New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 1997111	0 (0.000)	40 (0.450)	30/98	1.2	100%	coding (704/753 nt)	tcyN	cystine ABC transporter ATP binding subunit
	?	NC_000913	2023679 =	0 (0.000)					intergenic (+1/‑289)	fliR/rcsA	flagellar biosynthesis protein FliR/DNA‑binding transcriptional activator RcsA

TTGCAGCAGAAACTTCTCGAGGAACTGGCGGGTGCGAGGCTGCTCGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/1997065‑1997111 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATAC  >  NC_000913/2023679‑2023727                                                                                                  TTGCAGCAGAAACTTCTCGAGGAACTGGCGGGTGCGAGGCTGCTCGGTTC                                                >  1:4060274/1‑50   GCAGCAGAAACTTCTCGAGGAACTGGCGGGTGCGAGGCTGCTCGGTTCC                                               <  1:871268/49‑1    CAGCAGAAACTTCTCGAGGAACTGGCGGGTGCGAGGCTGCCCGGTTCCG                                              >  1:2332531/1‑49       CAGAAACTTCTCGAGGAACTGGCGGGCGCGAGGCCGCTCGGTTCCGGAAC                                          >  1:6318070/1‑50        AGAAACTTCTCGAGGAACTGGCGGGTGCGAGGCTGCTCGGTTCCGTAACG                                         <  1:6346775/50‑1        AGAAACTTCTCGAGGAACTGGCGGGTGCGAGGCTGCTCGGTTCCGTAACG                                         >  1:2480136/1‑50        AGAAACTTCTCGAGGAACTGGCGGGTGCGAGGCTGCTCGGTTCCGTAACG                                         <  1:3417350/50‑1         GAAACTTCTCGAGGAACTGGCGGGTGCGAGGCTGCTCGGTTCCGTAACGT                                        <  1:6493128/50‑1           AACTTCTCGAGGAACTGGCGGGTGCGAGGCTGCTCGGTTCCGTAACGTTT                                      <  1:2814480/50‑1           AACTTCTCGAGGAACTGGCGGGGGCGCGGCTGCTCGGTTCCCTAACGTTT                                      >  1:3376462/1‑50                   GAGGAACTGGCGGGTGCGAGGCTGCTCGGTTCCGTAACGTTTATCATGTT                              <  1:4321187/50‑1                   GAGGAACTGGCGGGTGCGAGGCTGCTCGGTTCCGTAACGTTTATCATGTT                              <  1:3531707/50‑1                   GAGGAACTGGCGGGTGCGAGGCTGCTCGGTTCCGTAACGTTTATCATG                                <  1:2228302/48‑1                   GAGGAACTGGCGGGTGCGAGGCTGCTCGGTTCCGTAACGTTTATCATG                                <  1:5897722/48‑1                     GGAACTGGCGGGTGCGAGGCTGCTCGGTTCCGTAACGTTTATCATGTTAT                            <  1:3440703/50‑1                       AACTGGCGGGTGCGAGGCTGCTCGGTTCCGTAACGTTTATCATGTTATCC                          >  1:1832077/1‑50                         CTGGCGGGTGCGAGGCTGCTCGGTTCCGTAACGTTTATCATGTTATCCTA                        <  1:321619/50‑1                              GGGTGCGAGGCTGCTCGGTTCCGTAACGTTTATCATGTTATCCTAAGGAT                   >  1:1873997/1‑50                               GGTGCGAGGCTGCTCGGTTCCGTAACGTTTATCATGTTATCCTAAGGATT                  <  1:622103/50‑1                               GGTGCGAGGCTGCTCGGTTCCGTAACGTTTATCATGTTATCCTAAGGATT                  <  1:5048318/50‑1                                GTGCGAGGCTGCTCGGTTCCGTAACGTTTATCATGTTATCCTAAGGATTA                 <  1:5319186/50‑1                                  GCGAGGCTGCTCGGTTCCGTAACGTTTATCATGTTATCCTAAGGATTATC               >  1:1149002/1‑50                                   CGAGGCTGCTCGGTTCCGTAACGTTTATCATGTTATCCTAAGGATTATCC              <  1:265621/50‑1                                   CGAGGCTGCTCGGTTCCGTAACGTTTATCATGTTATCCTAAGGATTATC               <  1:6191177/49‑1                                     AGGCTGCTCGGTTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGA            <  1:5301358/50‑1                                      GGCTGCTCGGTTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGA            >  1:3055859/1‑49                                      GGCTGCTCGGTTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGA            >  1:6389009/1‑49                                         TGCTCGGTTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAA        >  1:1875434/1‑50                                          GCTCGGTTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAA        >  1:4994281/1‑49                                          GCTCGGTTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAA        >  1:1292002/1‑49                                          GCTCGGTTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAA        >  1:6628212/1‑49                                           CTCGGTTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAA        <  1:455803/48‑1                                            TCGGTTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAA     >  1:4465853/1‑50                                             CGGTTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAA     >  1:3597082/1‑49                                              GGTTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATA   >  1:5761685/1‑50                                               GTTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATAC  >  1:5686599/1‑50                                               GTTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATAC  <  1:1368661/50‑1                                               GTTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATAC  >  1:791649/1‑50                                               GTTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATAC  <  1:272940/50‑1                                               GTTCCGTAACGTTTATCATCTTATCCTAAGGATTATCCGAAAAATAATAC  <  1:2293883/50‑1                                                                                                  TTGCAGCAGAAACTTCTCGAGGAACTGGCGGGTGCGAGGCTGCTCGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/1997065‑1997111 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATAC  >  NC_000913/2023679‑2023727

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ 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.