New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_bme_pgi	= 20563	NA (NA)	40 (0.880)	34/290	0.4	88.9%	intergenic (‑55/+252)	insA/rpsT	IS1 repressor TnpA/30S ribosomal subunit protein S20
	?	NC_000913_3_bme_pgi	= 61489	5 (0.110)					coding (1776/2907 nt)	rapA	RNA polymerase remodeling/recycling factor ATPase; RNA polymerase‑associated, ATP‑dependent RNA translocase

GCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGAAGAGTTCAGATAGTACAACGGCATGTCTCTTTTGAC  >  NC_000913_3_bme_pgi/20424‑20711                                                                                                                                            |                                                                                                                                                     gttGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAAt                                                                                                                                             <  2:85038/147‑1 (MQ=25)   tGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCACGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCCCAAtgt                                                                                                                                           >  2:624126/1‑149 (MQ=25)               gTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAACCAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAatat                                                                                                                               >  1:626911/1‑149 (MQ=255)               gTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAatat                                                                                                                               >  1:512982/1‑149 (MQ=255)               gTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAatat                                                                                                                               >  1:374470/1‑149 (MQ=255)                 gCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATCGACACCGGAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATcc                                                                                                                             <  1:587858/149‑1 (MQ=255)                   ttttGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCat                                                                                                                           >  1:473769/1‑149 (MQ=255)                   ttttGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAACTCAATGCGTATCACCATATCCat                                                                                                                           >  1:503245/1‑149 (MQ=255)                          gTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCttt                                                                                                                    <  1:693673/149‑1 (MQ=255)                           ttACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCGGCACCTACCTCAATGTGTATCACAATATCCATATTCTTtg                                                                                                                   >  1:750148/1‑149 (MQ=255)                           ttACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTtg                                                                                                                   <  1:361411/149‑1 (MQ=255)                           ttACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTtg                                                                                                                   >  1:498865/1‑149 (MQ=255)                            tACGCACCACGCCGTGAGTAGCAGAACAGGCGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACCCCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTtgt                                                                                                                  <  1:464304/149‑1 (MQ=18)                            tACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTtgt                                                                                                                  <  1:711676/149‑1 (MQ=255)                               gCACCCCCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACATAAGCCACTGGAGCACCTCAAAAACACCATCATACTCTAATTCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTggg                                                                                                               <  2:601493/149‑1 (MQ=255)                                 accaacCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACACAGGCCGCTGGGGCACCTCAAAAACACCATCATAGACTAAATGAGTAAGATGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTggggg                                                                                                             >  2:607667/1‑149 (MQ=18)                                         gTCAGTAGCTGAACAGGAGCGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCATAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTggc                                                                                                     <  1:762153/149‑2 (MQ=255)                                               aGCTGAACAGGAAGGACAGCTTATAGAAACAGAATCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTTGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGa                                                                                               <  1:290038/149‑1 (MQ=255)                                                 cTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGt                                                                                             >  1:155530/1‑149 (MQ=255)                                                 cTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGt                                                                                             <  1:456256/149‑1 (MQ=255)                                                   gAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAg                                                                                           >  1:202259/1‑149 (MQ=255)                                                              aCAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGtt                                                                                <  1:532153/149‑1 (MQ=255)                                                               cAGCTGATATAAACATAAGCCACTGGTGCACCTCAAAAACACCATTATACATTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTc                                                                               <  1:370227/149‑1 (MQ=37)                                                                 gCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTCCAg                                                                             >  2:629167/1‑149 (MQ=255)                                                                 gCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGACATTCTTTTTCAg                                                                             >  2:178586/1‑149 (MQ=255)                                                                   tGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGaa                                                                           <  2:469729/149‑1 (MQ=255)                                                                     aTAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGAAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGCGATTGAGGAGATATTCTTGTTCatactg                                                                         >  2:225495/1‑144 (MQ=255)                                                                      tAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGt                                                                        >  1:451199/1‑149 (MQ=255)                                                                        gAAACCGAGACCACCGGAGGATCCCGAAATCACCATCATACACTAGATGGCTGAGTTGGCCGCATTACCTACCTAAATGCGTATCACAATCTCCATATTCTTGGTGGGGGTGTCTGGAGATTCAGTAGATATTCTTGTTCAGAATGTAt                                                                      <  2:658277/149‑1 (MQ=255)                                                                          agcAGGAGCCACTGGAGCACCTCAAAAACACCATCATACCTTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATTACAATATCCATATTCTTTGTGGGGGAGTCTGGCGATTGAGTAGATATTCTTGTTCAGAATGTATCa                                                                    <  2:515336/147‑1 (MQ=37)                                                                          aaCAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCGGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCa                                                                    >  1:240865/1‑149 (MQ=255)                                                                               aaaccACTGGATCACCACAAAAACACCATCATACACTAAAACAGTAAGTTGTCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGa                                                               <  2:684422/146‑1 (MQ=38)                                                                                    aacggaggaCCGAAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCGCCTACCCCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGtt                                                          <  2:311495/146‑1 (MQ=38)                                                                                             ccTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGATTAGATATTCTTGTTCAGaa                                                                           <  2:577865/123‑1 (MQ=255)                                                                                             ccTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGaa                                                                           >  1:577865/1‑123 (MQ=255)                                                                                              cTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCt                                                >  1:534686/1‑149 (MQ=255)                                                                                              cTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCt                                                >  1:156985/1‑149 (MQ=255)                                                                                               tCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTCTCACAATATCCATATTCTTTGTGGGGGAGTCTGGCGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACAATTCtt                                               >  2:604781/1‑149 (MQ=255)                                                                                               tCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCtt                                               >  1:582419/1‑149 (MQ=255)                                                                                                  aaaaCACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTTTTTTTTTTTTTGAACATTGAATAGCTATTCTTGTTCATAATGTATCATCCGATGGTTCTCCTCTTCTTatc                                            >  2:123583/1‑147 (MQ=21)                                                                                                         catcatACACTAAATCAATAAGTTGGCATCATCACCTACCCCAATGTGTATCACAATATCCATATTCTTTGTAGAGGACTCTGTAAATTGACTATATATTCTTGTTCAGAATGTATCAGCCGATTCTTCTACGATTCTTAAGCCACGaa                                     <  2:750250/149‑1 (MQ=255)                                                                                                           tggtACACTACATCAGTTACTTGGGGGCATGACCTATCTCAATTTGTATTACAATATCCATATTCTTTGTGGGGGATTCTGGAGATTGATTAGATATTCTTGTTTAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGAaga                                   <  2:420554/146‑1 (MQ=255)                                                                                                           tcacACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGTCGATGGTTCTACGCTTCTTAAGCCACGAaga                                   >  2:75179/1‑149 (MQ=255)                                                                                                            catACCCTAAATCAGTAAGTTAGCAGCATCACCTACCTTAATTTGTATGACAATATCCATATTCTTTCTGGGGGTGTCTGGAGATTGTGTGGAGATTCTTGTTCAGTATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGAagag                                  <  2:693465/149‑1 (MQ=255)                                                                                                                cacTAAATCAGTAAGTTGGCAGCATCACCTACCTGAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGAAGAGTTCa                              <  1:575126/149‑1 (MQ=255)                                                                                                                  cTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGAAGAGTTCAGa                            <  1:356847/149‑1 (MQ=255)                                                                                                                     aaTCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGAAGAGTTCAGATAg                         <  2:202259/149‑1 (MQ=255)                                                                                                                       tCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATGCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGAAGAGTTCAGATAGTa                       >  1:636119/1‑149 (MQ=255)                                                                                                                          gTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGAAGAGTTCAGATAGTACaa                    >  1:243878/1‑149 (MQ=255)                                                                                                                           tAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGAAGAGTTCAGATAGTACAAc                   >  1:271714/1‑149 (MQ=255)                                                                                                                           tAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATGGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGAAGAGTTCAGATAGTGCAAc                   >  1:619245/1‑149 (MQ=255)                                                                                                                               ttGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGAAGAGTTCAGATAGTACAACGGCa               >  1:115431/1‑149 (MQ=255)                                                                                                                               ttGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGAAGAGTTCAGATAGTACAACGGCa               >  1:604205/1‑149 (MQ=255)                                                                                                                                  gcagcaTCACCCACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGGCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGAAGAGTTCAGATAGTACAACGGCATGt            <  1:404028/149‑1 (MQ=255)                                                                                                                                       aTCACCTACCTCAATGTGTATCAAAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGAAGAGTTCAGATAGTACAACGGCATGTCTCtt       >  2:680129/1‑149 (MQ=255)                                                                                                                                           cctacctCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGAAGAGTTCAGATAGTACAACGGCATGTCTCTTTTGa   <  2:271714/149‑1 (MQ=255)                                                                                                                                           cctacctCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGAAGAGTTCAGATAGTACAACGGCATGTCTCTTTTGa   >  1:638782/1‑149 (MQ=255)                                                                                                                                            ctacctCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGAAGAGTTCAGATAGTACAACGGCATGTCTCTTTTGAc  >  2:653252/1‑149 (MQ=255)                                                                                                                                            |                                                                                                                                                     GCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGAGTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGAAGAGTTCAGATAGTACAACGGCATGTCTCTTTTGAC  >  NC_000913_3_bme_pgi/20424‑20711

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.