New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	3904713 =	45 (0.830)	3 (0.060)	3/248	NT	6.7%	coding (30/1593 nt)	ilvA‑I	threonine deaminase
	?	NC_002947	3904749 =	41 (0.800)					intergenic (‑7/+4)	ilvA‑I/PP_mr42	threonine deaminase/P9 ncRNA

CGTTTCAATGGCCAGGTCGTACACCGGCGCCGCAAGAATGCGACGCACCTGCTCCGACAGCAGTTGCTGGGGGGTGACGGTAGTACGAGGGACACTGAAGCTGGTCATCGATGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCAGAGAGAAAAAACCCGCCTCCAGGGCGGGTTCGGTGCACGTACGCGCTAGCCCGCCAAGCTGATAATGGCGGTAATAATAATGGCGTTCACGTGCGGGAATGTATTCATTGGGGTAGGAACTTAGCCTGCCTCGCAGCCGAAAGTCAACA  >  NC_002947/3904602‑3904897                                                                                                                                                    |                                                                                                                                                     ccaatgaatacattcccgcacgtgaacgccattattattaccgccattatcagcttggcgggctagcgcgtacgtgcaccgaacccgccctggaggcgggttttttctctcTGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCaga                                                                                                                                                     >  3:302734‑M1/112‑149 (MQ=255)           gCCAGGTCGTACACCGGCGCCGCAAGAATGCGACGCACCTGCTCCGACAGCAGTTGCTGGGGGGTGACGGTAGTACGAGGGACACTGAAGCTGGTCATCGATGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCAGAGAGaaaaaa                                                                                                                                            <  5:112325/148‑1 (MQ=255)           gCCAGGTCGTACACCGGCGCCGCAAGAATGCGACGCACCTGCTCCGACAGCAGTTGCTGGGGGGTGACGGTAGTACGAGGGACACTGAAGCTGGTCATCGATGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCAGAGAGAAAAAAc                                                                                                                                           >  6:127336/1‑149 (MQ=255)            attcccgcacgtgaacgccattattattaccgccattatcagcttggcgggctagcgcgtacgtgcaccgaacccgccctggaggcgggttttttctctcTGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCagaga                                                                                                                                                   >  6:311116‑M1/101‑140 (MQ=255)            attcccgcacgtgaacgccattattattaccgccattatcagcttggcgggctagcgcgtacgtgcaccgaacccgccctggaggcgggttttttctctcTGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCagaga                                                                                                                                                   <  5:311116‑M1/40‑1 (MQ=255)             cAGGTCGTACACCGGCGCCGCAAGAATGCGACGCACCTGCTCCGACAGCAGTTGCTGGGGGGTGACGGTAGTACGAGGGACACTGAAGCTGGTCATCGATGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCAGAGAGaaa                                                                                                                                               <  6:160775/143‑1 (MQ=255)             cAGGTCGTACACCGGCGCCGCAAGAATGCGACGCACCTGCTCCGACAGCAGTTGCTGGGGGGTGACGGTAGTACGAGGGACACTGAAGCTGGTCATCGATGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCAGAGAGaaa                                                                                                                                               >  5:160775/1‑143 (MQ=255)             cAGGTCGTACACCGGCGCCGCAAGAATGCGACGCACCTGCTCCGACAGCAGTTGCTGGGGGGTGACGGTAGTACGAGGGACACTGAAGCTGGTCATCGATGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCAGAGAGAAAAAAccc                                                                                                                                         <  5:245263/149‑1 (MQ=255)               ggTCGTACACCGGCGCCGCAAGAATGCGACGCACCTGCTCCGACAGCAGTTGCTGGGGGGTGACGGTAGTACGAGGGACACTGAAGCTGGTCATCGATGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCAGAGAGAAAAAACCCGc                                                                                                                                       >  6:205377/1‑149 (MQ=255)                    tACACCGGCGCCGCAAGAATGCGACGCACCTGCTCCGACAGCAGTTGCTGGGGGGTGACGGTAGTACGAGGGACACTGAAGCTGGTCATCGATGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCAGAGAGAAAAAACCCGCCTc                                                                                                                                    >  1:55640/1‑147 (MQ=255)                    tACACCGGCGCCGCAAGAATGCGACGCACCTGCTCCGACAGCAGTTGCTGGGGGGTGACGGTAGTACGAGGGACACTGAAGCTGGTCATCGATGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCAGAGAGAAAAAACCCGCCTc                                                                                                                                    >  1:50644/1‑147 (MQ=255)                     acacCGGCGCCGCAAGAATGCGACGCACCTGCTCCGACAGCAGTTGCTGGGGGGTGACGGTAGTACGAGGGACACTGAAGCTGGTCATCGATGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCAGAGAGAAAAAACCCGCCTCCAg                                                                                                                                 >  7:113151/1‑149 (MQ=255)                      cacCGGCGCCGCAAGAATGCGACGCACCTGCTCCGACAGCAGTTGCTGGGGGGTGACGGTAGTACGAGGGACACTGAAGCTGGTCATCGATGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCAGAGAGAAAAAACCCGCCTCCAgg                                                                                                                                >  2:287229/1‑149 (MQ=255)                       acCGGCGCCGCAAGAATGCGACGCACCTGCTCCGACAGCAGTTGCTGGGGGGTGACGGTAGTACGAGGGACACTGAAGCTGGTCATCGATGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCAGAGAGAAAAAACCCGccctggagg                                                                                                                               >  3:81409/1‑142 (MQ=255)                           gcgcCGCAAGAATGCGACGCACCTGCTCCGACAGCAGTTGCAGGGGGGTGACGGTAGTACGAGGGACACTGAAGCTGGTCATCGATGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCAGAGAGAAAAAACCCGCCTCCAGGGCggg                                                                                                                           <  1:287229/149‑1 (MQ=255)                                  aaGAATGCGACGCACCTGCTCCGACAGCAGTTGCTGGGGGGTGACGGTAGTACGAGGGACACTGAAGCTGGTCATCGATGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCAGAGAGAAAAAACCCGCCTCCAGGGCGGGTTCgg                                                                                                                      <  4:42845/147‑1 (MQ=255)                                  aaGAATGCGACGCACCTGCTCCGACAGCAGTTGCTGGGGGGTGACGGTAGTACGAGGGACACTGAAGCTGGTCATCGATGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCAGAGAGAAAAAACCCGCCTCCAGGGCGGGTTCgg                                                                                                                      >  3:42845/1‑147 (MQ=255)                                   aGAATGCGACGCACCTGCTCCGACAGCAGTTGCTGGGGGGTGACGGTAGTACGAGGGACACTGAAGCTGGTCATCGATGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCAGAGAGAAAAAACCCGCCTCCAGGGCGGGTTCGGTGc                                                                                                                   <  2:50644/149‑1 (MQ=255)                                   aGAATGCGACGCACCTGCTCCGACAGCAGTTGCTGGGGGGTGACGGTAGTACGAGGGACACTGAAGCTGGTCATCGATGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCAGAGAGAAAAAACCCGCCTCCAGGGCGGGTTCGGTGc                                                                                                                   <  2:55640/149‑1 (MQ=255)                                           aCGCACCTGCTCCGACAGCAGTTGCTGGGGGGTGACGGTAGTACGAGGGACACTGAAGCTGGTCATCGATGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCAGAGAGAAAAAACCCGCCTCCAGGGCGGGTTCGGTGCACGTAcgc                                                                                                           >  1:117151/1‑149 (MQ=255)                                                   gCTCCGACAGCAGTTGCTGGGGGGTGACGGTAGTACGAGGGACACTGAAGCTGGTCATCGATGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCAGAGAGAAAAAACCCGCCTACAGGGCGGGTTCGGTGCACGTACGCGCTAGccc                                                                                                   >  8:312683/1‑149 (MQ=255)                                                    cTCCGACAGCAGTTGCTGGGGGGTGACGGTAGTACGAGGGACACTGAAGCTGGTCATCGATGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCAGAGAGAAAAAACCCGCCTCCAGGGCGGGTTCGGTGCACGTACGCGCTAGccc                                                                                                   <  8:113151/148‑1 (MQ=255)                                                    cTCCGACAGCAGTTGCTGGGGGGTGACGGTAGTACGAGGGACACTGAAGCTGGTCATCGATGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCAGAGAGAAAAAACCCGCCTCCAGGGCGGGTTCGGTGCACGTACGCGCTAGCCCg                                                                                                  <  5:205377/149‑1 (MQ=255)                                                       cGACAGCAGTTGCTGGGGGGTGACGGTAGTACGAGGGACACTGAAGCTGGTCATCGATGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCAGAGAGAAAAAACCCGCCTCCAGGGCGGGTTCGGTGCACGTACGCGCTAGCCCGcc                                                                                                >  1:94/1‑148 (MQ=255)                                                         aCAGCAGTTGCTGGGGGGTGACGGTAGTACGAGGGACACTGAAGCTGGTCATCGATGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCAGAGAGAAAAAACCCGCCTCCAGGGCGGGTTCGGTGCACGTACGCGCTAGCCCGcc                                                                                                >  7:152761/1‑146 (MQ=255)                                                         aCAGCAGTTGCTGGGGGGTGACGGTAGTACGAGGGACACTGAAGCTGGTCATCGATGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCAGAGAGAAAAAACCCGCCTCCAGGGCGGGTTCGGTGCACGTACGCGCTAGCCCGcc                                                                                                <  8:152761/146‑1 (MQ=255)                                                          cagcagTTGCTGGGGGGTGACGGTAGTACGAGGGACACTGAAGCTGGTCATCGATGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCAGAGAGAAAAAACCCGCCTCCAGGGCGGGTTCGGTGCACGTACGCGCTAGCCCGCCAAGc                                                                                            <  2:96474/149‑1 (MQ=255)                                                          cagcagTTGCTGGGGGGTGACGGTAGTACGAGGGACACTGAAGCTGGTCATCGATGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCAGAGAGAAAAAACCCGCCTCCAGGGCGGGTTCGGTGCACGTACGCGCTAGCCCGCCAAGc                                                                                            <  5:127336/149‑1 (MQ=255)                                                             cagTTGCTGGGGGGTGACGGTAGTACGAGGGACACTGAAGCTGGTCATCGATGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCAGAGAGAAAAAACCCGCCTCCAGGGCGGGTTCGGTGCACGTACGCGCTAGCCCGCCAAGCTGa                                                                                         <  4:255474/149‑1 (MQ=255)                                                                         ggTGACGGTAGTACGAGGGACACTGAAGCTGGTCATCGATGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCAGAGAGAAAAACCCCGCCTCCAGGGCGGGTTCGGTGCACGTACGCGCTAGCCCGCCAAGCTGATAATGGCGGtaa                                                                             <  3:218839/149‑1 (MQ=255)                                                                             aCGGTAGTACGAGGGACACTGAAGCTGGTCATCGATGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCAGAGAGAAAAAACCCGCCTCCAGGGCGGGTTCGGTGCACGTACGCGCTAGCCCGCCAAGCTGATAATGGCGGtaataa                                                                          <  1:316426/148‑1 (MQ=255)                                                                                    taCGAGGGACACTGAAGCTGGTCATCGATGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCAGAGAGAAAAAACCCGCCTCCAGGGCGGGTTCGGTGCACGTAGGCGCTAGCCCGCCAAGCTGATAATGGCGGTAATAATAATGGc                                                                   >  4:158403/1‑148 (MQ=255)                                                                                    taCGAGGGACACTGAAGCTGGTCATCGATGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCAGAGAGAAAAAACCCGCCTCCAGGGCGGGTTCGGTGCACGTAAGCGCTAGCCCGCCAAGCTGATAATGGCGGTAATAATAATGGc                                                                   <  3:158403/148‑1 (MQ=255)                                                                                     aCGAGGGACACTGAAGCTGGTCATCGATGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCAGAGAGAAAAAACCCGCCTCCAGGGCGGGTTCGGTGCACGTACGCGCTAGCCCGCCAAGCTGATAATGGCGGTAATAATAATGGCGt                                                                 >  7:80948/1‑149 (MQ=255)                                                                                      cGAGGGACACTGAAGCTGGTCATCGATGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCAGAGAGAAAAAACCCGCCTCCAGGGCGGGTTCGGTGCACGTACGCGCTAGCCCGCCAAGCTGATAATg                                                                                    >  2:343972/1‑129 (MQ=255)                                                                                      cGAGGGACACTGAAGCTGGTCATCGATGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCAGAGAGAAAAAACCCGCCTCCAGGGCGGGTTCGGTGCACGTACGCGCTAGCCCGCCAAGCTGATAATg                                                                                    <  1:343972/129‑1 (MQ=255)                                                                                       gAGGGACACTGAAGCTGGTCATCGATGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCAGAGAGAAAAAACCCGCCTCCAGGGCGGGTTCGGTGCACGTACGCGCTAGCCCGCCAAGCTGATAATGGCGGTAATAATAATGGCGTTc                                                               <  2:94/149‑1 (MQ=255)                                                                                         gggACACTGAAGCTGGTCATCGATGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCAGAGAGAAAAAACCCGCCTCCAGGGCGGGTTCGGTGCACGTACGCGCTAGCCCGCCAAGCTGATAATGGCGGTAATAATAATGGCGTTCAc                                                             <  8:80948/149‑1 (MQ=255)                                                                                                      tGGTCATCGATGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCAGAGAGAAAAAACCCGCCTCCAGGGCGGGTTCGGTGCACGTACGCGCTAGCCCGCCAAGCTGATAATGGCGGTAATAATAATGGCGTTCACGTGCGGGAATGTa                                                >  2:141791/1‑149 (MQ=255)                                                                                                           aTCGATGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCAGAGAGAAAAAACCCGCCTCCAGGGCGGGTTCGGTGCACGTACGCGCTAGCCCGCCAAGCTGATAATGGCGGTAATAATAATg                                                                     <  6:198090/123‑1 (MQ=255)                                                                                                           aTCGATGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCAGAGAGAAAAAACCCGCCTCCAGGGCGGGTTCGGTGCACGTACGCGCTAGCCCGCCAAGCTGATAATGGCGGTAATAATAATGGCGTTCACGTGCGGGAATGTATTCAt                                           >  2:6916/1‑149 (MQ=255)                                                                                                            tctctgactcttgggcaacgtaaaaatagccaaggagtcaGAGAGAAAAAACCCGCCTCCAGGGCGGGTTCGGTGCACGTACGCGCTAGCCCGCCAAGCTGATAATGGCGGTAATAATAATGGCGTTCACGTGCGGGAAt                                                   <  5:311116‑M2/100‑1 (MQ=255)                                                                                                            tctctgactcttgggcaacgtaaaaatagccaaggagtcaGAGAGAAAAAACCCGCCTCCAGGGCGGGTTCGGTGCACGTACGCGCTAGCCCGCCAAGCTGATAATGGCGGTAATAATAATGGCGTTCACGTGCGGGAAt                                                   >  6:311116‑M2/41‑140 (MQ=255)                                                                                                              tctgactcttgggcaacgtaaaaatagccaaggagtcaGAGAGAAAAAACCCGCCTCCAGGGCGGGTTCGGTGCACGTACGCGCTAGCCCGCCAAGCTGATAATGGCGGTAATAATAATGGCGTTCACGTGCGGGAATGTATTCATTgg                                        >  3:302734‑M2/39‑149 (MQ=255)                                                                                                                   CTCCTTGGCTATTTTTACGTTGCCCAAGAGTCAGAGAGAAAAAACCCGCCTCCAGGGCGGGTTCGGTGCACGTACGCGCTAGCCCGCCAAGCTGATAATGGCGGTAATAATAATGGCGTTCACGTGCGGGAATGTATTCATTGGGGTAg                                   >  8:155076‑M1/1‑149 (MQ=255)                                                                                                                   CTCCTTGGCTATTTTTACGTTGACCAAGAGTCAGAGAGAAAAAACCCGCCTCCAGGGCGGGTTCGGTGCACGTACGCGCTAGCCCACAAAGCTGATAATGGCGGTAATAATAATGGCGTGCACGTGCGGGAATGTATTCATTTGGGTAg                                   <  4:87535‑M1/149‑1 (MQ=255)                                                                                                                            tATTTTTACGTTGCCCAAGAGTCAGAGAGAAAAAACCCGCCTCTAGGGCGGGTTCGGTGCACGTACGCGCTAGCCCGCCAAGCTGATAATGGCGGTAATAATAATGGCGTTCACGTGCGGGAATGTATTCAtt                                          >  2:108658/1‑133 (MQ=255)                                                                                                                            tATTTTTACGTTGCCCAAGAGTCAGAGAGAAAAAACCCGCCTCTAGGGCGGGTTCCGTGCACGTACGCGCTAGCCCGCCAAGCTGATAATGGCGGTAATAATAATGGCGTTCACGTGCGGGAATGTATTCAtt                                          <  1:108658/133‑1 (MQ=255)                                                                                                                                     gTTGCCCAAGAGTCAGAGAGAAAAAACCCGCCTCCAGGGCGGGTTCGGTGCACGTACGCGCTAGCCCGCCAAGCTGATAATGGCGGTAATAATAATGGCGTTCACGTGCGGGAATGTATTCATTGGGGTAGGAACTTAGCCTGCCTCGc                 >  7:95813/1‑149 (MQ=255)                                                                                                                                            aaGAGTCAGAGAGAAAAAACCCGCCTCCAGGGCGGGTTCGGTGCACGTACGCGCTAGCCCGCCAAGCTGATAATGGCGGTAATAATAATGGCGTTCACGTGCGGGAATGTATTCATTGGGGTAGGAACTTAGCCTGCCTCGCAGCCGa           >  2:318580/1‑148 (MQ=255)                                                                                                                                              gagtcaGAGAGAAAAAACCCGCCTCCAGGGCGGGTTCGGTGCACGTACGCGCTAGCCCGCCAAGCTGATAATGGCGGTAATAATAATGGCGTTCACGTGCGGGAATGTATTCATTGGGGTAGGAACTTAGCCTGCCTCGCAGCCGAAAg        <  4:302734‑M2/143‑1 (MQ=255)                                                                                                                                                   aGAGAGAAAAAACCCGCCTCCAGGGCGGGTTCGGTGCACGTACGCGCTAGCCCGCCAAGCTGATAATGGCGGTAATAATAATGGCGTTCACGTGCGGGAATGTATTCATTGGGGTAGGAACTTAGCCTGCCTCGCAGCCGAAAGTCaa    <  2:117151‑M2/147‑1 (MQ=255)                                                                                                                                                    gagagaAAAAACCCGCCTCCAGGGCGGGTTCGGTGCACGTACGCGCTAGCCCGCCAAGCTGATAATGGCGGTAATAATAATGGCGTTCACGTGCGGGAATGTATTCATTGGGGTAGGAACTTAgcct                        <  6:216071/127‑1 (MQ=255)                                                                                                                                                    gagagaAAAAACCCGCCTCCAGGGCGGGTTCGGTGCACGTACGCGCTAGCCCGCCAAGCTGATAATGGCGGTAATAATAATGGCGTTCACGTGCGGGAATGTATTCATTGGGGTAGGAACTTAgcct                        >  5:216071/1‑127 (MQ=255)                                                                                                                                                    gagagaAAAAACCCGCCTCCAGGGCGGGTTCGGTGCACGTACGCGCTAGCCCGCCAAGCTGATAATGGCGGTAATAATAATGGCGTTCACGTGCGGGAATGTATTCATTGGGGTAGGAACTTAGCCTGCCTCGCAGCCGAAAGTCAaca  >  4:288936/1‑149 (MQ=255)                                                                                                                                                    gagagaAAAAACCCGCCTCCAGGGCGGGTTCGGTGCACGTACGCGCTAGCCCGCCAAGCTGATAATGGCGGTAATAATAATGGCGTTCACGTGCGGGAATGTATTCATTGGGGTAGGAACTTAGCCTGCCTCGCAGCCGAAAGTCAaca  <  1:6916/149‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                     CGTTTCAATGGCCAGGTCGTACACCGGCGCCGCAAGAATGCGACGCACCTGCTCCGACAGCAGTTGCTGGGGGGTGACGGTAGTACGAGGGACACTGAAGCTGGTCATCGATGACTCCTTGGCTATTTTTACGTTGCCCAAGAGTCAGAGAGAAAAAACCCGCCTCCAGGGCGGGTTCGGTGCACGTACGCGCTAGCCCGCCAAGCTGATAATGGCGGTAATAATAATGGCGTTCACGTGCGGGAATGTATTCATTGGGGTAGGAACTTAGCCTGCCTCGCAGCCGAAAGTCAACA  >  NC_002947/3904602‑3904897

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ 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.