New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 1651547	NA (NA)	53 (1.190)	38/274	NT	100%	intergenic (+10/‑4)	insD1/intQ	IS2 transposase TnpB;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related/pseudogene, Qin prophage; phage integrase family;Phage or Prophage Related
	?	NC_000913	1652253 =	0 (0.000)					pseudogene (703/1158 nt)	intQ	pseudogene, Qin prophage; phage integrase family;Phage or Prophage Related

GGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCT‑TGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGATTTAACCATAAAAGAACTGGCTGAAAAATT  >  NC_000913/1651417‑1651690                                                                                                                                    |                                                                                                                                                ggCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCT‑TGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGctcc                                                                                                                               >  1:309052/1‑149 (MQ=255)  gCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCT‑TGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTCAACTACGctcct                                                                                                                              >  2:240240/1‑149 (MQ=255)    gTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCT‑TGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCctct                                                                                                                            >  2:697575/1‑149 (MQ=255)        gAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCT‑TGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCtgttt                                                                                                                        <  1:234101/149‑1 (MQ=255)          gCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCT‑TGTAATGGGTTAAGTGATAACAGATGTCTGGGAATATAGGGGCAAATCCCCAGGTGAACTACGCTCCTCtgtttgt                                                                                                                      >  2:131765/1‑149 (MQ=255)                taACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCT‑TGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCa                                                                                                                >  1:580973/1‑149 (MQ=255)                 aaCGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCT‑TGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATGGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCaa                                                                                                               >  1:430319/1‑149 (MQ=255)                          cATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGGATATCTGCGGCAGCGGGCT‑TGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTg                                                                                                      >  2:793854/1‑149 (MQ=255)                                    gTGCGCTGGGTTATCGCTCGCCACCGGAATATCTGCGGCAGCGGGCTACGTGA‑GAGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGa                                                                                            <  1:749982/149‑1 (MQ=21)                                            ggtgctcgcgcgcCACGGGGCTATCTTGGGCGGCGGGCT‑TGTAATGGGTTAAGCGATAACAGATGTCTGGAAATATCGGGGCAAAGCCACAGGTGAACTACGCTCTTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCaa                                                                                    <  2:631803/144‑1 (MQ=21)                                            ggTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCT‑TGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCaa                                                                                    <  1:156206/149‑1 (MQ=255)                                                  cgctcgcCACGGGAATATCTGCGGCAGCGGGCT‑TGTAATGGGTTAAGTGTTAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTAAGCTCCTCTGTTTGTTACGCAATAACAACTGGGGTTTTCGACTATGCAAAACAGt                                                                              >  2:522539/1‑149 (MQ=255)                                                   gctcgcCACGGGAATATCGGCGGCAGCGGGCT‑TGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGtt                                                                             <  1:461940/149‑1 (MQ=255)                                                    ctcggCACGGGAATATCTGCGGCAGCGGGCT‑TGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGttt                                                                            <  1:165480/149‑1 (MQ=255)                                                    ctcgcCACGGGAATATCTGCGGCAGCGGGCT‑TGTAATGGGGTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACATGTGAGCTACGCTCCTCTGTTTGTTCCGCAATAAAAACTGGTGTTTTCGACTTTGCAAAACAGttt                                                                            <  1:547636/149‑1 (MQ=21)                                                         cACGGAAATTCCGGCGGCAGCGGGCT‑TGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCcctc                                                                       <  2:333568/149‑1 (MQ=255)                                                           cGGGGATAGCTGCGGCAGCGGGCT‑TGTAATGGGTTAAGTGATAACAGATTTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCcctcct                                                                     <  2:247593/149‑1 (MQ=255)                                                              gAATAACGGCGGCAGCGGGCT‑AGGAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCAc                                                                  <  1:342406/149‑1 (MQ=255)                                                               aaTCTCTGCGGCAGCGGGCT‑TGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACGACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTGCCCTCCTCatg                                                                 <  2:15561/149‑3 (MQ=255)                                                                    ccgCGGCAGCGGGCT‑TGTAATGGGTTAAGTGATAACAGATGTCCGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATc                                                            <  1:320395/147‑1 (MQ=255)                                                                    cTGCGGCAGCGGGCT‑TGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAGACAGTTTCCCTCCTCACGCAATc                                                            >  2:416135/1‑149 (MQ=255)                                                                         gCAGCGGGCT‑TGTAATGGGTTAAGTGATAGCAGATGTGTGGAAATATGGGAGCAAATCCACAGGGGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCCCCTAACGCaaccgcgac                                                       >  2:428352/1‑142 (MQ=37)                                                                            gCGGGCT‑TGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGCTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGaaaaa                                                    <  2:742548/149‑1 (MQ=255)                                                                              gggCT‑TGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAAtt                                                  >  2:613304/1‑149 (MQ=255)                                                                                      tAATGGGTTAAGTGATAACAGATGTCTGGAAATATGGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAg                                           <  2:430319/149‑1 (MQ=255)                                                                                                aGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGTAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAg                                 <  1:755365/149‑1 (MQ=255)                                                                                                aGTCATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACAATGCACACCAGTTTCCCTCCTCCCGCAATCTGGAAAAATTTGGTGAGGCCCGACAAg                                 <  1:755398/149‑1 (MQ=39)                                                                                                      aaCAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGATTTaa                           <  1:574991/149‑1 (MQ=255)                                                                                                              ccTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCCGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAATATTTAACCATaaaa                   <  2:285923/148‑1 (MQ=255)                                                                                                                tGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAGACTGGTGGGTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGATTTAACCATAAAAGa                 >  1:483556/1‑149 (MQ=255)                                                                                                                tGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGGTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGAGTTAACCATAAAAGa                 >  1:483571/1‑149 (MQ=255)                                                                                                                     atatAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGATTTAACCATAAAAGAACTgg            <  2:512192/149‑1 (MQ=255)                                                                                                                     atatAGGGGCAAATCCACAGGGGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGATTTAACCATAAAAGAACTgg            <  1:572211/149‑1 (MQ=255)                                                                                                                               aaaTCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGATTTAACCATAAAAGAACTGGCTGAAAAAtt  >  2:636095/1‑149 (MQ=255)                                                                                                                                    |                                                                                                                                                GGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCT‑TGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGATTTAACCATAAAAGAACTGGCTGAAAAATT  >  NC_000913/1651417‑1651690

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.