New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	= 1391495	NA (NA)	4 (0.260)	4/272	NT	40.0%	intergenic (+146/‑127)	insH1/ynaJ	IS5 transposase and trans‑activator/DUF2534 family putative inner membrane protein
	?	CP009273	= 1972751	6 (0.390)					intergenic (‑297/‑483)	flhD/uspC	flagellar class II regulon transcriptional activator, with FlhC/universal stress protein

GCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATG  >  CP009273/1391364‑1391630                                                                                                                                    |                                                                                                                                        gCCATAAATGGCAAAGAAGATGTTCAAATATGCTTATGCAAGGCATGTACGGTAGAAAAAATCGGCTCAAACATGAATAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCaa                                                                                                                             <  1:166321/144‑1 (MQ=11)        tgggCGAAGAAACGGTCTAAATTGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATTACTGAGTCAGCCGAGAAGAATTTTCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGt                                                                                                                 <  2:119438/147‑1 (MQ=255)                                    aTTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGtt                                                                                          >  1:222500/1‑144 (MQ=255)                                        aaGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCATTGCGTTGATTGTAAATCCAGCGAAGAGGTGAGGTTTTCAGAGCa                                                                                 <  2:238000/149‑1 (MQ=255)                                         aGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCAAAGAGGTGAGGTTTTCag                                                                                     >  1:74581/1‑144 (MQ=255)                                            cATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCTCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGc                                                                                  <  1:233222/144‑1 (MQ=255)                                                                   tCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGt                                                           >  1:105464/1‑144 (MQ=255)                                                                                   gaaatgaCTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTCCGTTTAGGt                                           >  1:280/1‑144 (MQ=255)                                                                                                                      ttATTCGCACCTTCCCTACCTAATCAATGCGTTGATTGTAAATCCAGCTAAGTGGTGAGGTTTTCAGAGCAGACAACGGGGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATg        >  1:153000/1‑144 (MQ=255)                                                                                                                       tATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGa       <  1:198769/144‑1 (MQ=255)                                                                                                                       tATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATg  <  2:243707/149‑1 (MQ=255)                                                                                                                                    |                                                                                                                                        GCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATG  >  CP009273/1391364‑1391630

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