New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	3319134 =	49 (0.830)	4 (0.080)	4/232	NT	9.4%	intergenic (‑98/+94)	treSA/PP_2919	trehalose synthase A/LysR family transcriptional regulator
	?	NC_002947	3319193 =	34 (0.650)					intergenic (‑157/+35)	treSA/PP_2919	trehalose synthase A/LysR family transcriptional regulator

CTCTTTGCGTGTCGGCACCGGCTCAGGTTATGACGGCGCTGCGGCCTGAACGTTCGGCTCAAGATGGGTGTTGGTTTCTTCGCGGGCTTGCCCGCTCCCACAGGCGGACATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGCATCATGGAAGTAATTGCGCACCGCCTGCATCGCCGGGCTGAATGCCCGTTCCCGGTGCCAGGCCAAC  >  NC_002947/3319045‑3319333                                                                                                                                                     |                                                                                                                                             ctctTTGCGTGTCGGCACCGGCTCAGGTTATGACGGCGCTGCGGCCTGAACGTTCGGCTCAAGATGGGTGTTGGTTTCTTCGCGGGCTTGCCCGCTCCCACAGGCGGACATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGgcg                                                                                                                                              >  6:352844/1‑149 (MQ=255)  tctTTGCGTGTCGGCACCGGCTCAGGTTATGACGGCGCTGCGGCCTGAACGTTCGGCTCAAGATGGGTGTTGGTTTCTTCGCGGGCTTTCCCACGACCCCAGGCGGACAAACCGCGGGAGATTTGCGCTGCACCAGTGGGAACGGgcgc                                                                                                                                             >  3:298042/1‑149 (MQ=255)  tctTTGCGTGTCGGCACCGGCTCAGGTTATGACGGCGCTGCGGCCTGAACGTTCGGCTCAAGATGGGTGTTGGTTTCTTCGCGGGCTTGCCCGCGGCCACAGGGGGGCCTAGCGGTGAATGTTTGCGCGGGACCGGTTGGGGCCGgcgc                                                                                                                                             >  3:351016/1‑149 (MQ=255)       gCGTGTCGGCACCGGCTCAGGTTATGACGGCGCTGCGGCCTGAACGTTCGGCTCAAGATGGGTGTTGGTTTCTTCGCGGGCTTGCCCGCTCCCACAGGCGGACATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGccc                                                                                                                                         <  7:245944/148‑1 (MQ=255)            gcGGCACCGGCTCAGGTTATGACGGCGCTGCGGCCTGAACGTTCGGCTCAAGATGGGTGTTGGTTTCTTCGCGGGCTTGCCCGCTCCCACAGGCGGACATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGaa                                                                                                                                    <  5:366328/147‑1 (MQ=255)                  ccGGCTCAGGTTATGACGGCGCTGCGGCCTGAACGTTCGGCTCAAGATGGGTGTTGGTTTCTTCGCGGGCGTGCCCGCGCCCACAGGCGGACATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCg                                                                                                                             <  5:5293/149‑1 (MQ=255)                        cAGGTTACGACGGCGCTGCGGCCTGAACGATCGGCTCAAGCTGGGTGTTGGCTGCTTCGCGGGCTTGCCCGCTCCCACAGGCGGACATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTg                                                                                                                       <  5:354449/149‑1 (MQ=38)                                gACGGCGCTGCGGCCTGAACGTTCGGCTCAAGATGGGTGTTGGTTTCTTCGCGGGCTTGCCCGCTCCCACAGGCGGACATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCgg                                                                                                                            <  7:165548/136‑1 (MQ=255)                                gACGGCGCTGCGGCCTGAACGTTCGGCTCAAGATGGGTGTTGGTTTCTTCGCGGGCTTGCCCGCTCCCACAGGCGGACATACCGCGGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCgg                                                                                                                            >  8:165548/1‑136 (MQ=255)                                 aCGGCGCTGCGGCCTGAACGTTCGGCTCAAGATGGGTGTTGGTTTCTTCGCGGGCTTGCCCGCTCCCACAGGCGGACATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAg                                                                                                              <  5:258710/149‑1 (MQ=255)                                          cGGCCTGAACGTTCGGCTCAAGATGGGTGTTGGTTTCTTCGCGGGCTTGCCCGCTCCCACAGGCGGACATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAgc                                                                                                       <  5:352844/147‑1 (MQ=255)                                                gAACGTTCGGCTCAAGATGGGTGTTGGTTTCTTCGCGGGCTTGCCCGCTCCCACAGGCGGACATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCgg                                                                                                                            <  7:65537/120‑1 (MQ=255)                                                gAACGTTCGGCTCAAGATGGGTGTTGGTTTCTTCGCGGGCTTGCCCGCTCCCACAGGCGGACATACCGCGGAAGATTTGCGCTGCACCGGTGGGAGCGGGCGCGCCCGCGAAGAGGCCgg                                                                                                                            >  8:65537/1‑120 (MQ=255)                                                   cGTTCGGCTCAAGATGGGTGTTGGTTTCTTCGCGGGCTTGCCCGCTCCCACAGGCGGACATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGa                                                                                             >  3:231583/1‑148 (MQ=255)                                                         gCTCAAGATGGGTGTTGGTTTCTTCGCGGGCTTGCCCGCTCCCACAGGCGGACATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAActgc                                                                                      >  1:231791/1‑149 (MQ=255)                                                           tCAAGATGGGTGTTGGTTTCTTCGCGGGCTTGCCCGCTCCCACAGGCGGACATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAActgctg                                                                                    >  6:157862/1‑149 (MQ=255)                                                             aaGATGGGTGTTGGTTTCTTCGCGGGCTTGCCCGCTCCCACAGGCGGACATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAg                                                                                                              >  3:272982/1‑121 (MQ=255)                                                             aaGATGGGTGTTGGTTTCTTCGCGGGCTTCCCCGCTCCCACAGGCGGACATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAg                                                                                                              <  4:272982/121‑1 (MQ=255)                                                                aTGGGTGTTGGTTTCTTCGCGGGCTTGCCCGCTGCCACAGGCGGACCTACCGCTGAAGATTTGCGCTGGACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGCTCGGCGCGGGGGCGCCAACTGCTGCgggg                                                                               >  8:284328/1‑147 (MQ=38)                                                                aTGGGTGTTGGTTTCTTCGCGGGCTTGCCCGCTCCCACAGGCGGACATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGt                                                                                <  4:351016/148‑1 (MQ=255)                                                                    gtgtGGGTTCCTGCGCGGGCTTGCCCGCCCCCCCCGGCCGACAACCCGCGCAAGATTGGCGCTGCACCTGGGGGCGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCCAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAg                                                                           <  3:18588/149‑1 (MQ=255)                                                                         ggTTTCTTCGCGGGCTTGCCCGCTCCCACAGGCGGACATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGt                                                                                >  7:351859/1‑139 (MQ=255)                                                                         ggTTTCTTCGCGGGCTTGCCCGCTCCCACAGGCGGACATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGt                                                                                <  8:351859/139‑1 (MQ=255)                                                                                  gcgGGCTTGCCCGCTCCCACAGGCGGACATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGCATCATgg                                                              <  2:231791/148‑1 (MQ=255)                                                                                   cgGGGTTGCCGGCTCCCACAGGGGGACATACCGGTGAAGATTGGCGCTGTTCCTGGGGGAGCGGGGGGGCCCGCGAAGAGGCCGGGCCTGGAATGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGCATCATGGaa                                                            <  4:298042/149‑1 (MQ=255)                                                                                   cgGGCTTGCCCGCTCCCACAGGCGGACATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGCATCATgg                                                              >  5:104732/1‑147 (MQ=255)                                                                                   cgGGCTTGCCCGCTCCCACAGGCGGACATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGGGCCAGAAACGCATCATGGaa                                                            <  6:308544/149‑1 (MQ=255)                                                                                   ccggCTTGCCCGCTCCCACACGCGGACATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGCATCATGGaa                                                            <  8:87375/147‑1 (MQ=255)                                                                                    gggCTTGCCCGCTCCCACAGGCGGACATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGCATCATGGAAg                                                           >  5:81766/1‑149 (MQ=255)                                                                                                  ccacaggtgcagcgcaaatcttcagcggtatgtccgcctgtgggagcgggcGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGCATCATGGAAGTAATTGCGCACCGc                                             >  4:224255‑M2/52‑149 (MQ=255)                                                                                                  CCACAGGCGGACATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGCATCATGGAAGTAATTGCGCACCGc                                             <  4:251850‑M1/149‑1 (MQ=255)                                                                                                  CCACAGGCGGACATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGCATCATGGAAGTAATTGCGCACCGc                                             <  3:92221‑M1/149‑1 (MQ=255)                                                                                                    ACAGGCGGACATACCGCTGAAGATTTGCACTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAAc                                                                       <  5:285311‑M1/121‑1 (MQ=255)                                                                                                    ACAGGCGGACATACCGCTGAAGATTTGCACTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAAc                                                                       >  6:285311‑M1/1‑121 (MQ=255)                                                                                                     CAGGCGGACATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGCATCATGGAAGTAATTGCGCACCGCCTg                                          >  6:81766‑M1/1‑149 (MQ=255)                                                                                                      AGGCGGACATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGCATCATGGAAGTAATTGCGCACCGCCTGc                                         >  4:231583‑M1/1‑149 (MQ=255)                                                                                                       GGCGGACATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGcatc                                                                  >  4:272774‑M1/1‑123 (MQ=255)                                                                                                       GGCGGACATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGcatc                                                                  <  3:272774‑M1/123‑1 (MQ=255)                                                                                                       GGCGGACATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGCATCATGGAAGTAATTGCGCACCGCCTGCa                                        >  2:134693‑M1/1‑149 (MQ=255)                                                                                                        gtgcagcgcaaatcttcagcggtatgtccgcctgtgggagcgggcGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGa                                                                                                            <  1:12552‑M2/35‑1 (MQ=255)                                                                                                        gtgcagcgcaaatcttcagcggtatgtccgcctgtgggagcgggcGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGa                                                                                                            >  2:12552‑M2/46‑80 (MQ=255)                                                                                                        GCGGACATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGCATCATGGAAGTAATTGCGCACCGCCTGCAt                                       <  6:175620‑M1/149‑1 (MQ=255)                                                                                                          ggACATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGCATCATGGAAGTAATTGCGCACCGCCTGCATCg                                     >  7:24265/1‑149 (MQ=255)                                                                                                               tACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACCGCTGCGGTGCCAGCAACGCATCATGGAAGTAATTGCGCACCGCCTGCATCGCCggg                                >  2:186909/1‑149 (MQ=255)                                                                                                                    cTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGCATCATGGAAGTAATTGCGCACCGCCTGCATCGCCGGGCTGaa                           >  7:42124/1‑149 (MQ=255)                                                                                                                       aaGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGCATCATgg                                                              >  3:126794/1‑111 (MQ=255)                                                                                                                       aaGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGCATCATgg                                                              <  4:126794/111‑1 (MQ=255)                                                                                                                         gATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGCATCATGGAAGTAATTGCGCACCGCCTGCATCGCCGGGCTGAATGccc                      >  2:27734/1‑149 (MQ=255)                                                                                                                           cggtatgtccgcctgtgggagcgggcGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGCATCATGGAAGTAATTGCGCACCGCCTGCATCGCCGGGCTGAATGCCCGt                    <  3:224255‑M2/123‑1 (MQ=255)                                                                                                                               cgcTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGCATCATGGAAGTAATTGCGCACCGCCTGCATCGCCGGGCTGAATGc                        <  4:282744/141‑1 (MQ=255)                                                                                                                               cgcTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGCATCATGGAAGTAATTGCGCACCGCCTGCATCGCCGGGCTGAATGc                        >  3:282744/1‑141 (MQ=255)                                                                                                                                    cACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGCATCATGGAAGTAATTGCGCACCGCCTGCATCGCCGGGCTGAATGCCCGTTCCCGGTGc           >  3:212714/1‑149 (MQ=255)                                                                                                                                       ctgtgggagcgggcGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGCATCATGGAAGTAATTGCGCACCGCCTGCATCGCCGGGCTGAATGCCCGTTCCCGGTGCCAg        >  7:80269‑M2/15‑149 (MQ=255)                                                                                                                                       ctgtgggagcgggcGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGCATCATGGAAGTAATTGCGCACCGCCTGCATCGCCGGGCTGAATGCCCGTTCCCGGTGCCAg        >  2:271193‑M2/15‑149 (MQ=255)                                                                                                                                       ctgtgggagcgggcGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGCATCATGGAAGTAATTGCGCACCCCCTGCATCGCCGGGCTGAATGCCCGTTCCCGGTGCCAg        >  3:212416‑M2/15‑149 (MQ=255)                                                                                                                                       ctgtgggagcgggcGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGCATCATGGAAGTAATAGCGCACCGCCTGCATCGCCGGGCTGAATGCCCGTTCCCGGTGCCAg        >  8:1799‑M2/15‑149 (MQ=255)                                                                                                                                             gagcgggcGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGCATCATGGAAGTAATTGCGCACCGCCTGCATCGCCGGGCTGAATGCCCGTTCCCGGTGCCAGGCCAAc  >  3:350926‑M2/9‑149 (MQ=255)                                                                                                                                                     |                                                                                                                                             CTCTTTGCGTGTCGGCACCGGCTCAGGTTATGACGGCGCTGCGGCCTGAACGTTCGGCTCAAGATGGGTGTTGGTTTCTTCGCGGGCTTGCCCGCTCCCACAGGCGGACATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGCATCATGGAAGTAATTGCGCACCGCCTGCATCGCCGGGCTGAATGCCCGTTCCCGGTGCCAGGCCAAC  >  NC_002947/3319045‑3319333

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ 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.