New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 1311719	49 (0.810)	4 (0.070)	4/240	NT	9.1%	intergenic (‑187/+91)	PP_1144/rapA	membrane protein/RNA polymerase‑associated protein RapA
	?	NC_002947	= 1311778	36 (0.660)					intergenic (‑246/+32)	PP_1144/rapA	membrane protein/RNA polymerase‑associated protein RapA

TGGCACAATGATTTCTACGATTTGGTTATAACTCCAATCGCAGTGAGGAATAAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGT‑GCCCGCTCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGCCTTCTCCAGCATTGCCAGGCCATCTTCGCGCCGCTTGCGCAGGGCGTCGATTTCGCTGTCACGCACACTTG  >  NC_002947/1311632‑1311925                                                                                                                                                   |                                                                                                                                                     tGGCACAATGATTTCTACGATTTGGTTATAACTCCAATCGCAGTGAGGAATAAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGTgc                                                                                                                                                    >  4:96581‑M2/1‑147 (MQ=255)   gCACAATGATTTCTACGATTTGGTTATAACTCCAATCGCAGTGAGGAATAAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGTgcc                                                                                                                                                   >  5:180002‑M2/1‑145 (MQ=255)       aaTGATTTCTACGATTTGGTTATAACTCCAATCGCAGTGAGGAATAAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAATCATGCACTGCGGTGGATTCCAACGGCTTTGGCGGTGTTAGCGGGCGTgcccgcga                                                                                                                                              <  3:105629‑M2/149‑9 (MQ=255)               cTACGATTTGGTTATAACTCCAATCGCAGTGAGGAATAAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATACCCTGCGGTGGATGCCACCGGCTTTTGCGGTGTTAGCGGGCGT‑GCCCCCACCCACaact                                                                                                                                     >  6:80824/1‑147 (MQ=38)                tACGATTTGGTTATAACTCCAATCGCAGTGAGGAATAAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCCTCCCCGGCGGGGGGTGGCACCCGCGTTGGCGGGGTTCGGGGGCGT‑GCCCGGTCCCCCAAggg                                                                                                                                    >  8:162300/1‑149 (MQ=255)                  cGATTTGGTTATAACTCCAATCGCAGTGAGGAATAAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGT‑GCCCGCTCCCACAAgggg                                                                                                                                   <  5:74607/148‑1 (MQ=255)                         gTTATAACTCCACTCGCAGTGTCGAATAAATTTGGGGCCCTCATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGT‑GCCCGCTCCCACAAGGGGCGCgggg                                                                                                                            <  8:162647/148‑1 (MQ=255)                             taACTCCAATCGCAGTGAGGAATAAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGGGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGT‑GCCCGCTCCCACAAGGGGCGCGGGGCCTgc                                                                                                                       <  7:259065/149‑1 (MQ=255)                               aCTCCAATCGCAGTGAGGAATAAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGT‑GCCCGCTCCCACAAGGGGCGCGGGGCCTgcgc                                                                                                                     <  5:329388/149‑1 (MQ=255)                                      tCGCAGTGAGGAATAAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGCAGCATCCACTGCGGTGGATGCCACCGGCTTTGGCGGTGTTAGCGGGCGT‑GCCCGCTCCCACAAGGGGCGCGGGGCCTGCGCGagccag                                                                                                              >  1:305442/1‑149 (MQ=255)                                        gCAGTGAGGAATAAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGT‑GCCCGCTCCCACAAGGGGCGCGGGGCCTGCGCTagccagc                                                                                                             <  2:22238/148‑1 (MQ=255)                                           gtcagcaaTAAATTTGGGCCCCTAATGCCTCCCTGTGGCAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGT‑GCCCGCTCCCACAAGGGGCGCggg                                                                                                                             <  1:784/123‑1 (MQ=25)                                                           gggCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGT‑GCCCGCTCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCt                                                                                          <  1:240435/148‑1 (MQ=255)                                                             gCCCTAATGCCTTCCGGGGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGGGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGT‑GCCCGCTCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTcc                                                                                       <  4:167320/149‑1 (MQ=255)                                                                 tAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCCGCTTTGCCGGTGTTCGCGGGCGT‑GCCCGCGCCCACAA‑GGGCGCGGGGCCTGCGCTAGCCAGCCCCCAGCACGCGAATGGCTTCCAGgcg                                                                                  >  2:280860/1‑149 (MQ=255)                                                                    tGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGT‑GCCCGCTCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGgc                                                                                   <  3:206382/146‑1 (MQ=255)                                                                    tGCCTTCCTGTGGGAGCGGGCGAGCCCCCGCAGCATACACAGGGGGGGATGGCACCCGCGTTGGCGGTGTTGGCGGGCGT‑GGCCGCGCCCCCAAGGGGCGCGGGGGCAGCGGAAGCCAGCCCCCCGCCCCCGCATGGCGTACAGgggcg                                                                                >  4:206382/1‑148 (MQ=255)                                                                           cTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGT‑GCCCGCTCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGggcggc                                                                         <  8:346146/149‑1 (MQ=255)                                                                              tgGGAGCGGGCTAGCCGGCGAAGCATCCACTGCGGTGTATGCCACCGGCTTTGCCGGTGTTCGCGGGCGT‑GCCCGCTCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGcc                                                                        <  6:31653/147‑1 (MQ=255)                                                                              tgGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGT‑GCCCGCTCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGcc                                                                        <  5:134352/147‑1 (MQ=255)                                                                              tgGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGT‑GCCCGCTCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGcc                                                                        <  2:58437/147‑1 (MQ=255)                                                                              tgGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTCCGCGGGCGT‑GCCCGCTCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGcc                                                                        <  8:6442/147‑1 (MQ=255)                                                                                   gCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGT‑GCCCGCTCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGTCGCAGGGCGGCCTTCTCCa                                                                 <  6:151756/149‑1 (MQ=255)                                                                                      ggCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCCGCTTTGCCGGTGTTCGCGGGCGT‑GCCCGCTCCCACAAGGGGCGCGGGGCCTGCGCTAGCCACCCACCACCACCCGAATGGCTTCCACGCGCAGGGCGGCCTTATCCAGc                                                               >  2:92807/1‑148 (MQ=38)                                                                                       gCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGTgcccgctcccacaggaaggcattagggccccaaatttattcctcactgcgattggagttataaccaaatcgtagaaatcattgtgcca                                                              <  1:118519‑M2/149‑89 (MQ=255)                                                                                       gCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGT‑GCCCGCTCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGCCTTCTCCAGCAt                                                             >  1:80978/1‑149 (MQ=255)                                                                                         gAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGT‑GCCCGCTCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGCCTTCTCCAGCATTg                                                           <  2:310596/149‑1 (MQ=255)                                                                                          gccccgcGAAGCATCCACTGCGGGGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGTgcccgctcccacaggaaggcattagggccccaaatttattcctcactgcgattggagttataaccaaatcgtagaaatcattgtgccatta                                                           >  2:125235‑M2/3‑58 (MQ=255)                                                                                          aGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGTgcccgctcccacaggaaggcattagggccccaaatttattcctcactgcgattggagttataaccaaatcgtagaaatcattgtgccat                                                             <  1:144738‑M2/147‑90 (MQ=255)                                                                                              cgcgAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGT‑GCCCGCTCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGCCTTCTCCAGCATTGCCAgg                                                      >  5:99104/1‑149 (MQ=255)                                                                                              cgcgAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGT‑GCCCGCTCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGCCTTCTCCAGCATTGCCAgg                                                      <  5:80824/149‑1 (MQ=255)                                                                                                cgAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGT‑GCCCGCTCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGCCTTCTCCAGCATTGCCAGGcc                                                    <  2:305442/149‑1 (MQ=255)                                                                                                      aTCCACCGCAGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGT‑GCCCCCTCCCACAAAGGGCGCCGGGCCTGCGCTAGCAAGCCACCAGCACGCGAATGGCTTACACGCGCAGGGCGGGCTTCTCCAGCATTTCCAGGGCATCTTc                                              >  7:129625/1‑149 (MQ=37)                                                                                                         cACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGT‑GCCCGCTCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGCCTTCTCCAGCATTGCCAGGCCATCTTcgcg                                           >  3:34424/1‑149 (MQ=255)                                                                                                                gTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGT‑GCCCGCTCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGCCTTCTCCAGCATTGCCAGGCCATCTTCGCGCCGCTTg                                    >  1:170797/1‑149 (MQ=255)                                                                                                                 tGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGTgcccgctcccacaggaaggcattagggccccaaatttattcctcactgcgattggagttataaccaaatcgtagaaatcattgtgccattagtcaggaaggcttaagtactcct                                    >  3:221450‑M2/1‑35 (MQ=255)                                                                                                                 tGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGT‑GCCCGCTCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGCCTTCTCCAGCATTGCCAGGCCATCTTCGCGCCGCTTgc                                   <  3:290394/149‑1 (MQ=255)                                                                                                                   gcgaacACCGGCTTTGCCGGTGTTCGCGGGCGT‑GCCCGCTCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGCCTTCTCCAGCATTGCCAGGCCATCTTCGCGCCGCTTgcg                                  >  7:224286/6‑148 (MQ=255)                                                                                                                        cACCGGCTTTGCCGGTGTTCGCGGGCGTGGCCCGCTCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGCCTTCTCCAGCATTGCCAGGCCATCTTCGCGCCGCTTGCGCAggg                             >  1:213220/1‑149 (MQ=255)                                                                                                                               tttGCCGGTGTTCGCGGGCGT‑GCCCGCTCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCCCCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGCCTTCTCCAGCATTGCCAGGCCATCTTCGCGCCGCTTGCGCAGGGCGTCGAtt                     >  3:251589/1‑149 (MQ=255)                                                                                                                                   ccGGTGTTCGCGGGCGT‑GCCCGCTCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGCCTTCTCCAGCATTGCCAGGCCATCTTCGCGCCGCTTGCGCAGGGCGTCGATTTCg                  <  4:105629/148‑1 (MQ=255)                                                                                                                                    cGGTGTTCGCGGGCGT‑GCCCGCTCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGCCTTCTCCAGCATTGCCAGGCCATCTTCGCGCCGCTTGCGCAGGGCGTCGATTTCGCt                >  3:310055/1‑149 (MQ=255)                                                                                                                                         ttCGCGGGCGT‑GCCCGCTCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGCCTTCTCCAGCATTGCCAGGCCATCTTCGCGCCGCTTGCGCAGGGCGTCGATTTCGCTGTCAc           >  8:118520/1‑149 (MQ=255)                                                                                                                                         ttCGCGGGCGT‑GCCCGCTCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGCCTTCTCCAGCATTGCCAGGCCATCTTCGCGCCGCTTGCGCAGGGCGTCGATTTCGCTGTCAc           <  2:170797/149‑1 (MQ=255)                                                                                                                                          tCGCGGGCGT‑GCCCGCGGCCCCAAGGGGGGCGGGGCCAGCCCTAGCCAGCCACCAGCACGCGCAAGGCTTGCAGGCCCAGGGCGGCCGTCGCCAGCATTGCCCGGCCATCTTCGCGCCGCTTGCGCAGGGGGTCGGTTTCGCTGTGAcc          >  2:363052/1‑148 (MQ=255)                                                                                                                                              gggCGT‑GCCCGCTCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCAAGGCGAAGGGCGGCCTTCTCCAGCATTGCCAGGCCATCTTCGCGCCGCTTGCGCAGGGCGTCGATTTCGCTGGCACGcaca      >  5:349959/1‑149 (MQ=255)                                                                                                                                                  gT‑GCCCGCTCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGCCTTCTCCAGCATTGCCAGGCCATCTTCGCGCCGCTTGCGCAGGGCGTCGATTTCGCTGTCACGCACACTTg  >  5:33955/1‑149 (MQ=255)                                                                                                                                                   |                                                                                                                                                     TGGCACAATGATTTCTACGATTTGGTTATAACTCCAATCGCAGTGAGGAATAAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGT‑GCCCGCTCCCACAAGGGGCGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGCCTTCTCCAGCATTGCCAGGCCATCTTCGCGCCGCTTGCGCAGGGCGTCGATTTCGCTGTCACGCACACTTG  >  NC_002947/1311632‑1311925

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.