New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 6020434	40 (0.740)	3 (0.060)	3/250	NT	7.4%	coding (215/1305 nt)	dadA‑II	D‑amino acid:quinone oxidoreductase
	?	NC_002947	= 6020469	37 (0.710)					coding (180/1305 nt)	dadA‑II	D‑amino acid:quinone oxidoreductase

CTCGTCGAGGCAGTCACGGCTGTACTCGGACAGGCGCACCATGCGCTCCTTGTTCACCGCGTAGCGGCTGGCAGTGCAGTTGCGCAGCATCTGTGCCATCCACAGG‑TACTGGTCGACATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTGACGCTCCAGCAGCCACTTGATGGCTTTGAGCGGTACGCCAGGCGCAGCCCAGGGCGAGGCATAGCCGGGCGAGATCTGGCCGGCGTTGGCAAAGCTGGTTTCCATGGCCACCGCCGGCTGGCGGTCGACCACCGTGACTTCGAAACC  >  NC_002947/6020286‑6020582                                                                                                                                                       |                                                                                                                                                     gtggtcgAGGCAGTCTCGGATGTACTCGGACATGCGGACCATGCGGTCGTTGTTGACGGGGTAGCGGCTGGCATTGGAGTTGCGCATGATTTGTGCCATGCACAGG‑TACTGGTTGTCATCGGCCGTGTGGTTGAT‑GGCCAGGGGGGCGt                                                                                                                                                      <  2:335657/146‑1 (MQ=255)    gtcgAGGCAGTCACGGCTGTACTCGGACAGGCGCACCATGCGCTCCTTGTTCACCGCGTAGCGGCTGGCAGTGCAGTTGCGCAGCATCTGTGCCATCCACAGGACACTGGTCGACATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTGa                                                                                                                                                    <  1:244866/149‑1 (MQ=255)    gtcgAGGCAGTCACGGCTGTACTCGGACAGGCGCACCATGCGCTCCTTGTTCACCGCGTAGCGGCTGGCAGTGCAGTTGCGCAGCATCTGTGCCATCCACAGG‑TACTGGTCGACATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTGa                                                                                                                                                    <  7:224411/148‑1 (MQ=255)        aGGCAGTCACGGCTGTACTCGGACAGGCGCACCATGCGCTCCTTGTTCACCGCGTAGCGGCTGGCAGTGCAGTTGCGCAGCATCTGTGCCATCCACAGG‑TACTGGTCGACATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTGACGCTc                                                                                                                                               >  7:156265/1‑149 (MQ=255)              tCACGGCTGTACTCGGACAGGCGCACCATGCGCTCCTTGTTCACCGCGTAGCGGCTGGCAGTGCAGTTGCGCAGCATCTGTGCCATCCACAGG‑TACTGGTCGACATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTGAc                                                                                                                                                   <  5:63976/139‑1 (MQ=255)              tCACGGCTGTACTCGGACAGGCGCACCATGCGCTCCTTGTTCACCGCGTAGCGGCTGGCAGTGCAGTTGCGCAGCATCTGTGCCATCCACAGG‑TACTGGTCGACATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTGAc                                                                                                                                                   >  6:63976/1‑139 (MQ=255)              tCACGGCTGTACTCGGACAGGCGCACCATGCGCTCCTTGTTCACCGCGTAGCGGCTGGCAGTGCAGTTGCGCAGCATCTGTGCCATCCACAGG‑TACTGGTCGACATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTGACGCTCcagcag                                                                                                                                         >  1:70631/1‑149 (MQ=255)                    cTGTACTCGGACAGGCGCACCATGCGCTCCTTGTTCACCGCGTAGCGGCTGGCAGTGCAGTTGCGCAGCATCTGTGCCATCCACAGG‑TACTGGTCGACATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTGACGCTCCAGCAGCCACtt                                                                                                                                   >  2:47472/1‑149 (MQ=255)                       tACTCGGACAGGCGCACCATGCGCTCCTTGTTCACCGCGTAGCGGCTGGCAGTGCAGTTGCGCAGCATCTGTGCCATCCACAGG‑TACTGGTCGACATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTGACGCTCCAGCAGCCACTTGAt                                                                                                                                <  3:204478/149‑1 (MQ=255)                          tCGGACAGGCGCACCATGCGCTCCTTGTTCACCGCGTAGCGGCTGGCAGTGCAGTTGCGCAGCATCTGTGCCATCCACAGG‑TACTGGTCGACATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTGACGCTCCAGCAGCCACTTGATGGc                                                                                                                             >  3:154484/1‑149 (MQ=255)                              aCAGGCGCACCATGCGCTCCTTGTTCACCGCGTAGCGGCTGGCAGTGCAGTTGCGCAGCATCTGTGCCATCCACAGG‑TACTGGTCGACATCGCCCGTGAGCTTGAT‑GGCCA‑GGGGGCGTGACGCTCCAGCAGCCACTTGATGGCTTTGa                                                                                                                        <  3:273142/149‑1 (MQ=255)                               cAGGCGCACCATGCGCTCCTTGTTCACCGCTTAGCGGCTGGCAGTGCAGTTGCGCAGCATCTGTGCCATCCACAGG‑TACTGGTCGAAATCGCCCGTTATCTTGAT‑GGCCAGGGGGGCGTGACGCTCCAGCAGCCACTTGATGGCTTTGa                                                                                                                        <  3:45550/149‑1 (MQ=255)                               cAGGCGCACCATGCGCTCCTTGTTCACCGCGTAGCGGCTGGCAGTGCAGTTGCGCAGCATCTGTGCCATCCACAGG‑TACTGGTCGACATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTGACGCTCCAGCAGCCACTTGATGGCTTTGa                                                                                                                        <  1:270198/149‑1 (MQ=255)                                  gcgcACCATGCGCTCCTTGTTCACCGCGTAGCGGCTGGCAGTGCAGTTGCGCAGCATCTGTGCCATCCACAGG‑TACTGGTCGACATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTGACGCTCCAGCAGCCACTTGATGGCTTTGAGCg                                                                                                                     >  7:18880/1‑149 (MQ=255)                                    gcACCATGCGCTCCTTGTTCACCGCGTAGCGGCTGGCAGTGCAGTTGCGCAGCATCTGTGCCATCCACAGG‑TACTGGTCGACATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTGACGCTCCAGCAGCCACTTGATGGCTTTGAGCgg                                                                                                                    >  1:186889/1‑148 (MQ=255)                                      aCCATGCGCTCCTTGTTCACCGCGTAGCGGCTGGCAGTGCAGTTGCGCAGCATCTGTGCCATCCACAGG‑TACTGGTCGACATCGCCCGTGAGCTTGATCGGCCAGGGGGGCGTGACGCTCCAGCAGCCACTTGATGGCTTTGAGCGGTa                                                                                                                  >  1:85962‑M2/1‑148 (MQ=255)                                      aCCATGCGCTCCTTGTTCACCGCGTAGCGGCTGGCAGTGCAGTTGCGCAGCATCTGTGCCATCCACAGG‑TACTGGTCGACATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTaccgctcaaagccatcaagtggctgctggagcgtcac                                                                                                                 <  7:198037‑M1/149‑38 (MQ=255)                                            cgcTCCTTGTTCACCGCGTAGCGGCTGGCAGTGCAGTTGCGCAGCATCTGTGCCATCCACAGG‑TACTGGTCGACATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTGACGCTCCAGCAGCCACTTGATGGCTTTGAGCGGTACGCCAg                                                                                                            <  2:70631/148‑1 (MQ=255)                                               tCCTTGTTCACCGCGTAGCGGCTGGCAGTGCAGTTGCGCAGCATCTGTGCCATCCACAGG‑TACTGGTCGACATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTGACGCTCCAGCAGCCACTTGATGGCTTTGAGCGGTACGCCAgg                                                                                                           <  5:251164/146‑1 (MQ=255)                                               tCCTTGTTCACCGCGTAGCGGCTGGCAGTGCAGTTGCGCAGCATCTGTGCCATCCACAGG‑TACTGGTCGACATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTGACGCTCCAGCAGCCACTTGATGGCTTTGAGCGGTACGCCAgg                                                                                                           >  6:251164/1‑146 (MQ=255)                                                 cTTGTTCACCGCGTAGCGGCTGGCAGTGCAGTTGCGCAGCATCTGTGCCATCCACAGG‑TACTGGTCGACATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTGACGCTCCAGCAGCCACTTGATGGCTTTGAGCGGTACGCCAGgcgc                                                                                                        <  5:137031/147‑1 (MQ=255)                                                 cTTGTTCACCGCGTAGCGGCTGGCAGTGCAGTTGCGCAGCATCTGTGCCATCCACAGG‑TACTGGTCGACATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTGACGCTCCAGCAGCCACTTGATGGCTTTGAGCGGTACGCCAGGCGCAg                                                                                                      >  7:127601/1‑149 (MQ=255)                                                    gTTCACCGCGTAGCGGCTGGCAGTGCAGTTGCGCAGCATCTGTGCCATCCACAGG‑TACTGGTCGACATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTGACGCTCCAGCAGCCACTTGATGGCTTTGAGCGGTACGCCAGGCGCAGcc                                                                                                    >  2:42826/1‑148 (MQ=255)                                                         ccccgTAGCGGCTGGCAGTGCAGTTGCGCAGCATCTGTGCCATCCACAGG‑TACTGGTCGACATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTGACGCTCCAGCAGCCACTTGATTGCTTTGAGCGGTACGCCAGGCGCAGCCCAGGGc                                                                                              <  2:83166/146‑1 (MQ=255)                                                          cgcgTAGCGGCTGGCAGTGCAGTTGCGCAGCATCTGTGCCATCCACAGG‑TACTGGTCGACATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTGACGCTCCAGCAGCCACTTGATGGCTTTGAGCGGTACGCCAGGCGCAGCCCAGGGc                                                                                              >  8:102167/1‑148 (MQ=255)                                                                     tGGCAGTGCAGTTGCGCAGCATCTGTGCCATCCACAGG‑TACTGGTCGACATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTGACGCTCCAGCAGCCACTTGATGGCTTTGAGCGGTACGCCAGGCGCAGCCCAGGGCGAGGCATAGCCg                                                                                  >  4:298915/1‑149 (MQ=255)                                                                        cagtgcagtTGCGCAGCATCTGTGCCATCCACAGG‑TACTGGTCGACATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTGACGCTCCAGCAGCCACTTGATGGCTTTGAGCGGTACGCCAGGCGCAGCCCAGGGCGAGGCATAGCCGGGc                                                                               >  3:298867/1‑149 (MQ=255)                                                                        cagtgcagtTGCGCAGCATCTGTGCCATCCACAGG‑TACTGGTCGACATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTGACGCTCCAGCAGCCACTTGATGGCTTTGAGCGGTACGCCAGGCGCAGCCCAGGGCGAGGCATAGCCGGGc                                                                               <  7:298372/149‑1 (MQ=255)                                                                          gtgcagtTGCGCAGCATCTGTGCCATCCACAGG‑TACTGGTCGACATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTGACGCTCCAGCAGCCACTTGATGGCTTTGAGCGGTACGCCAGGCGCAGCCCAGGGCGAGGCATAGCCGGGc                                                                               >  8:203432/1‑147 (MQ=255)                                                                           tgcagtTGCGCAGCATCTGTGCCATCCACAGG‑TACTGGTCGACATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTaccgctcaaagccatcaagtggctgctggagcgtcacgccc                                                                                                             >  6:229308‑M1/1‑75 (MQ=255)                                                                           tgcagtTGCGCAGCATCTGTGCCATCCACAGG‑TACTGGTCGACATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTaccgctcaaagccatcaagtggctgctggagcgtcacgccc                                                                                                             <  5:229308‑M1/116‑42 (MQ=255)                                                                                    gcagcaTCTGTGCCATCCACAGG‑TACTGGTCGACATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTGACGCTCCAGCAGCCACTTGATGGCTTTGAGCGGTACGCCAGGCGCAGCCCAGGGCGAg                                                                                           >  8:7346/1‑125 (MQ=255)                                                                                    gcagcaTCTGTGCCATCCACAGG‑TACTGGTCGACATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTGACGCTCCAGCAGCCACTTGATGGCTTTGAGCGGTACGCCAGGCGCAGCCCAGGGCGAg                                                                                           <  7:7346/125‑1 (MQ=255)                                                                                         aTCTGTGCCATCCACAGG‑TACTGGTCGACATCGCACGTGAGCTTGAT‑GGCCAGGGGGGCGTGACGCTCCAGCAGCCACTTGATGGCTTTGAGCGGTACGCCAGGCGCAGCCCAGGGCGAGGCATAGCC‑GGCCAGATCTCGcccggcta                                                              <  3:120983/148‑7 (MQ=255)                                                                                              tgCCATCCACAGG‑TACTGGTCGACATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTGACGCTCCAGCAGCCACTTGATGGCTTTGAGCGGTACGCCAGGCGCAGCCCAGGGCGAGGCATATCCGGGCGAGATCTGGCCGGCGTTg                                                             <  1:42826/145‑1 (MQ=255)                                                                                              tgCCATCCACAGG‑TACTGGTCGACATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTGACGCTCCAGCAGCCACTTGATGGCTTTGAGCGGTACGCCAGGCGCAGCCCAGGGCGAGGCATAGCCGGGCGAGATCTGGCCGGCGTTgg                                                            <  1:284925/146‑1 (MQ=255)                                                                                              tgCCATCCACAGG‑TACTGGTCGACATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTGACGCTCCAGCAGCCACTTGATGGCTTTGAGCGGTACGCCAGGCGCAGCCCAGGGCGAGGCATAGCCGGGCGAGATCTGGCCGGCGTTg                                                             <  8:18880/145‑1 (MQ=255)                                                                                                         gg‑TACTGGTCGACATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTGACGCTCCAGCAGCCACTTGATGGCTTTGAGCGGTACGCCAGGCGCAGCCCAGGGCGAGGCATAGCCGGGCGAGATCTGGCCGGCGTTGGCAAAGCTGGTTTcc                                              <  3:320143/149‑1 (MQ=255)                                                                                                            tACTGGTCGACATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTGACGCTCCAGCAGCCACTTGATGGCTTTGAGCGGTACGCCAGGCGCAGCCCAGGGCGAGGCATAGCCGGGCGAGATCTGGCCGGCGTTGGCAAAGCTGGTTTCCAt                                            <  8:148228/149‑1 (MQ=255)                                                                                                              cTGGTCGACATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTGACGCTCCAGCAGCCACTTGATGGCTTTGAGCGGTACGCCAGGCGCAGCCCAGGGCGAGGCATAGCCGGGCGATATCTGGCCGGCGTTGGCAAAGCTGGTTTCCATg                                           <  1:47472/148‑1 (MQ=255)                                                                                                                 gTCGACATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTGACGCTCCAGCAGCCACTTGATGGCTTTGAGCGGTACGCCAGGCGCAGCCCAGGGCGAGGCATAGCCGGGCGAGATCTGGCCGGCGTTGGCAAAGCTGGTTTCCATGGcc                                        <  7:203432/148‑1 (MQ=255)                                                                                                                 gTCGACATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTGACGCTCCAGCAGCCACTTGATGGCTTTGAGCGGTACGCCAGGCGCAGCCCAGGGCGAGGCATAGCCGGGCGAGATCTGGCCGGCGTTGGCAAAGCTGGTTTCCATGGc                                         <  1:294803/147‑1 (MQ=255)                                                                                                                  tCGACATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTGACGCTCCAGCAGCCACTTGATGGCTTTGAGCGGTACGCCAGGCGCAGCCCAGGGCGAGGCATAGCCGGGCGAGATCTGGCCGGCGTTGGCAAAGCTGGTTTCCATGGCCAc                                      >  4:257454/1‑149 (MQ=255)                                                                                                                  tCGACATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTGACGCTCCAGCAGCCACTTGATGGCTTTGAGCGGTACGCCAGGCGCAGCCCAGGGCGAGGCATAGCCGGGCGAGATCTGGCCGGCGTTGGCAAAGCTGGTTTCCATGGCCAc                                      >  6:231864/1‑149 (MQ=255)                                                                                                                      cATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTGACGCTCCAGCAGCCACTTGATGGCTTTGAGCGGTACGCGAGGCGCAGCCCAGGGCGAGGCATAGCCGGGCGAGATCTGGCCGGCGTTGGCAAAGCTGGTTTCCATGGCCAccgcc                                  <  2:186889/149‑1 (MQ=255)                                                                                                                                   cTTGAT‑GGCCAGGGGGGCGTGACGCTCCAGCAGCCACTTGATGGCTTTGAGCGGTACGCCAGGCGCAGCCCAGGGCGAGGCATAGCCGGGCGAGATCTGGCCGGCGTTGGCAAAGCTGGTTTCCATGGCCACCGCCGGCTGGCGGTCGa                     <  7:102167/149‑1 (MQ=255)                                                                                                                                           gCCAGGGGGGCGTGACGCTCCAGCAGCCACTTGATGGCTTTGAGCGGTACGCCAGGCGCAGCCCAGGGCGAGGCATAGCCGGGCGAGATCTGGCCGGCGTTGGCAAAGATGGTTTCCATGGACAACGACGGCTGGCGGTCTACCACCGt              >  8:168690/1‑149 (MQ=255)                                                                                                                                            ccAGGGGGGCGTGACGCTCCAGCAGCCACTTGATGGCTTTGAGCGGTACGCCAGGCGCAGCCCAGGGCGAGGCATAGCCGGGCGAGATCTGGCCGGCGTTGGCAAAGCTGGTTTCCATGGCCACCGCCGGCTGGCGGTCGACCACCGt              >  5:265364/1‑148 (MQ=255)                                                                                                                                                gggggCGTGACGCTCCAGCAGCCACTTGATGGCTTTGAGCGGTACGCCAGGCGCAGCCCAGGGCGAGGCATAGCCGGGCGAGATCTGGCCGGCGTTGGCAAAGCTGGTTTCCATGGCCACCGCCGGCTGGCGGTCGCCCACCGTGACtt         >  8:155304/1‑149 (MQ=255)                                                                                                                                                  gggCGTGACGCTCCAGCAGCCACTTGATGGCTTTGAGCGGTacgcccccctggccatcaagctcacgggcgatgtcgaccagtacctgtggatggcacagatgctgcgcaactgca                                        <  5:229308‑M2/116‑76 (MQ=255)                                                                                                                                                  gggCGTGACGCTCCAGCAGCCACTTGATGGCTTTGAGCGGTacgcccccctggccatcaagctcacgggcgatgtcgaccagtacctgtggatggcacagatgctgcgcaactgca                                        >  6:229308‑M2/1‑41 (MQ=255)                                                                                                                                                      gTGACGCTCCAGCAGCCACTTGATGGCTTTGAGCGGTacgcccccctggccatcaagctcacgggcgatgtcgaccagtacctgtggatggcacagatgctgcgcaactgcactgccagccgctacgcggtgaacaaggagcgcatggt   <  7:198037‑M2/149‑113 (MQ=255)                                                                                                                                                       taccgctcaaagccatcaagtggctgctggagcgtcacgcccccctggccgatcaagctcacgggcgatgtcgaccagtacctgtggatggcacagatgctgcgcaactgcactgccagccgctacgcggtgaacaaggagcgcatggt  >  1:85962‑M1/1‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                                     CTCGTCGAGGCAGTCACGGCTGTACTCGGACAGGCGCACCATGCGCTCCTTGTTCACCGCGTAGCGGCTGGCAGTGCAGTTGCGCAGCATCTGTGCCATCCACAGG‑TACTGGTCGACATCGCCCGTGAGCTTGAT‑GGCCAGGGGGGCGTGACGCTCCAGCAGCCACTTGATGGCTTTGAGCGGTACGCCAGGCGCAGCCCAGGGCGAGGCATAGCCGGGCGAGATCTGGCCGGCGTTGGCAAAGCTGGTTTCCATGGCCACCGCCGGCTGGCGGTCGACCACCGTGACTTCGAAACC  >  NC_002947/6020286‑6020582

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.