New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	AE015451	= 2472115	33 (0.810)	4 (0.100)	4/322	NT	12.0%	intergenic (+19/+130)	PP_2166/PP_2167	Anti‑anti‑sigma factor/putative PhoD‑like phosphatase
	?	AE015451	2472313 =	27 (0.690)					coding (1783/1851 nt)	PP_2167	putative PhoD‑like phosphatase

TGCAGTCGATGGGCTTCGATCAGGTGTTCAACATCGTCGATCGACCGATACCCTGCACCGATTGCCTGACCGACTTGCCGTCGCAGGACCAGAATGAAGATGTGGTGCGCTCCAAGGTGCTGGAGGCGCACAAGATCCTCATGGGCCTGAATGACTCCAACCGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACAGGCTGTAAAAACTCTGAATCTCACTACGCCCGGTTTTTAAACTCTGTAGCCTCACCCCCGCCAGCATCCAGCTGGTACACCCGCGCCGGCCGCCCCTGTTCATCAAAAAA  >  AE015451/2471891‑2472331                                                                                                                                                                                                                                 |                                                                                                                                                                                                                         tGCAGTCGATGGGCTTCGATCAGGTGTTCAACATCGTCGATCGACCGATACCCTGCACCGATTGCCTGACCGACTTGCCGTCGCAGGACCAGAATGAAGATGTGGTGCGCTCCAAGGTGCTGGAGGCGCACAAGATCCTCATGGGCCTGAATGACTCCAACCGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGt                                                                                                                                                                                                               >  1:522854/1‑236 (MQ=255)                   aTCAGGTGTTCAACATCGTCGATCGACCGATACCCTGCACCGATTGCCTGACCGACTTGCCGTCGCAGGACCAGAATGAAGATGTGGTGCGCTCCAAGGTGCTGGAGGCGCACAAGATCCTCATGGGCCTGAATGACTCCAACCGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTacg                                                                                                                                                                                                >  2:713556/1‑233 (MQ=255)                       ggTGTTCAACATCGTCGATCGACCGATACCCTGCACCTATTGCCTGACCGACTTGCCGTCGCAGGACCAGAATGAAGATGTGGTGCGCTCCAAGGTGCTGGAGGCGCACAAGATCCTCATGGGCCTGAATGACTCCAACCGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGTaa                                                                                                                                                                                                             <  1:57135/216‑1 (MQ=255)                           ttCAACATCGTCGATCGACCGATACCCTGCACCGATTGCCTGACCGACTTGCCGTCGCAGGACCAGAATGAAGATGTGGTGCGCTCCAAGGTGCTGGAGGCGCACAAGATCCTCATGGGCCTGAATGACTCCAACCGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTacg                                                                                                                                                                                                >  1:431403/1‑225 (MQ=255)                            tCAACATCGTCGATCGACCGATACCCTGCACCGATTGCCTGACCGACTTGCCGTCGCAGGACCAGAATGAAGATGTGGTGCGCTCCAAGGTGCTGGAGGCGCACAAGATCCTCATGGGCCTGAATGACTCCAACCGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTgcgc                                                                                                                                                                                     <  1:652394/235‑1 (MQ=255)                                         tcgaCCGATACCCTGCACCGATTGCCTGACCGACTTGCCGTCGCAGGACCAGAATGAAGATGTGGTGCGCTCCAAGGTGCTGGAGGCGCACAAGATCCTCATGGGCCTGAATGACTCCAACCGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTGCGcc                                                                                                                                                                                    <  1:713557/223‑1 (MQ=255)                                                 tACCCTGCACCGATTGCCTGACCGACTTGCCGTCGCAGGACCAGAATGAAGATGTGGTGCGCTCCAAGGTGCTGGAGGCGCACAAGATCCTCATGGGCCTGAATGACTCCAACCGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCAc                                                                                                                                                               <  1:693657/236‑1 (MQ=255)                                                  gcccTGCACCGATTGCCTGACCGACTTGCCGTCGCAGGACCAGAATGAAGATGTGGTGCGCTCCAAGGTGCTGGAGGCGCACAAGATCCTCATGGGCCTGAATGACTCCAACCGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCAc                                                                                                                                                               <  1:222071/234‑1 (MQ=255)                                                    ccTGCACCGATTGCCTGACCGACTTGCCGTCGCAGGACCAGAATGAAGATGTGGTGCGCTCCAAGGTGCTGGAGACGCACAAGATCCTCATGGGCCTGAATGACTCCAACCGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCAcccc                                                                                                                                                            <  1:422385/236‑1 (MQ=255)                                                      agCACCGATTGCCTGACCGACTTGCCGTCGCAGGACCAGAATGAAGATGTGGTGCGCTCCAAGGTGCTGGAGGCGCACAAGATCCTCATGGGCCTGAATGACTCCAACCGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCa                                                                                                                                                          <  2:522853/235‑1 (MQ=255)                                                          ccGATTGCCTGACCGACTTGCCGTCGCAGGACCAGAATGAAGATGTGGTGCGCTCCAAGGTGCTGGAGGCGCACAAGATCCTCATGGGCCTGAATGACTCCAACCGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCgcccctgttcatcaaaaaacacctgtcccagcccggcaccattccacagccgttccccggccttg                                                                                                                                                         >  2:542296‑M1/1‑168 (MQ=255)                                                                  cTGACCGACTTGCCGTCGCAGGACCAGAATGAAGATGTGGTGCGCTCCAAGGTGCTGGAGGCGCACAAGATCCTCATGGGCCTGAATGACTCCAACCGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTGTa                                                                                                                                                <  1:349307/234‑1 (MQ=255)                                                                     aCCGACTGGCCGTCGCAGGACCAGAATGAAGAGGTGGTGCGCTCCAAGGTGCTGGAGGCGCACAAGATCCTCATGGGCCTGAATGACTCCAACCGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGAGTAAACCCGCTCCTACGACGGCCTgcg                                                                                                                                                                                      <  2:114558/193‑1 (MQ=255)                                                                              ccGTCGCAGGACCAGAATGAAGATGTGGTGCGCTCCAAGGTGCTGGAGGCGCACAAGATCCTCATGGGCCTGAATGACTCCAACCGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCa                                                                                                                                                          >  2:427272/1‑212 (MQ=255)                                                                              ccGTCGCAGGACCAGAATGAAGATGTGGTGCGCTCCAAGGTGCTGGAGGCGCACAAGATCCTCATGGGCCTGAATGACTCCAACCGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCa                                                                                                                                                          <  1:427273/212‑1 (MQ=255)                                                                                                 aaGATGTGTTGCGCTCCAAGGTGCTGGAGGCGCACAAGCTCCTCATGGGCCTGAATGACTCCAACCGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTCTAGCCTGTGCCGGCCTCTTCCCGGGTAAACCCGCTCCTACGACGGCCTgcg                                                                                                                                                                                      <  1:230122/165‑1 (MQ=255)                                                                                                 aaGATGTGGTGCGCTCCAAGGTGCTGGAGGCGCACAAGATCCTCATGGGCCTGAATGACTCCAACCGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGcaca                                                                                                                <  1:456466/235‑1 (MQ=255)                                                                                                          tgCGCTCCAAGGTGCTGGAGGCGCACAAGATCCTCATGGGCCTGAATGACTCCAACCGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTACAGCCTGTGCCGGACTCTTCGCGGGTAAACCCGCTCCTACGACGGCCCGCGccc                                                                                                                                                                                   >  2:99538/1‑159 (MQ=255)                                                                                                            cgcTCCAAGGTGCTGGAGGCGCACAAGATCCTCATGGGCCTGAATGACTCCAACCGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTgcg                                                                                                                                                                                      <  1:83851/154‑1 (MQ=255)                                                                                                              cTCCAAGGTGCTGGAGGCGCACAAGATCCTCATGGGCCTGAATGACTCCAACCGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCgcccctgctcatcaaaaaacacctgtcccagcccggcaccattccac                                                                                                                                                                           >  2:70336‑M1/1‑116 (MQ=255)                                                                                                                 cAAGGTGCTGGAGGCGCACAAGATCCTCATGGGCCTGAATGACTCCAACCGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCgcccctgttcatcaaaaaacacctgtcccagcccggcaccattccacagccgttccccggccttgctgtggctgggcgtacgcggcaccacctccatttctcggcgcttggtaaaccagttg                                                                                                >  1:435087‑M1/1‑113 (MQ=255)                                                                                                                            aGGCGCACAAGATCCTCATGGGCCTGAATGACTCCAACCGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACAGGCTGTAAAAACTCTGAATCTCACTACg                                                                                    <  1:419707/236‑1 (MQ=255)                                                                                                                                   caAGATCCTCATGGGCCTGAATGACTCCAACCGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCAAATCAGGTGTAGGAGCGGGTTTGCCCGCGAAGAGGCCGGCACAGGCTGTAAAAACTCTGa                                                                                               >  2:419706/1‑218 (MQ=255)                                                                                                                                      gctCCTCATGGGCCTGAATGACTCCAACCGCGAAGCCTCCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCGCTTCGCGGGTAAACCCGCTCCTACGACGGCCTGCGCCCAAACAcc                                                                                                                                                                            <  2:218425/136‑1 (MQ=255)                                                                                                                                          cTCATGGGCCTGAATGACTCCAACCGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGca                                                                                                                  <  2:431402/192‑1 (MQ=255)                                                                                                                                           tCATGGGCCTGAATGACTCCAACCGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCAcccc                                                                                                                                                            <  2:281612/149‑1 (MQ=255)                                                                                                                                               gggCCTGAATGACTCCAACCGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCAcccc                                                                                                                                                            <  2:193245/145‑1 (MQ=255)                                                                                                                                                              cAACCGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGGTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTacga                                                                                                                                                                                               >  1:711075/1‑95 (MQ=255)                                                                                                                                                              cAACCGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTgcg                                                                                                                                                                                      >  1:717207/1‑104 (MQ=255)                                                                                                                                                              cAACCGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTgcg                                                                                                                                                                                      <  2:717206/104‑1 (MQ=255)                                                                                                                                                                gccGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACAGGCTGTAAAAACTCTGAATCTCACTACGCCCGGttttt                                                                          <  2:674308/209‑1 (MQ=255)                                                                                                                                                                                               gcTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCa                                                                                                                                                          >  1:748994/1‑99 (MQ=255)                                                                                                                                                                                               gcTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCa                                                                                                                                                          <  2:748993/99‑1 (MQ=255)                                                                                                                                                                                                cTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACAGGCTGTAAAAACTCTGAATCTCACTACg                                                                                    <  1:518177/168‑1 (MQ=255)                                                                                                                                                                                                               tCTATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACAGGCTGTAAAAACTCTGAATCTCACTACGCCCGGTTTTTAAACTCTGTAGCCTCACCCCCGCCAGCATCCAGCTGGTACACCCGCGCCGGCCGCCCCTGTTCATCaaaaaa  <  1:636112/235‑1 (MQ=255)                                                                                                                                                                                                                 tataGCCTGTGCCGGCCgcccctgttcatcaaaaaacacctgtcccagcccggcaccattccacagccgttccccggccttgctgtggctgggcgtacgcggcaccacctccatttctcggcgcttggtaaaccagtt                                                                                                 >  2:192294‑M1/1‑17 (MQ=255)                                                                                                                                                                                                                      ccTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTGCGCCCACACACCAAGGTGTGTCCACCCCCAATCAGGTGTAGGAGCGGGTTTACCCGCGAaga                                                                                                                          <  2:28132/108‑1 (MQ=255)                                                                                                                                                                                                                           gccggccgcccctgttcatca                                                                                                                                                                                                            >  2:188222‑M1/1‑7 (MQ=255)                                                                                                                                                                                                                             cGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCAccccc                                                                                                                                                           <  2:414078/68‑1 (MQ=255)                                                                                                                                                                                                                             cGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCAccccc                                                                                                                                                           >  1:414079/1‑68 (MQ=255)                                                                                                                                                                                                                             cGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTGTAGCAGCGGGTTTACCCGCGAAGAGGCCGGCACAGGCTGTAAAAACTCTGAATCTCACTACg                                                                                    >  1:421197/1‑139 (MQ=255)                                                                                                                                                                                                                             cGGCCTCTTCGCGGGTAAACCCGCCCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACAGGCTGTAAAAACTCTGAATCTCACTACg                                                                                    <  2:421196/139‑1 (MQ=255)                                                                                                                                                                                                                              ggccgcccctgttcatcaaaaaacacctgtcccagcccggcaccattccacagccgttccccggccttgctgtggctgggcgtacgcggcaccacctccatttctcggcgcttggtaaaccagttgagcggcgagcgc                                                                                    >  2:89517‑M1/1‑4 (MQ=255)                                                                                                                                                                                                                              ggCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACAGGCTGTAAAAACTCTGAATCTCACTACGCCCGGTTTTTAAACTCTGTAGCCTCAc                                                         <  2:624124/165‑1 (MQ=255)                                                                                                                                                                                                                               gccgcccctgttcatcaaaaaacacctgtcccagcccggcaccattccacagccgttccccggccttgctgtggctgggcgtacgcggcaccacctccatttctcggcgcttggtaaaccagttgagcggcga                                                                                        <  1:761080‑M1/133‑131 (MQ=255)                                                                                                                                                                                                                                 |                                                                                                                                                                                                                         TGCAGTCGATGGGCTTCGATCAGGTGTTCAACATCGTCGATCGACCGATACCCTGCACCGATTGCCTGACCGACTTGCCGTCGCAGGACCAGAATGAAGATGTGGTGCGCTCCAAGGTGCTGGAGGCGCACAAGATCCTCATGGGCCTGAATGACTCCAACCGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACAGGCTGTAAAAACTCTGAATCTCACTACGCCCGGTTTTTAAACTCTGTAGCCTCACCCCCGCCAGCATCCAGCTGGTACACCCGCGCCGGCCGCCCCTGTTCATCAAAAAA  >  AE015451/2471891‑2472331

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ 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.