New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	= 1483730	16 (0.410)	11 (0.280)	10/276	NT	40.7%	coding (670/3903 nt)	hrpA	putative ATP‑dependent helicase
	?	NC_000913_3_pae_tpiA	= 2290113	NA (NA)					intergenic (‑32/+1)	insH1/yejO	IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system

CGACGGTATCCTGCTGGCGGAGATCCAGCAAGACCGCCTGCTGATGCAGTACGACACTATCATTATTGACGAAGCGCACGAACGCAGCCTGAATATCGATTTTTTGCTCGGCTATTTGAAAGAGTTGCTGCCGCGGCGTCCTGACCTAAAAATCATTATCACTTCCGCGACTATCGACCCGGAACGCTTTTCGCGCCACTTTAATAATGCGCCGATTATTGAAGTCTCCGGTCGGACCTATCCGGTGGAAGTGCGCTATCGCCCGATTGTTGAAGAAGCCGATGACACCGAGCGCG  >  NC_000913_3_pae_tpiA/1483582‑1483877                                                                                                                                                     |                                                                                                                                                    aactggggataacgccttaaatggcgaagaaacggtctaaataggctgattcaaggcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcCCTaa                                                                                                                                                     >  1:554220‑M1/145‑149 (MQ=255)  gACGGTATCCTGCTGGTGGAGATCCAGCAAGACCGCCTGCTGATGCAGTACGACACTATCATTATTGACGAAGCGCACGAACGCAGCCTGAATATCGATTTTTTGCTCGGCTATTTGAAAGAGTTGCTGCCGCGGCGTCCTGACCTAAg                                                                                                                                                    <  2:226346‑M1/149‑2 (MQ=255)  atcgcggaaaaggccgtacagggcggtgaaacggtcgaaataggctgattcaaggcatttacgggagaaaaaatcgtctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcCCTaaa                                                                                                                                                    >  2:221410‑M1/144‑149 (MQ=255)  actggggataacgccttaaatggcgaagaaacggtctaaataggctgattcaaggcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcCCTaaa                                                                                                                                                    <  1:229702‑M1/6‑1 (MQ=255)       tATCCTGCTGGCGGAGATCCAGCAAGACCGCCTGCTGATGCAGTACGACACTATCATTATTGACGAAGCGCACGAACGCAGCCTGAATATCGATTTTTTGCTCGGCTATTTGAAAGAGTTGCTGCCGCGGCGTCCTGACCTAAAAATCa                                                                                                                                               <  2:139345/149‑1 (MQ=255)         gccTGCTGGAGGAGTTCCAGCAAGACCGGCTGCTGATGCAGTACGACACTATCATTATTGACGGCGCGCACGAACGCAGCCTTAATATCGATTTTTTGCTCGGCTATTTGAAAGAGTTGCTGCCGCGGCGTCCTGACCTAAAAATCAtt                                                                                                                                             <  2:445634/148‑1 (MQ=255)                     agttccaGCAAGCCCGCCTGCTGATGCAGTACGACACTATCATTATTGACGAAGCGCACGAACGCAGCCTGAATATCGATTTTTTGCTCGGCTATTTGAAAGAGTTGCTGCCGCGGCGTCCTGACCTAAggaaggtgcgaacaagtccc                                                                                                                                 <  1:671565‑M1/146‑21 (MQ=255)                      gaTCCAGCAAGACCGCCTGCTGAGGCAGTACGACACTATCATTATTGACGAAGCGCACGAACGCAGCCTGAATATCGATTTTTTGCTCGGCTATTTGAAAGAGTTGCTGCCGCGGCGTCCTGACCTAAggaaggtgcgaacaagtccct                                                                                                                                <  1:732‑M1/149‑22 (MQ=255)                       ggcgaagaaacggtctaaataggctgattcaaggcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcCCTAAAAATCATTATCACTTCCGCGAc                                                                                                                               >  2:286748‑M1/123‑149 (MQ=255)                       ggcgaagaaacggtctaaataggctgattcaaggcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcCCTAAAAATCATTATCACTTCCGCGAc                                                                                                                               >  1:683677‑M1/123‑149 (MQ=255)                             cAATACCGCCTGCTGATGCAGTACGACACTATCATTATTGACGAAGCGCACGAACGCAGCCTGAATATCGATTTTTTGCTCGGCTATTTGAAAGAGTTGCTGCCGCGGCGTCCTGACCTAAAAATCATTATCACTTCCGCGACTATCGa                                                                                                                         >  1:649383/1‑149 (MQ=255)                              aaGACCGCCTGCTGATGCAGTACGACACTATAATTATTGACGAAGCGCACGAACGCAGCCTGAATATCGATTTTTTGCTCGGCTATTTGACAGAACTGCTGCCGCGGAGTAAAGATATTACCACCATTAGCACTTCCGCGACTATCGAc                                                                                                                        >  1:650666/1‑149 (MQ=255)                               aGACCGCCTGCTGATGCAGTACGACACTATCATTATTGACGAAGCGCACGAACGCAGCCTGAATATCGATTTTTTGCTCGGCTATTTGAAAGAGTTGCTGCCGCGGCGTCCTGACCTAAAAATCATTATCACTTCCGAGACTATCGAcc                                                                                                                       >  1:388665/1‑149 (MQ=255)                                      ctgctgATGCAGTACGACACTATCATTATTGACGAAGCGCACGAACGCAGCCTGAATATCGATTTTTTGCTCGGCTATTTGAAAGAGTTGCTGCCGCGGCGTCCTGACCTAAggaaggtgcgaacaagtccctgatatgagctcatgtt                                                                                                                >  2:616932‑M1/1‑112 (MQ=255)                                       tgctgATGCAGTACGACACTATCATTATTGACGAAGCGCACGAACGCAGCCTGAATATCGATTTTTTGCTCGGCTATTTGAAAGAGTTGCTGCCGCGGCGTCCTGACCTAAggaaggtgcgaacaagtccctgatatgagatcatgttt                                                                                                               <  1:368044‑M1/149‑39 (MQ=255)                                       tgctgATGCAGTACGAAACTATCATTATTGACGAAGCGCACGAACGCAGCCTGAATATCGATTTTTTGCTCGGGTATTTGAAAGAGTTGCTGCCGCGGCGTCCTGACCTAAggaaggtgcgaacaagtccctgatatgagatcacgttt                                                                                                               <  2:557910‑M1/149‑39 (MQ=255)                                        gctgATGCAGTACGACACTATCATTATTGACGAAGCGCACGAACGCAGCCTGAATATCGATTTTTTGCTCGGCTATTTGAAAGAGTTGCTGCCGCGGCGTCCTGACCTAAggaaggtgcgaacaagtccctgatatgagatcatgtttg                                                                                                              <  2:51009‑M1/149‑40 (MQ=255)                                            ggctgattcaaagcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcCCTAAAAATCATTATCACTTCCGCGACTATCGACCCGGAACGCTTTTc                                                                                                          >  1:105207‑M1/102‑149 (MQ=255)                                                aGTACCCCACTATCATTATTGCCGAAGCGCACGAACGCAGCCTGAACATCGGTTTTTTGCCCGGCTATTTGAAAGAGTTGCTGCCGCGGCGTCCTGACCTAAAAATCATTATCACTTCCGCGACTATCGACCCGGAACGCTTTTCgcgc                                                                                                      <  1:396993/149‑1 (MQ=255)                                                  tACGACACTATCATTATTGACGAAGAGCACGAACGCAGCCTGAATACCGATTTTTTGCTCGGCTATAAGAAAGAGTTGCTGCCGAGGCGTCCTGACCTAAggaaggtgcgaacaagtccctgagatgagatcatgtttggcagctggag                                                                                                    >  1:665472‑M1/1‑100 (MQ=255)                                                   tcaaggcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaattactgagtcagccgagaagaatttccccgcttattcgcaccttcCCTAAAAATCATTATCACATCCACTACTAGCTACCCGGAACGCTTTTCGCGCCAc                                                                                                   >  2:712088‑M1/95‑149 (MQ=255)                                                   aCGACATTAGTATTATTGACGAAGCGCACTAACTCAGTCTGAATATCGATTTCTTGCTCGGCTATTTGAAAGAGGTGCTGCCGCGGCCTCCTGACCTAAAAATCATTATCACTTCCGCGACTATCGACCCGGAACGCTTTTCGCGCCAc                                                                                                   <  2:234929/149‑1 (MQ=255)                                                     gACACTATCATTATTGACGAAGCGCACGAACGCAGCCTGAATATCGATTTTTTGCTCGGCTATTTGAAAGAGTTGCTGCCGCGGCGTCCTGACCTAAAAATCATTATCACTTCCGCGACTATCGACCCGGAACGCTTTTCGCGACACtt                                                                                                 >  1:149238/1‑149 (MQ=255)                                                        gcagtgacgtgagaaaaaatcggcacaaacctgaagaaatgaaatgactgactcagccgagaagaatctccccgcttattcgcaccttcCCTAAAAATCATTATCACTTCCGCGACTATCGATCCGGAACGCTTTTCGCGCCACTTtaa                                                                                              >  2:513546‑M1/90‑149 (MQ=255)                                                              attatcGACGAAGCGCACGAACGCAGCCTGAATATCGAGTTTTTGCTCGGCTATTTGAAAGAGTTGCTGCCGCGGCGTCCTGACCTAAAAATCATTATCACTTCCGCGACTATCGACCCGGAACGCTTTTCGCGCCACTTTAATAATgc                                                                                        <  1:315184/149‑1 (MQ=255)                                                                tattGACGAAGCGCACGAACGCAGCCTGAATATCGATTTTTTGCTCGGCTATTTGAAAGAGTTGCTGCCGCGGCGTCCTGACCTAAAAATCATTATCACTTCCGCGACTATCGACCCGGAACGCTTTTCGCGCCACTTTAATAATgcgc                                                                                      <  1:162251/149‑1 (MQ=255)                                                                   tGAGGAAGAGCACGAACGCAGCCTGAATATCGATTTTTTGCTCGGCTATTTGAAAGAGTTGCTGCCGCGGGGTCCCGACCCAAAAATCCGCAGCCCGTTGTTTGCTATCGACCCGGAACGCTTTTCGCGCCACTTTAATAACGCGCCGa                                                                                   <  2:674087/149‑1 (MQ=255)                                                                    gACGAAGCGCACGAACGCTGCCTGAATACCTCGTTTTTGCACGGCCCTTTGAAAGCGTTGCTGCCGCGGCGTCCTGACCTAAAAATCATTATCACTTCCGCGACTATCTACCCGGAACGCTTTTCGCGCCACTTTAATCATCCGCCGat                                                                                  >  2:157453/1‑149 (MQ=255)                                                                    gACGAAGCGCACGAACGCAGCCTGAATATCGATTTTTTGCTCGGCTATTTGAAAGAGTTGCTGCCGCGGCGTCCTGACCTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcat                                                                                  <  1:201999‑M1/149‑68 (MQ=255)                                                                        aaatcggctcaaacatgaagaaatgacatgactgagtcagccgagaagaatttccccgcttattcgcaccttcCCTAAAAATCATTATCACTTCCGCGACTATCGACCCGGAACGCTTTTCGCGCCACTTTAATAATGCGCCGattatt                                                                              >  1:89031‑M1/74‑149 (MQ=255)                                                                          gcgcACGAACGCAGCCTGAATATCGATTTTTTTCTCGTCTATTTGAAAGAGTTGCTGCCGCGGCGTCCTGAACTAAggaaggtgccaacgagtgcctgatatgagatcatgcttgtcatctggagccatagagcagggttcatcatgag                                                                            >  2:680065‑M1/1‑76 (MQ=255)                                                                           cgcACGAACGCAGCCTGAATATCGATTTTTTGCTCGGCTATTTGAAAGAGTTGCTGCCGCGGCGTCCTGACCTAAAAATCATTATCACTTCCGCGACTATCGACCCGGAACGCTTTTCGCGCCACTTTAATAATGCGCCGATTATTGaa                                                                           <  1:205091/149‑1 (MQ=255)                                                                                tcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcCCTAAAAATCATTATCACTTCCGCGACTATCGACCCGGAACGCTTTTCGCGCCCCTTTACTAATGCGCCGATTATTGAAGtctc                                                                      <  2:689433‑M1/84‑1 (MQ=255)                                                                                              tgtCGATTTGTTGCTTGCCTATTTGAAAGAGTTGCTGCCGGGGCGTCCTGACCTAAAAATCATTATCACTTCCGCGACTATCGGCCCGGAACGCTTTTCGCGCCACTTTAATAATGCGCCGATTATTGAAGTCTCCGGTCGGACCTATc                                                        <  2:379103/147‑1 (MQ=255)                                                                                              tatCGATTTTTTGCTCGGCTATTTGAAAGAGTTGCTGCCGCGGCGTCCTGACCTAAAAATCATTATCACTTCCGCGACTATCGACCCGGAACGCTTTTCGCGCCACTTTAATAATGCGCCGATTATTGAAGTCTCCGGTCGGACCTATc                                                        <  1:529927/149‑1 (MQ=255)                                                                                                      actgagtcagccgagaagaatttccccgcttattcgcaccttcCCTACAAATCATGATCACTTCCGCGACTATCGACCCGGAACGCTTTTCGCGCCACTTTAATAATGCGCCGATTATTGAAGTCTCCGGTCGGACCTATCCGGTGGaa                                                >  1:573518‑M1/44‑149 (MQ=255)                                                                                                                 cgagaagaatttccccgcttattcgcaccttcCCTAAAAATCATTATCACTTCCGCGACTATCGACCCGGAACGCTTTTCGCGCCACTTTAATAATGCGCCGATTATTGAAGTCTCCGGTCGGACCTATCCGGTGGAAGTGCGCTATCg                                     <  1:108349‑M1/117‑1 (MQ=255)                                                                                                                         agagTTGCTGCCGCGGCGTCCTGACCTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgagtcatcaacttaccttcgccgacagtgaattcagcagtaagcgccgtc                             >  1:711548‑M1/1‑29 (MQ=255)                                                                                                                                      ttcgcaccttcCCTAAAAATCATTATAACTTCCGCGACTATCGACCCGGAACGCTTTTCGCGCCACTTTAATAATGCGCCGATTATTGACGTCTCCGGTCGGACCTATCCGGTGGAACTGCGCTGCCGCCCGATGGTTTAAGAagccag                <  2:230578‑M1/138‑3 (MQ=255)                                                                                                                                      ctagcatcttcCCTAAACATCATTATCACTTCCGCGACTATCGACCCGGAACGTTTTTCGCGCCACTTTAATAATGCGCCGATTATTGAAGTCTCCGGTCGGACCTATCCGGTGTGTGGGCTGGGTCGCCCGATTGTTGAAGAAGCCGa                >  2:157042‑M1/12‑149 (MQ=255)                                                                                                                                           tCCTGACCTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgagtcatcaacttaccttcgccgacagtgaattcagcagtaagcgccgtcagaccagaaaagagattt           >  1:716278‑M1/1‑11 (MQ=255)                                                                                                                                               gACCTAACAATAATTACCTCTTCCGCGACTATCCACCCGGAACTCTTTTCGCTCCACTTTAATAATGCGCCGATTATTGAATTCTCCGGTCTGACCTATCCGGTGGAAGTCCGCTATCGCCCTATTTTTGAAGATGCCGATGCCACCGa       <  2:562101/149‑1 (MQ=255)                                                                                                                                                 ccTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgagtcatcaacttaccttcgccgacagtgaattcagcagtaagcgccgtcagaccagaaaagagattttcttgt     <  2:84807‑M1/149‑145 (MQ=255)                                                                                                                                                 ccTAAggaaggtgcgaacaagtccctgatatgagaaaaggttggtcatctggagccatagaacagggttcatcatgagtcatcaacttaccttcgccgacagtgaattcagcagtaagcgccgtcagaccagacaagagattttcttgt     >  1:728952‑M1/1‑5 (MQ=255)                                                                                                                                                  cTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgagtcatcaacttaccttcgccgacagtgaattcagcagtaagcgccgtcagaccagaaaagagattttcttgtc    >  1:716618‑M1/1‑4 (MQ=255)                                                                                                                                                  cTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctgaagccatagaacagggttcatcatgagtcatcaacttaccttcgccgacagtgaattcagcagtaagcgccgtaagaccagaaaagagattttcttgtc    >  2:164627‑M1/1‑4 (MQ=255)                                                                                                                                                  cTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatcgggaaacatataatagggttcatcctgagtcatcaacttaccttcgccgacagtgaattcagcagtaagcgccgtcagaccagaaaagagcttttcttgtt    >  2:673935‑M1/1‑4 (MQ=255)                                                                                                                                                  cTAAggaaggtgcgaacaagtccctgatatgagataatgtttgtcatcttgagccatagaacagggttcatcatgagtcatcaacttaccttcgccgacagtgaattcagcagtaagcgccgtcagaccagaaaagagattttcttgtc    <  1:689343‑M1/149‑146 (MQ=255)                                                                                                                                                   tAAAAATCATTATCACTTCCGCGACTATCGACCCGGAACGCTTTTCGCGCCACTTTAATAATGCGCCGCTTATTGAAGTCTCCGGTCGGACCTATCCGGTGGAAGTGCGCTATCGCCCGCTTGTTGAAGAAGCCGATGACACCgcgcgc   >  2:288960/1‑149 (MQ=255)                                                                                                                                                    aaggaaggtgcgaacaagtccctgatatgatatcatgtttgtcatctggagccatagaacagggttcatcatgagtcatcaacttaccttcgccgacagtgaattcagcagtaagcgccgtcagaccagaaaagagattttcttgtccc  <  2:378168‑M1/149‑148 (MQ=255)                                                                                                                                                     |                                                                                                                                                    CGACGGTATCCTGCTGGCGGAGATCCAGCAAGACCGCCTGCTGATGCAGTACGACACTATCATTATTGACGAAGCGCACGAACGCAGCCTGAATATCGATTTTTTGCTCGGCTATTTGAAAGAGTTGCTGCCGCGGCGTCCTGACCTAAAAATCATTATCACTTCCGCGACTATCGACCCGGAACGCTTTTCGCGCCACTTTAATAATGCGCCGATTATTGAAGTCTCCGGTCGGACCTATCCGGTGGAAGTGCGCTATCGCCCGATTGTTGAAGAAGCCGATGACACCGAGCGCG  >  NC_000913_3_pae_tpiA/1483582‑1483877

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.