New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	= 287112	NA (NA)	10 (0.490)	8/278	NT	62.5%	noncoding (1/768 nt)	IS1	repeat region
	?	CP009273	= 1973068	6 (0.290)					intergenic (‑614/‑166)	flhD/uspC	flagellar class II regulon transcriptional activator, with FlhC/universal stress protein

GCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  CP009273/286995‑287112 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑AGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTCATTAACATTAAGTTGATTGTTGCCTTTCTTTGTATTTAATTAGTTTGTTGTGCGGTAAGTGTCTGTTTAAAAA  <  CP009273/1973068‑1972937                                                                                                                                                                                                                                                            GCCGGTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCAGAAAATAGTGTACTGATTCTCCGCATTAAAC                                                                                                      <  1:139721/150‑1      TACGCACCACCCCGGCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTG                                                                                                 <  1:179504/150‑1                 CCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATG                                                                                      <  2:200299/150‑1                            TGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTC                                                                           <  2:37850/150‑1                                                                     CACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATGTGTAAGACCTTTCATTAACATTAAGCTGATTGTTGCTTTTCTTTGTATTTATTT                                  >  1:14215/1‑150                                                                     CACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTCGTTAACATTAAGTTGATTGTTGCCTTTCTTTGTATTTAATT                                  >  1:19196/1‑150                                                                     CACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTCATTAACATTAAGTTGATTGTTGCCTTTCTTTGTATTTAATT                                  >  2:139324/1‑150                                                                                                   AGTAAGTTGGCAGCATCAAGAAAAAATATTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTCATTAACATTAAGTTGATTGTTGCCTTTCTTTGTATTTAATTAGTTTGTTGTGCGGTAAGTGTCTGTTTAAA    >  1:167722/1‑150                                                                                                    GTAAGTTGGCATCATCACCAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTCATTAACATTAAGTTGATTGTTGCCTTTCTTTGTATTTAATTAGTTTGTTGTGCGGTAAGTGTCTGTTTAAAA   <  2:342863/150‑1                                                                                                     TAAGTTGGCACCACCACAACAAAATAGTGTACTGATTCTCCTCATTAAACAAGTGGTTAATATATGTAAAACATTTCATTAACATTAAGGTGATTGTTGCCTTTCTTTGTATTTAATTAGTTTGTTGTGCGGTAAGTGTCTGTTTAAAAA  <  1:203503/150‑1                                                                                                                                                                                                                                                            GCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  CP009273/286995‑287112 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑AGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTCATTAACATTAAGTTGATTGTTGCCTTTCTTTGTATTTAATTAGTTTGTTGTGCGGTAAGTGTCTGTTTAAAAA  <  CP009273/1973068‑1972937

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ 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.