New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	= 20563	NA (NA)	12 (0.440)	11/226	NT	30.8%	noncoding (1/768 nt)	IS1	repeat region
	?	CP009273	= 879040	27 (0.990)					intergenic (‑196/‑89)	ybjG/mdfA	undecaprenyl pyrophosphate phosphatase/multidrug efflux system protein

GGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGAAGAGTTCAGATAGTACAACGGCATGTCTCTTTTGACTATCTGGCAACCGGCAGTGTGTTCTCTCACGCATCACAAAAGCAGCAGGCATAAAAAAACCCGCTTGCGCGGGCTTTTTCACAAAGCTTCAGCAAATTGGCGATTAAGCCA  >  CP009273/20360‑20822                                                                                                                                                                                                            |                                                                                                                                                                                                                                                                    gtaaaagagacGGGGTAATTTAACTGCAGGTGCCATGTTTTTCGGCAGGGAGAGCAGGGATAGGGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGtt                                                                                                                                                                                               <  2:282752/264‑1 (MQ=18)                        cTGCAGTTGCCATGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTANCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTca                                                                                                                                                                       >  1:501609/1‑274 (MQ=255)                         tGCAGTTGCCATGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCt                                                                                                                                                                                                   >  1:282757/1‑246 (MQ=255)                                                cgaacagCAGACANGGCGCTTATGTCCGGCGGTGCCTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGAAGAGt                                                                                                                                                <  2:501600/269‑1 (MQ=255)                                                                                                         gTCAGTAGCTGAACAGGAGGGACAGCTGACAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTtg                                                                                                                                                                                                                                  >  2:86605/1‑135 (MQ=255)                                                                                                             gTAGCTGAACAGGAGGGACAGCTGACAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTggg                                                                                                                                                                                                                              <  1:86605/135‑1 (MQ=255)                                                                                                                   gAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTtgt                                                                                                                                                                                                                                 >  2:210375/1‑126 (MQ=255)                                                                                                                       aggaggGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTgggg                                                                                                                                                                                                                             <  1:210379/126‑1 (MQ=255)                                                                                                                           gggACAGCGGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTAAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTATTGTTGAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGAAGAGTTCAGATAGTACAACGGCATGTCTCTTTTGACTATCTGGCAACCGGCAGTGTGTTCTCTCACGCATCACAAAagca                                                                     >  1:588427/1‑274 (MQ=255)                                                                                                                                     aTAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCacctac                                                                                                                                                                                                                                                                  >  2:157706/1‑75 (MQ=32)                                                                                                                                         aaaCAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCa                                                                                                                                                                                                                                                              <  1:157709/75‑1 (MQ=39)                                                                                                                                                           cACCTCAAACACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAAtgt                                                                                                                                                                                                                                                          >  1:531954/1‑61 (MQ=255)                                                                                                                                                               tCAAAAACACCATCATACACTAAATCAGTAAGTAGGCAGCATCACCTACCTCAATGTGTAt                                                                                                                                                                                                                                                      <  2:531943/61‑1 (MQ=255)                                                                                                                                                                cAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTtgt                                                                                                                                                                                                                                 >  1:561057/1‑81 (MQ=255)                                                                                                                                                                    aaCACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTgggg                                                                                                                                                                                                                             <  2:561046/81‑1 (MQ=255)                                                                                                                                                                        ccATCATACACTAAATCAGCAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGTGGGACTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGac                                                                                                                                                    >  1:544749/1‑149 (MQ=255)                                                                                                                                                                                    aaaTCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGaa                                                                                                                                                    >  1:405620/1‑138 (MQ=255)                                                                                                                                                                                        cAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTTGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACCAAGAGt                                                                                                                                                <  2:405615/138‑1 (MQ=255)                                                                                                                                                                                           tAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGAAGAGTTCAGATAGTACAACGGCATGTCTCTTTTGACTATCTGGCAACCGGCAGTGTGTtctct                                                                                      >  1:55792/1‑193 (MQ=255)                                                                                                                                                                                              gggggCAGCATAAACTTACTCAATGTGTATAACAATATCCTGATTCGTTGGGGGGGAGTCGGGAGATTTATGAGATATTCTTGTTCAGAATGTATAAGCCGATGGTTCTACGATTCTTAAGCCACGAAGAGTTCAGATAGTACAACGGCATGTCTCTTTTGACTATCTGGCAACCGGCAGTGTGTTCTCTCATGCACCACAAAAGCAGCAGGCATAAAAATACCCGCTTGCTCGGGCTTTTTCAAAAAGCTTCAGCAAATTGGCGATTAAGCCa  <  2:588416/271‑1 (MQ=255)                                                                                                                                                                                               ttGGCAGCATAACCTACCTAAATGTGTATCACAATATCCATAGTCTTTGTGGGGGAGTCTGGAGATTGAGTAGAGATTCTTGTTCAGTATGTATCAGCCGATGGTGCCACGATTAGTAAGCCATGAAGAGCTCAGATAGTACAGCGGCACATCTCTTTTGACTATCTGGCAACCGGAAGTATGTTCTCTCACg                                                                                  <  2:55792/193‑1 (MQ=255)                                                                                                                                                                                                            |                                                                                                                                                                                                                                                                    GGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGAAGAGTTCAGATAGTACAACGGCATGTCTCTTTTGACTATCTGGCAACCGGCAGTGTGTTCTCTCACGCATCACAAAAGCAGCAGGCATAAAAAAACCCGCTTGCGCGGGCTTTTTCACAAAGCTTCAGCAAATTGGCGATTAAGCCA  >  CP009273/20360‑20822

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ 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.