New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	= 20563	NA (NA)	24 (0.930)	20/294	NT	100%	noncoding (1/768 nt)	IS1	repeat region
	?	CP009273	= 879039	0 (0.000)					intergenic (‑195/‑90)	ybjG/mdfA	undecaprenyl pyrophosphate phosphatase/multidrug efflux system protein

GGCTGTTGCCCGGCATCCAACGCCATTCATGGCCATATCAATGATTTTCTGGTGCGTACCGGGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGAAGAGTTCAGATAGTACAACGGCATGTCTCTTTTGACTATCTGGCAACCGGCAGTGTGTTCTCTCACGCATCACAAAAGCAGCAG  >  CP009273/20299‑20759                                                                                                                                                                                                                                                                         |                                                                                                                                                                                                     ggCTGTTGCCCGGCATCCAACGCCATTCATGGCCATATCAATGATTTTCTGGTGCGTACCGGGTTTAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACAATAAATCAGAAAATTGGCAGAATCACCTACCTCAAt                                                                                                                                                                                             >  1:168115/1‑274 (MQ=12)           cGGCATCCACCGCCATTCATGGCCATATCAATGATTTTCTGGTGCGTACCGGGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACaa                                                                                                                                                                                  <  1:174894/275‑1 (MQ=38)                          ttCATGGCCATATCAATGATTTTCTGGTGCGTACCGGGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGAAAGTTGGCAGACTCACCTACCTCAATGTGTATCACACTAACCCTATTATTtg                                                                                                                                                                   >  2:33479/1‑275 (MQ=255)                              tGGCCATATTAATGATTTTCTGGTGCGTACCGGGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATAtt                                                                                                                                                                        <  1:33480/266‑1 (MQ=255)                              tGGCCATATCAATGATTTTCTGGTGCGTACCGGGTTGAGAAGCGGTGTAAGTGAGCTGCAGTTGACATGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTAAGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACACTATCCATATTCTTTGTggg                                                                                                                                                               <  1:399782/275‑1 (MQ=255)                               ggCCATATCAATTATTTTCTGGTGTGTACCGGGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTgggg                                                                                                                                                              <  1:76645/275‑1 (MQ=255)                                                                              taGTGAACTGCAGTTGCCATGTTTTACTGCAGTGAGGGCAGAGATAGCGCTGATGGCCGGCTGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGa                                                                                                               <  1:234489/274‑1 (MQ=255)                                                                                     cTGCAGTTGCCATGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTAACACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGGAGAAATTCTTGTTCAGAATGTATctgtcgctctcta                                                                                                         >  2:79550/1‑262 (MQ=255)                                                                                           ttGCCATGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTAACAAAATAACCATATTCTTtgt                                                                                                                                                                  >  2:390051/1‑211 (MQ=255)                                                                                             gCCATGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCacctac                                                                                                                                                                                                   >  2:310182/1‑176 (MQ=31)                                                                                               cATGTTTTACGGCAGTGAGAGCAGAGANAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTgggg                                                                                                                                                              <  1:390064/211‑1 (MQ=255)                                                                                                 tGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCa                                                                                                                                                                                               <  1:310191/176‑1 (MQ=33)                                                                                                   ttttACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGcc                                                                                          >  1:295871/1‑275 (MQ=255)                                                                                                                                                            gCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTTATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGAAGAGTTCAGATAGTACAACGGCATGTCTCTTTTGACTATCTGGCAACCGGCa                                  <  1:79552/274‑1 (MQ=255)                                                                                                                                                                caccCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCa                                                                                                                                                                            >  2:89293/1‑132 (MQ=255)                                                                                                                                                                  ccccGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCCCCTACATCAATGTGTATCACAATATCCATATTCATtg                                                                                                                                                                   >  2:16877/1‑139 (MQ=255)                                                                                                                                                                    ccGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATAtt                                                                                                                                                                        <  1:89295/132‑1 (MQ=255)                                                                                                                                                                      gTCAGTAGCTGAACAGGAGGGACAGAGGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTggg                                                                                                                                                               <  1:16878/139‑1 (MQ=255)                                                                                                                                                                       tCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCacctac                                                                                                                                                                                                   >  1:483123/1‑102 (MQ=31)                                                                                                                                                                           tAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCa                                                                                                                                                                                               <  2:483110/102‑1 (MQ=35)                                                                                                                                                                                 aaCAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTtg                                                                                                                                                                   >  1:14658/1‑124 (MQ=255)                                                                                                                                                                                     ggaggGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTggg                                                                                                                                                               <  2:14658/124‑1 (MQ=255)                                                                                                                                                                                         ggACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCa                                                                                                                                                                            >  1:90198/1‑107 (MQ=255)                                                                                                                                                                                           aCAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGtt                                                                                                                                >  2:319417/1‑149 (MQ=255)                                                                                                                                                                                           aCAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGAAGAGTTCAGATAGTACAACGGCATGTCTCTTTTGACTATCTGGCAACCTGCAGTGTGTTCTCTCACGCATCACAAAAGcagcag  >  1:106806/1‑275 (MQ=255)                                                                                                                                                                                             aGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATgtgt                                                                                                                                                                                         >  1:83015/1‑90 (MQ=255)                                                                                                                                                                                             aGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATAtt                                                                                                                                                                        <  2:90196/107‑1 (MQ=255)                                                                                                                                                                                               cTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGa                                                                                                                            <  1:319427/149‑1 (MQ=255)                                                                                                                                                                                                 gATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATca                                                                                                                                                                                     <  2:83013/90‑1 (MQ=255)                                                                                                                                                                                                                                 aaCACCATCATACACTAAATCAGTAAGTTGGCAGCATCacctac                                                                                                                                                                                                   <  1:232412/44‑1 (MQ=35)                                                                                                                                                                                                                                                  aaTCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTtgt                                                                                                                                                                  >  2:279596/1‑60 (MQ=255)                                                                                                                                                                                                                                                  aaTCAGTAAGTTGGCAGCACCACCTACCTCAATGTGTATc                                                                                                                                                                                      >  1:398542/1‑40 (MQ=255)                                                                                                                                                                                                                                                      aGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACaa                                                                                                                                                                                  <  2:398529/40‑1 (MQ=255)                                                                                                                                                                                                                                                      aGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTgggg                                                                                                                                                              <  1:279604/60‑1 (MQ=255)                                                                                                                                                                                                                                                       gTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAg                                                                                                                   >  2:487166/1‑102 (MQ=255)                                                                                                                                                                                                                                                        tAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGat                                                                                                                                         >  1:464370/1‑79 (MQ=255)                                                                                                                                                                                                                                                           gTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGa                                                                                                               <  1:487179/102‑1 (MQ=255)                                                                                                                                                                                                                                                            ttGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTc                                                                                                                                     <  2:464357/79‑1 (MQ=255)                                                                                                                                                                                                                                                            ttGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAg                                                                                                                   >  1:123880/1‑97 (MQ=255)                                                                                                                                                                                                                                                              ggCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGaa                                                                                     >  2:338312/1‑125 (MQ=255)                                                                                                                                                                                                                                                                cagcaTCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGa                                                                                                               <  2:123874/97‑1 (MQ=255)                                                                                                                                                                                                                                                                  gcaTCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGAAGAGt                                                                                 <  1:338323/125‑1 (MQ=255)                                                                                                                                                                                                                                                                     tCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAg                                                                                                                   >  1:128466/1‑88 (MQ=255)                                                                                                                                                                                                                                                                         ctacctCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGa                                                                                                               <  2:128460/88‑1 (MQ=255)                                                                                                                                                                                                                                                                         |                                                                                                                                                                                                     GGCTGTTGCCCGGCATCCAACGCCATTCATGGCCATATCAATGATTTTCTGGTGCGTACCGGGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGAAGAGTTCAGATAGTACAACGGCATGTCTCTTTTGACTATCTGGCAACCGGCAGTGTGTTCTCTCACGCATCACAAAAGCAGCAG  >  CP009273/20299‑20759

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ 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.