New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	= 287112	NA (NA)	5 (0.350)	5/274	NT	55.6%	noncoding (1/768 nt)	IS1	repeat region
	?	CP009273	= 1973068	4 (0.280)					intergenic (‑614/‑166)	flhD/uspC	flagellar class II regulon transcriptional activator, with FlhC/universal stress protein

AGCGCTGATGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATATCTGGAAGCAATCATGGAGGCTCGTGTTACCGTTGCTGGCATGGGGCTGGTGATGGAGGTGCA  >  CP009273/286970‑287260                                                                                                                                               |                                                                                                                                                     aGCGCTGATGGCCGGCAGTGCTTTTGCCGGTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACATCATCATACACTAAATCATTCAGTTGCCCGCATCACCGaa                                                                                                                                                   <  2:119109/146‑1 (MQ=11)             cGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGCGGGACAGATGATAGAAACAGAAGCCACTGGAGCACATCAGAAACACCATCATACAATAACTAAGTACGTTGGCAGCATCACCGAATTTTGAGCCCGGTTGt                                                                                                                                   >  1:218208/1‑150 (MQ=11)                       tttgctctcaCGGACAACCCCGTCATTAGCCGAACAGGAGGGACAGCTGATATAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCACTCACTAACCCATTAAGTTTGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTAcc                                                                                                                         <  1:121753/141‑1 (MQ=17)                          gCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGGTAGAAAGTGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTAt                                                                                                                      >  1:248583/1‑150 (MQ=255)                           cctttACGCAGCCCCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTAcc                                                                                                                         <  2:24263/143‑1 (MQ=255)                                            gTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGAt                                                                                                    <  1:199638/150‑1 (MQ=255)                                                    cTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGc                                                                                            <  1:57883/150‑1 (MQ=255)                                                         cAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCg                                                                                           <  2:135241/146‑1 (MQ=255)                                                             aggGACAGCTGATAGACACAGAAGCCACTAAAACACCTAAAACACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATc                                                                                       <  2:49595/146‑1 (MQ=25)                                                                                                   cAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGAATGTTTCACGTACCTATGACGAATATCTGGCCGATAAGGTAGCGGATAGAGAAGAGGATGCAGAGGGATATCTGGAAGCAATCATGGCgg                                             >  1:66798/1‑150 (MQ=38)                                                                                                                atACACAAAAGCGGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTCCCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATATCTGGAAGCAATCATGGAGGCTCGTGTTa                                    <  2:52317/146‑1 (MQ=255)                                                                                                                             gTACGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCGCTGGCGAACATCTGGCAGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAACATCTGGAAGCAATCATGGAGGCTCGTGTTACCGTTGCTGGCAt                       <  2:114995/146‑1 (MQ=255)                                                                                                                                ggtgggcggggtCACCGAATTTTCAGCCGGGATGTTTCACCTACCTATGTGGAATATCTGGCCGATAAGGTTGCGGAGCGAGAAGAGGATGCAGAGGAATATCTGGAAGCAATCATGGAGGCTCGTGTTACCGTTGCTGGCATggg                    <  2:221591/135‑1 (MQ=255)                                                                                                                                              ccGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATATCTGGAAGCAATCATGGAGGCTCGTGTTACCGTTGCTGGCATGGGGCTGGGGATGGAgg      >  2:75889/1‑146 (MQ=255)                                                                                                                                              ccGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATATATGGAAGCAATCATGGAGGCTCGTGTTACCGGTGCAGGCCTGGGGCGGGTGATGGAggcgaa  >  1:229519/1‑146 (MQ=255)                                                                                                                                               |                                                                                                                                                     AGCGCTGATGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATATCTGGAAGCAATCATGGAGGCTCGTGTTACCGTTGCTGGCATGGGGCTGGTGATGGAGGTGCA  >  CP009273/286970‑287260

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ 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.