New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	1569744 =	41 (0.830)	8 (0.180)	7/236	NT	17.4%	coding (555/1203 nt)	pcaF‑I	beta‑ketoadipyl‑CoA thiolase
	?	NC_002947	1569779 =	38 (0.840)					coding (590/1203 nt)	pcaF‑I	beta‑ketoadipyl‑CoA thiolase

GTTTCATCAACCCGCTGATGAAGAGCCAGTACGGTGTGGATTCCATGCCGGAAACCGCCGACAACGTGGCCGACGACTATCAGGTTTCGCGTGCTGATCAGGACGCTTTCGCCCTGCGCAGCCAGCAGAAGGCTGCCGCTGCGCAGGCTGCCGGCTTCTTTGCCGAAGAAATCGTGCCGGTGCGTATCGCTCACAAGAAGGGCGAAATCATCGTCGAA‑CGTGACGAACACCTGCGCCCGGAAACCACGCTGGAGGCGCTGACCAAGCTCAAACCGGTCAACGGCCCG  >  NC_002947/1569632‑1569918                                                                                                                                                    |                                                                                                                                             tcttCATCAGCGGGTTGATGAAGAGCCAGTACGGTGTGGATTCCATGCCGGAAACCGCCGACAACGTGGCCGACGACTATCAGGTTTCGCGTGCTGATCAGGACGCTTTCGCCCTGCGCAGCCAGCAGAAGGCTGCCGCTGCGCAGGCt                                                                                                                                             >  6:18996/3‑149 (MQ=255)  gcgcctccagcgtggtttccgggcgcaggtgttcgtcacgttcgacgatgatttcgcccttcttgtgagcgatacgcaccggcacgatttcttcggcaaagaagccggcagCCTGCGCAGCCAGCAGCAGGCTGCCGCTGCGCAGGCTg                                                                                                                                            <  3:95824‑M1/38‑1 (MQ=255)       tcaACCCGCTGATGAAGAGCCAGTACGGTGTGGATTCCATGCCGGAAACCGCCGACAACGTGGCCGACGACTATCAGGTTTCGCGAGCTGATCAGGACGCTTTCGCCCTGCGCAGCCAGCAGAAGGCTGCCGCTGCGCAGGCTGCCGGc                                                                                                                                       >  3:13246/1‑149 (MQ=255)            ccGCTGATGAAGAGCCAGTACGGTGTGGATTCCATGCCGGAAACCGCCGACAACGTGGCCGACGACTATCAGGTTTCGCGTGCTGATCAGGACGCTTTCGCCCTGCGCAGCCAGCAGAAGGCTGCCGCTGCGCAGGCTGCCGGctt                                                                                                                                     >  6:20610/1‑146 (MQ=255)            ccGCTGATGAAGAGCCAGTACGGTGTGGATTCCATGCCGGAAACCGCCGACAACGTGGCCGACGACTATCAGGTTTCGCGTGCTGATCAGGACGCTTTCGCCCTGCGCAGCCAGCAGAAGGCTGCCGCTGCGCAGGCTGCCGGctt                                                                                                                                     <  5:20610/146‑1 (MQ=255)             cGCTGATGAAGAGCCAGTACGGTGTGGATTCCATGCCGGAAACCGCCGACAACGTGGCCGACGACTATCAGGTTTCGCGTGCTGATCAGGACGCTTTCGCCCTGCGCAGCCAGCAGAAGGCTGCCGCTGCGCAGGCTGCCGGCTTCttt                                                                                                                                 <  2:108787/149‑1 (MQ=255)                  atgaAGAGCCAGTACGGTGTGGATTCCATGCCGGAAACCGCCGACAACGTGGCCGACGACTATCAGGTTTCGCGTGCTGATCAGGACGCTTTCGCCCTGCGCAGCCAGCAGAAGGCTGCCGCTGCGCAGGCTGCCGGCTTCTTTGCCga                                                                                                                            <  5:12759/149‑1 (MQ=255)                   tgaAGAGCCAGTACGGTGTGGATTCCATGCCGGAAACCGCCGACAACGTGGCCGACGACTATCAGGTTTCGCGTGCTGATCAGGACGCTTTCGCCCTGCGCAGCCAGCAGAAGGCTGCCGCTGCGCAGGCTGCCGGCTTCTTTGCCgaa                                                                                                                           <  7:232898/149‑1 (MQ=255)                      agagCCTGTACGGTGGGGATTCCTTGCCGGAAACCGCCGACAACGTGGCCGAGGACTTTCTGGTTTGGCGTGCTGATCAGGACGCTTTCGCCCTGCGCAGCCAGCAGACGGCGGCCGCGGCGCTGGCTGCCGGCTTCTTTGCCgaagaa                                                                                                                        <  4:3374/149‑1 (MQ=255)                       ggcgatggtgttcgtcacgttcgacgatgatttcgcccttctggtgagctatacccaccgccaccatttctgcggcaaagacgccggcagCCTGCGCAGCCAGCAGAAGGCGGCCGCTGCGCAGGCTGCCGGCTTCTTTGCCGAAGaaa                                                                                                                       >  4:95824‑M1/91‑149 (MQ=255)                          ccAGTACGGTGTGGATTCCATGCCGGAAACCGCCGACAACGTGGCCGACGACTATCAGGTTTCGCGTGCTGATCAGGACGCTTTCGCCCTGCGCAGCCAGCAGAAGGCTGCCGCTGCGCAGGCTGCCGGCTTCTTTGCCGAAGAAATCg                                                                                                                    >  2:80999/1‑149 (MQ=255)                            aGTACGGTGTGGATTCCATGCCGGAAACCGCCGACAACGTGGCCGACGACTATCAGGTTTCGCGTGCTGATCAGGACGCTTTCGCCCTGCGCAGCCAGCAGAAGGCTGCCGCTGCGCAGGCTGCCGGCTTCTTTGCCGAAGAAATCGTg                                                                                                                  >  6:192523/1‑149 (MQ=255)                             gTACGGTGTGGATTCCATGCCGGAAACCGCCGACAACGTGGCCGACGACTATCAGGTTTCGCGTGCTGATCAGGACGCTTTCGCCCTGCGCAGCCAGCAGAAGGCTGCCGCTGCGCAGGCTGCCGGCTTCTTTGCCGAAGAAATCGTGc                                                                                                                 <  7:236576/149‑1 (MQ=255)                                   tgtgGATTCCATGCCGGAAACCGCCGACAACGTGGCCGACGACTATCAGGTTTCGCGTGCTGATCAGGACGCTTTCGCCCTGCGCAGCCAGCAGAAGGCTGCCGCTGCGCAGGCTGCCGGCTTCTTTGCCGAAGAAATCGTGCCGGTGc                                                                                                           <  8:179003/149‑1 (MQ=255)                                   tgtgGATTCCATGCCGGAAACCGCCGACAACGTGGCCGACGACTATCAGGTTTCGCGTGCTGATCAGGACGCTTTCGCCCTGCGCAGCCAGCAGAAGGCTGCCGCTGCGCAGGCTGCCGGCTTCTTTGCCGAAGAAATCGTGCCGGTGc                                                                                                           <  5:18996/149‑1 (MQ=255)                                        aTTCCATGCCGGAAACCGCCGACAACGTGGCCGACGACTATCAGGTTTCGCGTGCTGATCAGGACGCTTTCGCCCTGCGCAGCCAGCAGAAGGCTGCCGCTGCGCAGGCTGCCGGCTTCTTTGCCGAAGAAATCGTGCCGGTGCGTATc                                                                                                      <  8:164896/149‑1 (MQ=255)                                            cATGCCGGAAACCGCCGACAACGTGGCCGACGACTATCAGGTTTCGCGTGCTGATCAGGACGCTTTCGCCCTGCGCAGCCAGCAGAAGGCTGCCGCTGCGCAGGCTGCCGGCTTCTTTGCCGAAGAAATCGTGCCGGTGCGTATCGCTc                                                                                                  <  8:54599/149‑1 (MQ=255)                                             aTGCCGGAAACCGCCGACAACGTGGCCGACGACTATCAGGTTTCGCGTGCTGATCAGGACGCTTTCGCCCTGCGCAGCCAGCAGAAGGCTGCCGCTGCGCAGGCTGCCGGCTTCTTTGCCGAAGAAATCGTGCCGGTGCGTATCGCTca                                                                                                 <  2:223593/149‑1 (MQ=255)                                                    aaaCCGCCGACAACGTGGCCGACGACTATCAGGTTTCGCGTGCTGATCAGGACGCTTTCGCCCTGCGCAGCCAGCAGAAGGCTGCCGCTGCGCAGGCTGCCGGCTTCTTTGCCGAAGAAATCGTGCCGGTGCGTATCGCTCACaagaag                                                                                          <  5:192523/149‑1 (MQ=255)                                                       ccgccgACACCGTGGCCGACGAGTTTCAGGTTTCGCGTGCTGATCAGGCCGCTTTCGCCCTGCGCAGCCAGCAGAAGGCTGCCGCTGCGCAGGCTGCCGGCTTCTTTGCCGAAGAAATCGTGCCGGTGCGTATCGGTCACAAGAAGGGc                                                                                       <  8:4722/149‑1 (MQ=255)                                                           cgACAACGTGGCCGACGACTATCAGGTTTCGCGTGCTGATCAGGACGCTTTCGCCCTGCGCAGCCAGCAGAAGGCTGCCGCTGCGCAGGCTGCCGGCTTCTTTGCCGAAGAAATCGTGCCGGTGCGTATCGCTCACAAGAAGGGCGaaa                                                                                   <  1:306874/149‑1 (MQ=255)                                                                aCGTGGCCGACGACTATCAGGTTTCGCGTGCTGATCAGGACGCTTTCGCCCTGCGCAGCCAGCAGAAGGCTGCCGCTGCGCAGGCTGCCGGCTTCTTTGCCGAAGAAATCGTGCCGGTGCGTATCGCTCACAAGAAGGGCGAAatcatc                                                                              <  1:227968/149‑1 (MQ=255)                                                                              tATCAGGTTTCGCGTGCTGATCAGGACGCTTTCGCCCTGCGCAGCCAGCAGAAGGCTGCCGCTGCGCAGGCTGCCGGCTTCTTTGCCGAAGAAATCGTGCCGGTGCGTATCGCTCACAAGAAGGGCGAAATCATCGTCGAA‑CGTGACg                                                                >  7:234668/1‑148 (MQ=255)                                                                                tCAGGTTTCGCGTGCTGATCAGGACGCTTTCGCCCTGCGCAGCCAGCAGAAGGCTGCCGCTGCGCAGGCTGCCGGCTTCTTTGCCGAAGAAATCGTGCCGGTGCGTATCGCTCACAAGAAGGGCGAAATCATCGTCGAA‑CGTGACGaa                                                              >  1:184959/1‑148 (MQ=255)                                                                                tCAGGTTTCGCGTGCTGATCAGGACGCTTTCGCCCTGCGCAGCCAGCAGAAGGCTGCCGCTGCGCAGGCTGCCGGCTTCTTTGCCGAAGAAATCGTGCCGGTGCGTATCGCTCACAAGAAGGGCGAAATCATCGTCGAA‑CGTGACGaa                                                              >  2:207383/1‑148 (MQ=255)                                                                                  aGGTTTCGCGTGCTGATCAGGACGCTTTCGCCCTGCGCAGCCAGCAGAAGGCTGCCGCTGCGCAGGCTGCCGGCTTCTTTGCCGAAGAAATCGTGCCGGTGCGTATCGCTCACAAGAAGGGCGAAATCATCGTCGAA‑CGTGACGAacac                                                           <  2:184959/149‑1 (MQ=255)                                                                                    gTTTCGCGTGCTGATCAGGACGCTTTCGCCCTGCGCAGCCAGCAGAAGGCTGCCGCTGCGCAGGCTGCCGGCTTCttt                                                                                                                                 >  8:113512/1‑78 (MQ=255)                                                                                    gTTTCGCGTGCTGATCAGGACGCTTTCGCCCTGCGCAGCCAGCAGAAGGCTGCCGCTGCGCAGGCTGCCGGCTTCttt                                                                                                                                 <  7:113512/78‑1 (MQ=255)                                                                                         tttcttcggcaaagaagccggcagcctgcgcagcggccgccttctgctggctgcgcaggCTGCCGGCGTCTTTGCCGCAGAAATGGTGGCGGTGGGTATAGCTCACCAGAAGGGCGAAATCATCGTCGAA‑CGTGACGAACACCATCGcc                                                    >  4:95824‑M2/60‑149 (MQ=255)                                                                                           gagCTGATCAGGTCGCTTTCGCCCTGCGCAGCCAGCAGAAGGCTGCCGCTGCGCAGGCTGCCGGCTTCTTTGCCGAAGAAATCGTGCCGATGCGTATCGCTCACAAGAAGGGCGAAATCATCGTCGAA‑CGTGACGAACACCTGCGCCCg                                                  <  4:13246/147‑1 (MQ=255)                                                                                               tGATCAGGACGCTTTCGCCCTGCGCAGCCAGCAGAAGGCTGCCGCTGCGCAGGCTGCCGGCTTCTTTGCCGAAGAAATCGTGCCGGTGCGTATCGCTCACAAGAAGGGCGAAATCATCGTCGAA‑CGTGACGAACACCTGCGCCCGGaaa                                              >  2:159046/1‑149 (MQ=255)                                                                                                    aGGACGCTTTCGCCCTGCGCAGCCAGCAGAAGGCTGCCGCTGCGCAGGCTGCCGGCTTCTTTGCCGAAGAAATCGTGCCGGt                                                                                                             <  3:6173/82‑1 (MQ=255)                                                                                                    aGGACGCTTTCGCCCTGCGCAGCCAGCAGAAGGCTGCCGCTGCGCAGGCTGCCGGCTTCTTTGCCGAAGAAATCGTGCCGGt                                                                                                             >  4:6173/1‑82 (MQ=255)                                                                                                           tttCGCCCTGCGCAGCCAGCAGAAGGCTGCCGCTGCGCAGGCTGCCGGCTTCTTTGCCGAAGAAATCGTGCCGGTGCGTATCGCTCACAAGAAGGGCGAAATCATCGTCGAA‑CGTGACGAACACCTGCGCCCGGAAAc                                             <  7:173869/138‑1 (MQ=255)                                                                                                           tttCGCCCTGCGCAGCCAGCAGAAGGCTGCCGCTGCGCAGGCTGCCGGCTTCTTTGCCGAAGAAATCGTGCCGGTGCGTATCGCTCACAAGAAGGGCGAAATCATCGTCGAA‑CGTGACGAACACCTGCGCCCGGAAAc                                             >  8:173869/1‑138 (MQ=255)                                                                                                           tttCGCCCTGCGCAGCCAGCAGAAGGCTGCCGCTGCGCAGGCTGCCGGCTTCTTTGCCGAAGAAATCGTGCCGGTGCGTATCGCTCACAAGAAGGGCGAAATCATCGTCGAA‑CGTGACGAACACCTGCGCCCGGAAACCACGCTGGAgg                                  >  3:41999/1‑149 (MQ=255)                                                                                                            ttCGCCCTGCGCAGCCAGCAGAAGGCTGCCGCTGCGCAGGCTGCCGGCTTCTTTGCCGAAGAAATCGTGCCGGTGCGTATCGCTCACAAGAAGGGCGAAATCATCGTCGAA‑CGTGACGAACACCTGCGCCCGGAAACCACGCTGGAGgc                                 >  4:224864/1‑149 (MQ=255)                                                                                                             tCGCCCTGCGCAGCCAGCAGAAGGCTGCCGCTGCGCAGGCTGCCGGCTTCTTTGCCGAAGAAATCGTGCCGGTGCGTATCGCTCACAAGAAGGGCGAAATCATCGTCGAA‑CGTGACGAACACCTGCGCCCGGAAACCACGCTGGAgg                                  <  1:207383/147‑1 (MQ=255)                                                                                                              cagcctgcgcagcggcagcctgctgctggctgcgcaggCTGCCGGCTTCTTTGCCGAAGAAATCGTGCCGGTGCGTATCGCTCACAAGAAGGGCGAAATCATCGTCGAA‑CGTGACGAACACCTGCGCCCGGAAACCACGCTGGAGgcgc                               <  3:95824‑M2/111‑1 (MQ=255)                                                                                                               gCCCTGCGCAGCCAGCAGAAGGCTGCCGCTGCGCAGGCTGCCGGCTTCTTTGCCGAAGAAATCGTGCCGGTGCGTATCGCTCACAAGAAGGGCGAAATCATCGTCGAA‑CGTGACGAACACCTGCGCCCGGAAACCACGCTGGAGgcgc                               <  8:234668/148‑1 (MQ=255)                                                                                                                 CCTGCGCAGCCAGCAGAAGGCTGCCGCTGCGCAGGCTGCCGGCTTCTTTGCCGAAGAAATCGTGCCGGTGCGTATCGCTCACAAGAAGGGCGAAATCATCGTCGAA‑CGTGACGAACACCTGCGCCCGGAAACCGCGCTGGAGGCGCTGa                            <  6:148005‑M1/149‑1 (MQ=255)                                                                                                                 CCTGCGCAGCCAGCAGAAGGCTGCCGCTGCGCAGGCTGCCGGCTTCTTTGCCGAAGAAATCGTGCCGGTGCGTATCGCTCACAAGAAGGGCGAAATCATCGTCGAA‑CGTGACGAACACCTGCGCCCGGAAACCACGCTGGAGGCGCTGa                            >  3:224864‑M1/1‑149 (MQ=255)                                                                                                                   tgcgcagcggcagccttctgctggctgcgcaggCTGCCGGCTTCTTTGCCGAAGAAATCGTGCCGGTGCGTATCGCTCACAAGAAGGGCGaaa                                                                                   <  3:207595‑M2/60‑1 (MQ=255)                                                                                                                   tgcgcagcggcagccttctgctggctgcgcaggCTGCCGGCTTCTTTGCCGAAGAAATCGTGCCGGTGCGTATCGCTCACAAGAAGGGCGaaa                                                                                   >  4:207595‑M2/34‑93 (MQ=255)                                                                                                                   tgcgcagcggcagccttctgctggctgcgcaggCTGCCGGCTTCTTTGCCGAAGAAATCGTGCCGGTGCGTATCGCTCACAAGAAGGGCGAAATCATCGTCGAA‑CGTGACGAACACCTGCGCCCGGAAACCACGc                                        >  3:171464‑M2/34‑135 (MQ=255)                                                                                                                   tgcgcagcggcagccttctgctggctgcgcaggCTGCCGGCTTCTTTGCCGAAGAAATCGTGCCGGTGCGTATCGCTCACAAGAAGGGCGAAATCATCGTCGAA‑CGTGACGAACACCTGCGCCCGGAAACCACGc                                        <  4:171464‑M2/102‑1 (MQ=255)                                                                                                                          cggcagccttctgctggctgcgcaggCTGCCGGCTTCTTTGCCGAAGAAATCGTGCCGGTGCGTATCGCTCACAAGAAGGGCGAAATCATCGTCGAACCGTGACGAACACCTGCGCCCGGAAACCACGCTGGAGGCGCTGAc                           <  1:220678‑M2/116‑1 (MQ=255)                                                                                                                          cggcagccttctgctggctgcgcaggCTGCCGGCTTCTTTGCCGAAGAAATCGTGCCGGTGCGTATCGCTCACAAGAAGGGCGAAATCATCGTCGAA‑CGTGACGAACACCTGCGCCCGGAAACCACGCTGGAGGCGCTGAc                           >  2:220678‑M2/27‑141 (MQ=255)                                                                                                                            agcagAAGGCTGCCGCTGCGCAGGCTGCCGGCTTCTTTGCCGAAGAAATCGTGCCGGTGCGTATCGCTCACAAGAAGGGCGATATCATCGTCGAA‑CGTGACGAACACCTGCGCCCGGAAACCACGCTGGAGGCGCTGACCAAGCTCaaa                 >  5:308798/1‑149 (MQ=255)                                                                                                                             gcagAAGGCTGCCGCTGCGCAGGCTGCCGGCTTCTTTGCCGAAGAAATCGTGCCGGTGCGTATCGCTCACAAGAAGGGCGAAATCATCGTCGAA‑CGTGACGAACACCTGCGCCCGGAAACCACGCTGGAGGCGCTGACCAAGCTCAAAc                >  2:94117/1‑149 (MQ=255)                                                                                                                                  aGGCTGCCGCTGCGCAGGCTGCCGGCTTCTTTGCCGAAGAAATCGTGCCGGTGCGTATCGCTCACAAGAAGGGCGAAATCATCGTCGAA‑CGTGACGAACACCTGCGCCCGGAAACCACGCTGGAGGCGCTGACCAAGCTCAAACCGGt            <  1:159046/148‑1 (MQ=255)                                                                                                                                       gCCGCTGCGCAGGCTGCCGGCTTCTTTGCCGAAGAAATCGTGCCGGTGCGTATCGCTCACAAGAAGGGCGAAATCATCGTCGAA‑CGTGACGAACACCTGCGCCCGGAAACCACGCTGGAGGCGCTGACCAAGCTCAAACCGGTCAACgg      >  7:260842/1‑149 (MQ=255)                                                                                                                                           ctgcgcaggCTGCCGGCTTCTTTGCCGAAGAAATCGTGCCGGTGCGTATCGCTCACAAGAAGGGCGAAATCATCGTCGAA‑CGTGACGAACACCTGCGCCCGGAAACCACGCTGGAGGCGCTGACCAAGCTCAAACCGGTCAACGGCCCg  <  1:80999‑M2/140‑1 (MQ=255)                                                                                                                                                   gCTGCCGGCTTCTTTGCCGAAGAAATCGTGCCGGTGCCTATCGCTCACAAGAAGGGCGAAATCATCGTCGAA‑CGTGACGAACACCTGCGCCCGGAAACCACGCTGGAGGCGCTGACCAAg                       >  6:187899‑M2/2‑120 (MQ=255)                                                                                                                                                   gCTGCCGGCTTCTTTGCCGAAGAAATCGTGCCGGTGCCTATCGCTCACAAGAAGGGCGAAATCATCGTCGAA‑CGTGACGAACACCTGCGCCCGGAAACCACGCTGGAGGCGCTGACCAAg                       <  5:187899‑M2/119‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                             GTTTCATCAACCCGCTGATGAAGAGCCAGTACGGTGTGGATTCCATGCCGGAAACCGCCGACAACGTGGCCGACGACTATCAGGTTTCGCGTGCTGATCAGGACGCTTTCGCCCTGCGCAGCCAGCAGAAGGCTGCCGCTGCGCAGGCTGCCGGCTTCTTTGCCGAAGAAATCGTGCCGGTGCGTATCGCTCACAAGAAGGGCGAAATCATCGTCGAA‑CGTGACGAACACCTGCGCCCGGAAACCACGCTGGAGGCGCTGACCAAGCTCAAACCGGTCAACGGCCCG  >  NC_002947/1569632‑1569918

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ 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.