New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 1651547	NA (NA)	29 (0.670)	26/274	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

AAGAACCTTGCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGATTTAACCATAAAAGAACTGGCTGAAAAA  >  NC_000913/1651403‑1651688                                                                                                                                                 |                                                                                                                                              aaGACCATTGCAGGGGTGGTCGAGTATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGTATATCGGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAg                                                                                                                                           <  2:738417/149‑1 (MQ=11)          gCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTAc                                                                                                                                  >  1:640173/1‑149 (MQ=38)                    tCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTCTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCtgt                                                                                                                        <  2:449160/149‑1 (MQ=255)                         taTTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCtgtttgtt                                                                                                                   <  1:156840/148‑1 (MQ=255)                         gaTTATAACGAATGGCATCCGCATAGGGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCtgtttgtt                                                                                                                   <  1:138962/148‑1 (MQ=255)                         cagtataACGAGTGGCATCCGCATAGTGCGCTGGGATATCGCTCGCCACGCGAATATCCGCGGCAGCGGGCTTGCAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCtgtttgtt                                                                                                                   <  2:691524/146‑1 (MQ=17)                         cATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCtgtttgtt                                                                                                                   <  1:309043/149‑1 (MQ=255)                         cATTACAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCtgtttgtt                                                                                                                   <  1:253924/149‑1 (MQ=255)                           ttATCACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTAc                                                                                                                 <  1:385911/149‑1 (MQ=255)                           ttATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTAc                                                                                                                 <  1:385882/149‑1 (MQ=255)                            tataACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATCGGTGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTaag                                                                                                                >  2:550711/1‑147 (MQ=255)                                     tGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATaaaaa                                                                                                       <  1:773288/149‑1 (MQ=255)                                       gCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACt                                                                                                     >  1:681002/1‑149 (MQ=255)                                                  gTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGa                                                                                          <  1:397607/149‑1 (MQ=255)                                                  gTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGa                                                                                          <  1:320142/149‑1 (MQ=255)                                                                  ctcgcCACGGGAATAGCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAATCACTCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGttt                                                                          <  1:347080/149‑1 (MQ=255)                                                                   tcgcCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTCCGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTc                                                                         <  1:737406/149‑1 (MQ=255)                                                                   tcgcAACGGGAATGTCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTc                                                                         <  1:428679/149‑1 (MQ=255)                                                                     gcCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTccc                                                                       <  2:446684/149‑1 (MQ=255)                                                                         cGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTTCTAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCcctcct                                                                   <  2:102348/149‑1 (MQ=255)                                                                                           cGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAAt                                                 <  1:434176/149‑1 (MQ=255)                                                                                            gggCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGGCTATGCAAAACAGTTTCCCTCCTCACGCACTCTGaaaaaagt                                                >  2:745579/1‑147 (MQ=255)                                                                                            gggCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAAtt                                                >  2:72978/1‑149 (MQ=255)                                                                                               cTTGTAATGGGTTAAGTGAGAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTgg                                             <  2:634996/149‑1 (MQ=255)                                                                                                       tggTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGGGAACTACGCGCCTCTTTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGccc                                     <  1:745825/148‑1 (MQ=255)                                                                                                       ggggTAAGTGAGAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACGACGCTCCGCTGGTTGTTACGCAATAAAAACTGGTGTTTGCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGccc                                     <  1:745888/149‑1 (MQ=39)                                                                                                                 aTAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGAttt                           >  2:132359/1‑149 (MQ=255)                                                                                                                 aTAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGAttt                           >  2:67089/1‑149 (MQ=255)                                                                                                                             tGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAGATTTGGTGAGGCCCGACAAGATTTAACCATAAAAGa               >  1:235001/1‑149 (MQ=255)                                                                                                                             tGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGATTTAACCATaaaaaa               >  2:60461/1‑147 (MQ=255)                                                                                                                             tGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGATTTAACCATAAAAGa               >  2:323270/1‑149 (MQ=255)                                                                                                                             tGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGATTTAACCATAAAAGa               >  1:725063/1‑149 (MQ=255)                                                                                                                              ggAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGATTTAACCATAAAAGaa              <  1:558786/149‑1 (MQ=255)                                                                                                                              ggAAATATAGGGGCAAATCCACAGGTGAACTACGCGCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGTCCGACAAGATTTAACCATAAAAGaa              <  1:437041/149‑1 (MQ=255)                                                                                                                                         ggCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGATTTAACCATAAAAGAACTGGCTGaaaa   >  1:740120/1‑149 (MQ=255)                                                                                                                                          gCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAACACTGGTGTTTTCGACGATGCAAAACAGTTTCCCTCATCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGACTTACCCAGAAACGGCGTGGCTGaaaac  >  2:319998/1‑148 (MQ=255)                                                                                                                                                 |                                                                                                                                              AAGAACCTTGCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGATTTAACCATAAAAGAACTGGCTGAAAAA  >  NC_000913/1651403‑1651688

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.