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

TTATTGCAGCAGAAACTTCTCGAGGAACTGGCGGGTGCGAGGCTGCTCGGGGTCGGCAAATAACGCTTTTGCGGCCCCCTGCTCGACTATCCGCCCCTG  >  NC_000913/1997062‑1997160                                                  |                                                  ttattGCAGCAGAAACTTCTCGAGGAACTGGCGGGGGGGAGGGTGGTCgg                                                   >  1:6054799/1‑50 (MQ=37)    ttGCAGCAGAAACTTCTCGAGGAACTGGCGGGTGCGAGGCTGCTCGGttc                                                >  1:4060274‑M1/1‑47 (MQ=255)      gcagcaGAAACTTCTCGAGGAACTGGCGGGTGCGAGGCTGCTCGGttcc                                               <  1:871268‑M1/49‑5 (MQ=255)       cagcagAAACTTCTCGAGGAACTGGCGGGTGCGAGGCTGCCCGGttccg                                              >  1:2332531‑M1/1‑44 (MQ=255)          cagAAACTTCTCGAGGAACTGGCGGGCGCGAGGCCGCTCGGttccggaac                                          >  1:6318070‑M1/1‑41 (MQ=255)           agAAACTTCTCGAGGAACTGGCGGGTGCGAGGCTGCTCGGttccgtaacg                                         <  1:3417350‑M1/50‑11 (MQ=255)           agAAACTTCTCGAGGAACTGGCGGGTGCGAGGCTGCTCGGttccgtaacg                                         >  1:2480136‑M1/1‑40 (MQ=255)           agAAACTTCTCGAGGAACTGGCGGGTGCGAGGCTGCTCGGttccgtaacg                                         <  1:6346775‑M1/50‑11 (MQ=255)            gAAACTTCTCGAGGAACTGGCGGGTGCGAGGCTGCTCGGttccgtaacgt                                        <  1:6493128‑M1/50‑12 (MQ=255)              aaCTTCTCGAGGAACTGGCGGGTGCGAGGCTGCTCGGttccgtaacgttt                                      <  1:2814480‑M1/50‑14 (MQ=255)              aaCTTCTCGAGGAACTGGCGGGGGCGCGGCTGCTCGGttccctaacgttt                                      >  1:3376462‑M1/1‑37 (MQ=255)                      gAGGAACTGGCGGGTGCGAGGCTGCTCGGttccgtaacgtttatcatgtt                              <  1:3531707‑M1/50‑22 (MQ=255)                      gAGGAACTGGCGGGTGCGAGGCTGCTCGGttccgtaacgtttatcatgtt                              <  1:4321187‑M1/50‑22 (MQ=255)                      gAGGAACTGGCGGGTGCGAGGCTGCTCGGttccgtaacgtttatcatg                                <  1:5897722‑M1/48‑20 (MQ=255)                      gAGGAACTGGCGGGTGCGAGGCTGCTCGGttccgtaacgtttatcatg                                <  1:2228302‑M1/48‑20 (MQ=255)                        ggAACTGGCGGGTGCGAGGCTGCTCGGttccgtaacgtttatcatgttat                            <  1:3440703‑M1/50‑24 (MQ=255)                          aaCTGGCGGGTGCGAGGCTGCTCGGttccgtaacgtttatcatgttatcc                          >  1:1832077‑M1/1‑25 (MQ=255)                            cTGGCGGGTGCGAGGCTGCTCGGttccgtaacgtttatcatgttatccta                        <  1:321619‑M1/50‑28 (MQ=255)                                 gggTGCGAGGCTGCTCGGttccgtaacgtttatcatgttatcctaaggat                   >  1:1873997‑M1/1‑18 (MQ=255)                                  ggTGCGAGGCTGCTCGGttccgtaacgtttatcatgttatcctaaggatt                  <  1:5048318‑M1/50‑34 (MQ=255)                                  ggTGCGAGGCTGCTCGGttccgtaacgtttatcatgttatcctaaggatt                  <  1:622103‑M1/50‑34 (MQ=255)                                   gTGCGAGGCTGCTCGGttccgtaacgtttatcatgttatcctaaggatta                 <  1:5319186‑M1/50‑35 (MQ=255)                                     gCGAGGCTGCTCGGttccgtaacgtttatcatgttatcctaaggattatc               >  1:1149002‑M1/1‑14 (MQ=255)                                      cGAGGCTGCTCGGttccgtaacgtttatcatgttatcctaaggattatcc              <  1:265621‑M1/50‑38 (MQ=255)                                      cGAGGCTGCTCGGttccgtaacgtttatcatgttatcctaaggattatc               <  1:6191177‑M1/49‑37 (MQ=255)                                        aGGCTGCTCGGttccgtaacgtttatcatgttatcctaaggattatccga            <  1:5301358‑M1/50‑40 (MQ=255)                                         ggCTGCTCGGttccgtaacgtttatcatgttatcctaaggattatccga            >  1:6389009‑M1/1‑10 (MQ=255)                                         ggCTGCTCGGttccgtaacgtttatcatgttatcctaaggattatccga            >  1:3055859‑M1/1‑10 (MQ=255)                                            tgctCGGttccgtaacgtttatcatgttatcctaaggattatccgaaaaa        >  1:1875434‑M1/1‑7 (MQ=255)                                             gctCGGttccgtaacgtttatcatgttatcctaaggattatccgaaaaa        >  1:1292002‑M1/1‑6 (MQ=255)                                             gctCGGttccgtaacgtttatcatgttatcctaaggattatccgaaaaa        >  1:4994281‑M1/1‑6 (MQ=255)                                             gctCGGttccgtaacgtttatcatgttatcctaaggattatccgaaaaa        >  1:6628212‑M1/1‑6 (MQ=255)                                              ctCGGttccgtaacgtttatcatgttatcctaaggattatccgaaaaa        <  1:455803‑M1/48‑44 (MQ=255)                                               tCGGttccgtaacgtttatcatgttatcctaaggattatccgaaaaataa     >  1:4465853‑M1/1‑4 (MQ=255)                                                cGGttccgtaacgtttatcatgttatcctaaggattatccgaaaaataa     >  1:3597082‑M1/1‑3 (MQ=255)                                                 ggttccgtaacgtttatcatgttatcctaaggattatccgaaaaataata   >  1:5761685‑M1/1‑2 (MQ=255)                                                  gttccgtaacgtttatcatgttatcctaaggattatccgaaaaataatac  >  1:5686599‑M1/1‑1 (MQ=255)                                                  gttccgtaacgtttatcatgttatcctaaggattatccgaaaaataatac  <  1:1368661‑M1/50‑50 (MQ=255)                                                  gttccgtaacgtttatcatgttatcctaaggattatccgaaaaataatac  <  1:272940‑M1/50‑50 (MQ=255)                                                  gttccgtaacgtttatcatgttatcctaaggattatccgaaaaataatac  >  1:791649‑M1/1‑1 (MQ=255)                                                  gttccgtaacgtttatcatcttatcctaaggattatccgaaaaataatac  <  1:2293883‑M1/50‑50 (MQ=255)                                                  |                                                  TTATTGCAGCAGAAACTTCTCGAGGAACTGGCGGGTGCGAGGCTGCTCGGGGTCGGCAAATAACGCTTTTGCGGCCCCCTGCTCGACTATCCGCCCCTG  >  NC_000913/1997062‑1997160

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.