New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	= 4236141	54 (0.950)	6 (0.110)	6/266	6.7	10.2%	intergenic (+77/‑37)	yjbE/yjbF	extracellular polysaccharide production threonine‑rich protein/extracellular polysaccharide production lipoprotein
	?	NC_000913_3_pae_tpiA	= 4236145	55 (1.040)					intergenic (+81/‑33)	yjbE/yjbF	extracellular polysaccharide production threonine‑rich protein/extracellular polysaccharide production lipoprotein
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

GCAACCGGTGGCGGTGATGGTTCTAATACCGGGACCACCACAACCACGACCACCAGTACCCAGTAATAAAGTATGTATCCCCAAAATAATTCGAGTCATTGCATCTGTGGCTAGAAGTATGAAGGGATTAACCATAACCACACTCCGGTGTGGTTATTCTGCCCCTCTGGAGAAGAGTCGTGAAGCGACCTGCACTCATTCTTATCTGCCTGTTATTACAGGCCTGTTCAGCCACGACTAAAGAGCTGGGCAATTCACTGTGGGACAGTCTGTTCGGCACGCCAGGCGTACAGC  >  NC_000913_3_pae_tpiA/4235999‑4236292                                                                                                                                                   |                                                                                                                                                    gCAACCGGTGGCGGTGATGGTTCTAATACCGGGACCACCACAACCACCACCACCAGTACCCAGTAATAAAGTATGTATCCCCAAAATAATTCGAGTCATTGCATCTGTGGCTAGAAGTATGAAGGGATTAACCATAACCACACTCCGgt                                                                                                                                                   <  1:557443/149‑1 (MQ=255)     ccGGTGGCGGTGATGGTTCTAATACCGGGACCACCACAACCACGACCACCAGTACCCAGTAATAAAGTATGTATCCCCAAAATAATTCGAGTCATTGCATCTGTGGCTAGAAGTATGAAGGGATTAACCATAACCACACTCCGGTGTgg                                                                                                                                               <  2:858803/149‑1 (MQ=255)          ggCGGTGATGGTTCTAATACCGGGACCACCACAACCACGACCACCAGTACCCAGTAATAAAGTATGTATCCCCAAAATAATTCGAGTCATTGCATCTGTGGCTAGAAGTATGAAGGGATTAACCATAACCACACTCCGGTGTGgttgtt                                                                                                                                          >  1:507128/1‑149 (MQ=255)                gATGGTTCTAATACCGGGACCACCACAACCACGACCACCAGTACCCAGTAATAAAGACTGTATCCCCAAAAAAATACGAGTCATTGCATCTCTAGCTAGAAGTATGAAGGGTATAACCACAACCACACTCGGATGTGGTTTTTCTGccc                                                                                                                                    >  2:435868/1‑149 (MQ=255)                     ttCTAATACCGGGACCACCACAACCACGACCACCAGTACCCAGTAATAAAGTATGTATCCCCAAACTAATTAGAGTCCATCCATCTGTGGCTAGCAGTATGAAGGGATTCACCACAACCCCACTCCGGTGTGGTTATTCTGCCCctctt                                                                                                                               >  2:501447/1‑148 (MQ=255)                     ttCTAATACCGGGACCACCACAACCACGACCACCAGTACCCAGTAATAAAGTATGTATCCCCAAAATAATTCGAGTCATTGCATCTGTGGCTAGAAGTATGAAGGGATTAACCATAACCACACTCCGGTGTGGTTATTCTGCCCCTCTg                                                                                                                               >  2:583628/1‑149 (MQ=255)                          aTACCGGGCCCACAACAACCACTACCACCAGTACCCAGGAATAAAGTATGTATCCCCAAAATAATTCGAGTCATTGCATCTGTGGCTAGAAGTATGAAGGGATTAACCATAACCACACTCCGGTGTGGTTATGCTGCCCCTCTGGagaa                                                                                                                          <  1:882966/149‑1 (MQ=255)                          aTACCGGGACCACCACAACCACGACCACCAGTACCCAGTAATAAAGTATGTATCCCCAAAATAATTCGAGTCATTGCATCTGTGGCTAGAAGTATGAAGGGATTAACCATAACCACACTCCGGTGTGGTTATTCTGCCCCTCTGGagaa                                                                                                                          <  1:159573/149‑1 (MQ=255)                            aCCGGGACCACCACAACCACGACCACCAGTACCCAGTAATAAAGTATGTATCCCCAAAATAATTCGAGTCATTGCATCTGTGGCTAGAAGTATGAAGGGATTAACCATAACCACACTCCGGTGTGGTTATTCTGCCCCTCTGGagaaga                                                                                                                        <  1:193354/149‑1 (MQ=255)                             ccGGGACCACCACAACCACGACCACCAGTACCCAGTAATAAAGTATGTATCCCCAAAATAATTCGAGTCATTGCATCTGTGGCTAGAAGTATGAAGGGATTAACCATAACCACACTCCGGTGTGGTTATTCTGCCCCTCTGGAGAagag                                                                                                                       >  1:961693/1‑149 (MQ=255)                                ggACCACCACAACCACGACCACCAGTACCCAGTAATAAAGTATGTATCCCCAAAATAATTCGAGTCATTGCATCTGTGGCTAGAAGTATGAAGGGATTAACCATAACCACACTCCGGTGTGGTTATTCTGCCCCTCTGGAGAAGAGTCg                                                                                                                    >  1:981831/1‑149 (MQ=255)                                    cccacaaaCCACGACCACCAGTACCCAGGAATAAAGTCTGTATCCCCAAAATAATTCGAGTCATTGCATCTGTGGCTAGAAGTATGAAGGCATTAACCATAACCACACTCCGGTGTGGTTATTCTGCCCCTCTGGAGAAGAGTCGTGaa                                                                                                                <  1:181855/143‑1 (MQ=255)                                    caccacAACCACGACCACCAGTACCCAGTAATAAAGTATGTATCCCCAAAATAATTCGAGTCATTGCATCTGTGGCTAGAAGTATGAAGGGATTAACCATAACCACACTCCGGTGTGGTTATTCTGCCCCTCTGGAGAAGAGTCGTGaa                                                                                                                <  2:981831/149‑1 (MQ=255)                                       cacaACCACGACCACCAGTACCCAGTAATAAAGTATGTATCCCCAAAATAATTCGAGTCATTGCATCTGTGGCTAGAAGTATGAAGGGATTAACCATAACCACACTCCGGTGTGGTTATTCTGCCCCTCTGGAGAAGAGTCGTGAAGCg                                                                                                             >  2:40848/1‑149 (MQ=255)                                                   caccaGTACCCAGTAATAAAGTATGTATCCCCAAAATAATTCGAGTCATTGCATCTGTGGCTAGAAGTATGAAGGGATTAACCATAACCACACTCCGGTGTGGTTATTCTGCCCCTCTGGAGAAGAGTCGTGAAGCGACCTGCACTCAt                                                                                                 <  1:766390/149‑1 (MQ=255)                                                      caGTACCCAGTAATAAAGTATGTATCCCCAAAATAATTCGAGTCATTGCATCTGTGGCTAGAAGTATGAAGGGATTAACCATAACCACACTCCGGTGTGGTTATTCTGCCCCTCTGGagaa                                                                                                                          >  1:486724/1‑121 (MQ=255)                                                      caGTACCCAGTAATAAAGTATGTATCCCCAAAATAATTCGAGTCATTGCATCTGTGGCTAGAAGTATGAAGGGATTAACCATAACCACACTCCGGTGTGGTTATTCTGCCCCTCTGGagaa                                                                                                                          <  2:486724/121‑1 (MQ=255)                                                         tACCCAGTAATAAAGTATGTATCCCCAAAATAATTCGAGTCATTGCATCTGTGGCTAGAAGTATGAAGGGATTAACCATAACCACACTCCGGTGTGGTTATTCTGCCGCTCTGGAGACGAGTCGTATCGCGACCGAGCTTCATTCTTAt                                                                                           >  2:446393/1‑149 (MQ=255)                                                           cccAGTAATAAAGTATGTATCCCCAAAATAATTCGAGTCATTGCATCTGTGGCTAGAAGTATGAACGGATTAACCATAACCACACTCCGGTGTGGTTATTCTGCCCCTCTAAAGAAGAATCGTAAGGCGACCTGCACTCCTTCTTATCt                                                                                         >  2:305548/1‑149 (MQ=255)                                                            ccAGTAATAAAGTATGTATCCCCAAAATAATTCGAGTCATTGCATCTGTGGCTAGAAGTATGAAGGGATTAACCATAACCACACTCCGGTGTGGTTATTCTGCCCCTCTGGAGAAGAGTCGTGAAGCGACCTGCACTCATTCTTATCTg                                                                                        >  2:667147/1‑149 (MQ=255)                                                            ccAGTAATAAAGTATGTATCCCCAAAATAATTCGAGTCATTGCATCTGTGGCTAGAAGTATGAAGGGATTAACCATAACCACACTCCAGCGCGGTTATTGTCCGCCTGTGGAGGAGAGACGTACAGCGACTTGGCCTCATTCTTATCTg                                                                                        >  2:614181/1‑149 (MQ=255)                                                             cAGTAATAAAGTATGTATCCCCAAAATAATTCGAGTCATTGCATCTGTGGCTAGAAGTATGAAGGGATTAACCATAACCACACTCCGGTGTGGTTATTCTGCCCCTCTGGAGAAGAGTCGTGAAGCGACCTGCACTCATTCTTATCTGc                                                                                       >  2:490389/1‑149 (MQ=255)                                                                        tatgtatCCCCAAAATAATTCGAGTCATTGCATCTGTGGCTAGACGTATGAAGGGATTAACCATAACCACACTCCGGTGTGGTTATTCTGCCCCTCTGGAGAAGAGTCGTGAAACAACCTGCACTCATTCTTATCTCCCGGTTATTACa                                                                            >  2:952088/1‑149 (MQ=255)                                                                        tatgtatCCCCAAAATAATTCGAGTCATTGCATCTGTGGCTAGAAGTATGAAGGGATTAACCATAACCACACTCCGGTGTGGTTATTCTGCCCCTCTGGAGAAGAGTGGTGAAGCGACCTGCACTCATTCTTATCTGCCTGTTATTACa                                                                            >  2:636070/1‑149 (MQ=255)                                                                        tatgtatCCCCAAAATAATTCGAGTCATTGCATCTGTGGCTAGAAGTATGAAGGGATTAACCATAACCACACTCCGGTGCGGTTATTCTGCCCCTCTGGAGAAGAGTCGTGAAGCGACCTGCACTCATTCTTATCTGCCTGTTATTACa                                                                            <  2:832859/149‑1 (MQ=255)                                                                        tatgtatCCCCAAAATAATTAGAGTCATTGCATCTGTGGCTACAAGTATGAAGGGATTAACCCTCACCACACCCCGCTGTAGTTATTCCGCCCCTCCGGAAAAGAATCGTGAACCGCCCTCCACTCACACTTAGCTGACTGAAATTACa                                                                            >  2:699703/1‑149 (MQ=255)                                                                              tCCCCAAAATAATTCGAGTCATTGCATCTGTGGCTAGAAGTATGAAGGGATTAACCATAACCACACTCCGGTGTGGTTATTCTGCCCCTCTGGAGAAGAGTCGTGAAGCGACCTGCACTCATTCTTATCTGCCTGTTATTACAGGCCTg                                                                      >  1:693536/1‑149 (MQ=255)                                                                                  cAAAATAATTCGAGTCATTGCATCTGTGGCTAGAAGTATGAAGGGATTAACCATAACCACACTCCGGTGTGGTTATTCTGCCCCTCTGGAGAAGAGTCGTGAAGCGACCTGCACTCATTCTTATCTGCCt                                                                                     >  1:537904/1‑130 (MQ=255)                                                                                  cAAAATAATTCGAGTCATTGCATCTGTGGCTAGAAGTATGAAGGGATTAACCATAACCACACTCCGGTGTGGTTATTCTGCCCCTCTGGAGAAGAGTCGTGAAGCGACCTGCACTCATTCTTATCTGCCt                                                                                     <  2:537904/130‑1 (MQ=255)                                                                                      ataatTCGAGTCATTGCATCTGTAGCAAGAAGTATGAACGGATTAACCATAACCACACTCCGGTGTGGCTATTCTACCCCCCTGGAAAAAAGTCGTGAAGCGACCTGCACTCATTCTTAACTGCCTGTTATTACAGGCCTGTTCAGCCa                                                              <  2:970012/149‑1 (MQ=255)                                                                                       taatTCGAGTCATTGCATCTGTGGCTAGAAGTATGAAGGGATTAACCATAACCACACTCCGGTGTGGTTATTCTGCCCCTCTGGAGAAGAGTCGTGAAGCGACCTGCACTCATTCTTATCTGCCTGTTATTACAGGCCTGTTCAGCCAc                                                             <  2:693536/149‑1 (MQ=255)                                                                                              aGTCATTGCATCTGTGGCTAGAAGTATGAAGGGAATAACCATAACCACACTCCAGTGAGGTTATTGTGCCCCTCTGGAGAAAAGTCGTGAAGCGAGCTGCACTCATCGTTATCTGCCTGTTATTACAGGCCCGTTCAGCCACGACtcag                                                      >  2:840092/1‑146 (MQ=255)                                                                                               gTCATTGCATCTGTGGCTAGAAGTATGAAGGGATTAACCATAACCACACTCCGGTGTGGTTATTCTGCCCCTCTGGAGAAGAGTCGTGAAGCGACCTGCACTCATTCTTATCTGCCTGTTATTACAGGCCTGTTCAGCCACGACTAAag                                                     <  2:961693/149‑1 (MQ=255)                                                                                                tCATTGCATCTGTGGCTAGAAGTATGAAGGGATTAACCATAACCACACTCCGGTGTGGTTATTCTGCCCCTCTGGAGAAGAGTCGTGAAGCGCCCTGCACTCATTCTTATCTGCCTGTTATTACAGGCCTGTTCCGCCACGCATAAagc                                                    >  2:586248/1‑148 (MQ=255)                                                                                                   ttGCATCTGTGGCTAGAAGTATGAAGGGATTAACCCTAACCACACTCCGGTGTGGTTATTCTGCCCCTCTGGAGAAGAGTCGTGAAGCGACCTGCACTCATTCTTATCTGCCTGTTATTACAGGCCTGTTCAGCCACGACTAAAGAGCt                                                 <  1:129979/149‑1 (MQ=255)                                                                                                   ttGCATCTGTGGCTAGAAGTATGAAGGGATTAACCATAACCACACTCCGGTGTGGTTATTCTGCCCCTCTGGAGAAGAGTCGTGAAGCGACCTGCACTCATTCTTATCTGCCTGTTATTACAGGCCTGTTCAGc                                                                >  1:132262/1‑134 (MQ=255)                                                                                                   ttGCATCTGTGGCTAGAAGTATGAAGGGATTAACCATAACCACACTCCGGTGTGGTTATTCTGCCCCTCTGGAGAAGAGTCGTGAAGCGACCTGCACTCATTCTTATCTGCCTGTTATTACAGGCCTGTTCAGc                                                                <  2:132262/134‑1 (MQ=255)                                                                                                      cATCTGTGGCTAGAAGTATGAAGGGGTTAACCATAACCACACTGCGGTGTGGTTATTCTGCCCCTCTGGTGAAGAGTCGTGAAGCGACCTGCACTCATTCTGATCTGCCAGTTATTACAGGCCTGTTCAGGCCCGACTAAAGGGCTggg                                              >  1:771033/1‑149 (MQ=255)                                                                                                       aTCTGTGGCTAGAAGTATGAAGGGATTAACCATAACAACATATCGGTGTGGTTATTCTGCCCCTCTGGAGAAGAGTCGTGAAGCGACCTGCACTCATTCTTATCTGCCTGTTATTACAGGCCTGTTCAGCCACGACTAAAACGCTGGGc                                             >  2:428271/1‑149 (MQ=255)                                                                                                              gCTAGAAGTATGAAGGGATTAACCATAACCACACTCCGGTGTGGTTATTCTGCCCCTCTGGAGAAGAGTCGTGAAGCGACCTGCACTCATTCTTATCTGCCTGTTATTACAGGCCTGTTCAGCCACGACTAAAGAGCTgg                                               <  2:259669/140‑1 (MQ=255)                                                                                                              gCTAGAAGTATGAAGGGATTAACCATAACCACACTCCGGTGTGGTTATTCTGCCCCTCTGGAGAAGAGTCGTGAAGCGACCTGCACTCATTCTTATCTGCCTGTTATTACAGGCCTGTTCAGCCACGACTAAAGAGCTgg                                               >  1:259669/1‑140 (MQ=255)                                                                                                               cTAGAAGTATGAAGGGATTAACCATAACCACACTCCGGTGTGGTTATTCTGCCCCTCTGGAGAAGGGTCGTGAAGCGACCTGCACTCATTCTTATCTGCCTGTTATTACAGGCCTGTTCAGCCACGACTAAAGAGCTGGGCAATTCACt                                     <  2:711350/149‑1 (MQ=255)                                                                                                                     gTATGAAGGGATTAACCATAACCACCCGCCGGTGTGGTTATTCTGCCCCTCTGGAGAAGAGTCGTGAAGCGACCTGCACTCATTCTTATCTGCCTGTTATTACAGGCCTGTTCAGCCACGACTAAAGAGCTGGGCAATTCACTGTGGGa                               <  1:220703/149‑1 (MQ=255)                                                                                                                      tATGAAGGGATTAACCATAACCACACTCCGGTGTGGTTATTCTGCCCCTCTGGAGAAGAGTCGTGAAGCGACCTGCACTCATTCTTATCTGCCTGTTATTACAGGCCTGTTCAGCCACGACTAAAGAGCTGGGCAATTCACTGTGGGAc                              >  1:1004845/1‑149 (MQ=255)                                                                                                                         gAAGGGATTAACCATAACCACACTCCGGTGTGGTTATTCTGCCCCTCTGGAGAAGAGTCGTGAAGCGACCTGCACTCATTCTTATCTGCCTGTTATTACAGGCCTGTTCAGCCACGACTAAAGAGCTGGGCAATTCACTGTGGGACAGt                           >  2:26208/1‑149 (MQ=255)                                                                                                                          aaGGGATTAACCATAACCACACTCCGGTGTGGTTATTCTGCCCCTCTGGAGAAGAGTCGTGAAGCGACCTGCACTCATTCTTATCTGCCTGTTATTACAGGCCTGTTCAGCCACGACTAAAGAGCTGGGCAATTACCTGTGGGACAGTc                          >  2:44054/1‑149 (MQ=255)                                                                                                                                ttactgataaccaCACTGCGGTGGGGTTAGTCGGCCCCTTGGGAGAAGAGGCGTGAAGCTAGCTGCACTCAGTCTTATCTGCCTGTTATTACAGGCCTGGTCAGCCACGACTAAAGAGCTGGGCAATTCACTGTGGGACAGTCTGTTCg                    <  2:838909/143‑1 (MQ=255)                                                                                                                                  aaccataaccaCACTCCGGTGTGGTTATTCTGCCCCTCTGGAGAAGAGTCGTGAAGCTACCTGCACTCATTCTTATCTGCCTGTTATTACAGGCCTGTTCAGCCACGACTAAAGAGCTGGGCAATTCACTGTGGGACAGTCTGTTCGGc                  >  1:542308/1‑149 (MQ=255)                                                                                                                                    ccataaccaCACTCCGGTGTGGTTATTCTGCCCCTCTGGAGAAGAGTCGTGAAGCGACCTGCACTCATTCTTATCTGCCTGTTATTACAGGCCTGTTCAGCCACGACTAAAGAGCTGGGCAATTCACTGTGGGACAGTCTGTTCGGccc                >  1:252234/1‑147 (MQ=255)                                                                                                                                     aataaccaCACCGGAGTGTGGTTATTCTGCCCCTCTGGAGAAGAGTCGTGAAGCGACCTGCACTCATTCTTATCTGCCTGTTATTACAGGCCTGTTCAGCCACGACTAAAGAGCTGGGCAATTCACTGTGGGACAGTCTGTTCGGCACg               >  2:267839/2‑149 (MQ=255)                                                                                                                                        aaccaCACTCCGGTGTGGTTATTCTGCCCCTCTGGAGAAGAGTCGTGAAGCGACCTGCACTCATTCTTATCTGCCTGTTATTACAGGCCTGTTCAGCCACGACTAAAGAGCTGGGCAATTCACtgtg                                  >  2:320282/1‑127 (MQ=255)                                                                                                                                        aaccaCACTCCGGTGTGGTTATTCTGCCCCTCTGGAGAAGAGTCGTGAAGCGACCTGCACTCATTCTTATCTGCCTGTTATTACAGGCCTGTTCAGCCACGACTAAAGAGCTGGGCAATTCACtgtg                                  <  1:320282/127‑1 (MQ=255)                                                                                                                                         accaCACTCCGGTGTGGTTATTCTGCCCCTCTGGAGAAGAGTCGTGAAGCGACCTGCACTCATTCTTATCTGCCTGTTATTACAGGCCTGTTCAGCCACGACTAAAGAGCTGGGCAATTCACTGTGGCACAGTCTGTTCGGCACGCCAg           >  1:98267/1‑149 (MQ=255)                                                                                                                                           cacaCTCCGGTGTGGTTATTCTGCCCCTCTGGAGAAGAGTCGTGAAGCGACCTGCACTCATTCTTATCTGCCTGTTATTACAGGCCTGTTCAGCCACGACTAAAGAGCTGGGCAATTCACTGTGGGACAGTCTGTTCGGCACGCCAGGc         >  2:822229/1‑149 (MQ=255)                                                                                                                                                tCCGGTGTGGTTATTCTGCCCCTCTGGAGAAGAGTCGTGAAGCGACCTGCACTCATTCTTATCTGCCTGTTATTACAGGCCt                                                                       <  2:738615/82‑1 (MQ=255)                                                                                                                                                tCCGGTGTGGTTATTCTGCCCCTCTGGAGAAGAGTCGTGAAGCGACCTGCACTCATTCTTATCTGCCTGTTATTACAGGCCt                                                                       >  1:738615/1‑82 (MQ=255)                                                                                                                                                  cGGTGTGGTTATTCTGCCCCTCTGGAGAAGAGTCGTGAAGCGACCTGCACTCATTCTTATCTGCCTGTTATTACAGGCCTGTTCAGCCACGACTAAAGAGCTGGGCAATTCACTGTGGGACAGTCTGTTCGGCACGCCAGGCGTACAGc  >  1:343871/1‑149 (MQ=255)                                                                                                                                                   |                                                                                                                                                    GCAACCGGTGGCGGTGATGGTTCTAATACCGGGACCACCACAACCACGACCACCAGTACCCAGTAATAAAGTATGTATCCCCAAAATAATTCGAGTCATTGCATCTGTGGCTAGAAGTATGAAGGGATTAACCATAACCACACTCCGGTGTGGTTATTCTGCCCCTCTGGAGAAGAGTCGTGAAGCGACCTGCACTCATTCTTATCTGCCTGTTATTACAGGCCTGTTCAGCCACGACTAAAGAGCTGGGCAATTCACTGTGGGACAGTCTGTTCGGCACGCCAGGCGTACAGC  >  NC_000913_3_pae_tpiA/4235999‑4236292

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.