGGTAATGACTCCAACTTATTGATAGTGTTT                                          >  1:4358382/1‑71                            TGCCTGGTTTTCAATGCTTCATTCAGGGTTATTGTTATTAGGG                                                                      >  1:2437589/1‑43                             GCCTGGTTTTCAATGCTTCATTCCGGGTTATTGTTATTAGGGTAATGACTCCAACTTATTGATAGTGTTT                                          >  1:3559757/1‑70                              CCTGGTTTTCAATGCTTCATTCCGGGTTATTGTTATTAGGGTAATGACTCCAACT                                                        <  1:4556974/55‑1                                TGGTTTTCAATGCTTCATTCCGGGTTATTGTTATTAGGGTAATGACTCCAACTTATTGATAGTGTTTTATG                                      >  1:2113505/1‑71                                 tGTTTTCAATGCTTCATTCCGGGTTATTGTTATTAGGGTAATGACT                                                              >  1:5108275/2‑46                                 GGTTTTCAATGCTTCATTCCGGGTTATTGTTATTAGGGTAATGA                                                                <  1:1861568/44‑1                                  GTTTTCAATGCTTCATTCCGGGTTATTGTTATTAGGGTAATGACTCCAATTTATTGATAGTGTTTTATGTT                                    <  1:2301679/71‑1                                  GTTTTCAATGCTTCATTCCGGGTTATTGTTATTAGGGTAATGACTCCAACTTATT                                                    >  1:4211835/1‑55                                  GTTTTCAATGCTTCATTCCGGGTTATTGTTATTAGGGTAA                                                                   >  1:1840212/1‑40                                   TTTTCAATGCTTCATTCCGGGTTATTGTTATTAGGGTAATGACTCCAACTTATTGATAGTGTTT                                          <  1:943461/64‑1                                    TTTCAATGCTTCATTCCGGGTTATTGTTATTAGGGTAATGACTCC                                                            >  1:365136/1‑45                                    TTTCAATGCTTCATTCCGGGTTATTGTTATTAGGGTAATG                                                                 >  1:4069059/1‑40                                     TTCAATGCTTCATTCCGGGTTATTGTTATTAGGGTAATGACTCCAACTTATTGATAGTGTTTT                                         >  1:4217041/1‑63                                      TCAATGCTTCATTCCGGGTTATTGTTATTAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTT                                    >  1:3941433/1‑67                                      TCAATGCTTCATTCCGGGTTATTGTTATTAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTT                                    >  1:1934487/1‑67                                        AATGCTTCATTCCGGGTTATTGTTATTAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTGAGAT                               <  1:1689703/70‑1                                        AATGCTTCATTCCGGGTTATTGTTATTAGGGTAATGACTCCAACTTATTGATAGTG                                             <  1:694338/56‑1                                        AATGCTTCATTCCGGGTTATTGTTATTAGGGTAATGA                                                                >  1:5094289/1‑37                                         ATGCTTCATTCTGGGTTATTGTTATTAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGAT                               <  1:1371408/69‑1                                         ATGCTTCATTCCGGGTTATTGTTATTAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGA                                <  1:1719966/68‑1                                         ATGCTTCATTCCGGGTTATTGTTATTAGGGTAATGACTCCAAATTATTGATAGTGTTTTATGTTCAGAT                               <  1:4780158/69‑1                                          TGCTTCATTCCGGGTTATTGTTATTAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAAT                            <  1:102979/71‑1                                          TGCTTCATTCCGGGTTATTGTTATTAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAAT                            >  1:266003/1‑71                                             TTCATTCCGGGTTATTGTTATTAGGGTAATGACTCCAACTTA                                                      >  1:1434369/1‑42                                               CATTCCGGGTTATTGTTATTAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCC                        >  1:2178347/1‑70                                               CATTCCGGGTTATTGTTATTAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCC                        >  1:2997052/1‑70                                                ATTCCGGGTTATTGTTATTAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCC                        <  1:2840973/69‑1                                                ATTCCGGGTTATTGTTATTAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAG                                 >  1:4878330/1‑60                                                   CCGGGTTATTGTTATTAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATG                    <  1:4185913/70‑1                                                   CCGGGTTATTGTTATTAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAA                             >  1:2782515/1‑61                                                   CCGGGTTATTGTTATTAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAA                             >  1:1872776/1‑61                                                      GGTTATTGTTATTAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATAACT                 <  1:1637661/70‑1                                                        TTATTGTTATTAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTG              <  1:5149065/71‑1                                                        TTATTGTTATTAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTG              <  1:446169/71‑1                                                           TTGTTATTAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCA           <  1:833993/71‑1                                                           TTGTTATTAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGA                      >  1:3515863/1‑60                                                            TGTTATTAGGGTAATGACTCCAACTTATTGTTAGTTTTTTA                                        <  1:581457/41‑1                                                            TGTTATTAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTT                                    <  1:1150763/45‑1                                                             GTTATTAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCAT          <  1:4444252/70‑1                                                             GTTATTAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCA                                  >  1:2834818/1‑46                                                                ATTAGGGTAATGACTCCAACTTATTGATAGTGTTTT                                         >  1:3541636/1‑36                                                                   AGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCT    <  1:3884702/70‑1                                                                    GGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCC  <  1:103252/71‑1                                                                                                                                            TTTCTGGGGTGCCTTTATCCTTATCATTGCCTGGTTTTCAATGCTTCATTCCGGGTTATTGTTATTAG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  AP009048/3748864‑3748797 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCC  >  AP009048/4056220‑4056289

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ 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.