New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 5101273	49 (0.970)	3 (0.060)	3/248	NT	6.1%	coding (354/1560 nt)	phhR	sigma‑54 dependent transcriptional regulator
	?	NC_002947	= 5101301	45 (0.930)					coding (326/1560 nt)	phhR	sigma‑54 dependent transcriptional regulator

ACATCACCTTTGACTTTGATGCGCAAGCCGTTGATGCGCGACTTGTTGGCCCGCACCAACTCCGGAAGATCGAAGTCTTCTACGTAGCGCGCCAGCGGCATGCCCGGCA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTCGCTGGGCATCAGGCCCACACGCTTAAC  >  NC_002947/5101154‑5101422                                                                                                                                                      |                                                                                                                          acaTCACCTTTGACTTTGATGCGCAAGCCGTTGATGCGCGACTTGTTGGCCCGCACCAACTCCGGAAGATCGAAGTCTTCTACGTAGCGCGCCAGCGGCATGCCCGGCA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACg                                                                                                                          >  2:132771‑M2/1‑148 (MQ=255)    tCACCTTTGACTTTGATGCGCAAGCCGTTGATGCGCGACTTGTTGGCCCGCACCAACTCCGGAAGATCGAAGTCTTCTACGTAGCGCGCCAGCGGCATGCCCGGCA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACggtt                                                                                                                       >  1:213716‑M2/1‑145 (MQ=255)    tCACCTTTGACTTTGATGCGCAAGCCGTTGATGCGCGACTTGTTGGCCCGCACCAACTCCGGAAGATCGAAGTCTTCTACGTAGCGCGCCAGCGGCATGCCCGGCA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACggtt                                                                                                                       >  1:319757‑M2/1‑145 (MQ=255)    tCACCTTTGACTTTGATGCGCAAGCCGTTGATGCGCGACTTGTTGGCCCGCACCAACTCCGGAAGATCGAAGTCTTCTACGTAGCGCGCCAGCGGCATGCCCGGCA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACggtt                                                                                                                       <  6:91866‑M2/149‑5 (MQ=255)             actttgaTGCGCAAGCCGTTGATGCGCGACTTGTTGGCCCGCACCAACTCCGGAAGATCGAAGTCTTCTACGTAGCGCGCCAGCGGCATGCCCGGCA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAAc                                                                                                              >  7:208385/1‑149 (MQ=255)               tttgaTGCGCAAGCCGTTGATGCGCGACTTGTTGGCCCGCACCAACTCCGGAAGATCGAAGTCTTCTACGTAGCGCGGCAGCGGCATGCCCGGCA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGa                                                                                                            >  1:102251/1‑149 (MQ=255)                        cAAGCCGTTGATGCGCGACTTGTTGGCCCGCACCAACTCCGGAAGATCGAAGTCTTCTACGTAGCGCGCCAGCGGCATGCCCGGCA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTgccgc                                                                                                   <  7:119818/149‑1 (MQ=255)                         aaGCCGTTGATGCGCGACTTGTTGGCCCGCACCAACTCCGGAAGATCGAAGTCTTCTACGTAGCGCGCCAGCGGCATGCCCGGCA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTgccgcc                                                                                                  <  4:257660/149‑1 (MQ=255)                            ccGTTGATGCGCGACTTGTTGGCCCGCACCAACTCCGGAAGATCGAAGTCTTCTACGTAGCGCGCCAGCGGCATGCCCGGCA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCAt                                                                                               >  5:301047/1‑149 (MQ=255)                             cGTTGATGCGCGACTTGTTGGCCCGCACCAACTCCGGAAGATCGAAGTCTTCTACGTAGCGCGCCAGCGGCATGCCCGGCA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATg                                                                                              <  5:91866/149‑1 (MQ=255)                              gTTGATGCGCGACTTGTTGGCCCGCACCAACTCCGGAAGATCGAAGTCTTCTACGTAGCGCGCCAGCGGCATGCCCGGCA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGt                                                                                             >  5:254966/1‑149 (MQ=255)                                      gcgACTTGTTGGCCCGCACCAACTCCGGAAGATCGAAGTCTTCTACGTAGCGCGCCAGCGGCATGCCCGGCA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGAc                                                                                     <  8:208385/149‑1 (MQ=255)                                        gACTTGTTGGCCCGCACCAACTCCGGAAGATCGAAGTCTTCTACGTAGCGCGCCAGCGGCATGCCCGGCA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAg                                                                                   >  3:260053/1‑149 (MQ=255)                                             gttgGCCCGCACCAACTCCGGAAGATCGAAGTCTTCTACGTAGCGCGCCAGCGGCATGCCCGGCA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCAcc                                                                               <  2:49150/148‑1 (MQ=255)                                              ttgGCCCGCACCAACTACGGAAGATCGAAGTCTTCTACGTAGCGCGCCAGCGGCATGCCCGGCA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCTCCCATGtcgat                                                                                         <  6:202177/137‑1 (MQ=255)                                              ttgGCCCGCACCAACTACGGAAGATCGAAGTCTTCTACGTAGCGCGCCAGCGGCATGCCCGGCA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAAAGATGCTGCCGCCCATGtcgat                                                                                         >  5:202177/1‑137 (MQ=255)                                                  cccGCACCAACTCCGGAAGATCGAAGTCTTCTACGTAGCGCGCCAGCGGCATGCCCGGCAATGCACATAAACCCGAACGCCAAGCAACTGCGCGGATGCACGTTTGGCCGCAACGATGATGCCGCCCATGTCCATCGACAGCACCggg                                                                            >  1:92977/1‑148 (MQ=255)                                                  cccGCACCAACTCCGGAAGATCGAAGTCTTCTACGTAGCGCGCCAGCGGCATGCCCGGCA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAg                                                                         >  4:112439/1‑149 (MQ=255)                                                  cccGCACCAACTCCGGAAGATCGAAGTCTTCTACGTAGCGCGCCAGCGGCATGCCCGGCA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAg                                                                         >  1:127422/1‑149 (MQ=255)                                                      cACCAACTCCGGAAGATCGAAGTCTTCTACGTAGCGCGCCAGCGGCATGCCCGGCA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTc                                                                       >  4:50144/1‑147 (MQ=255)                                                               cGGAAGATCGAAGTCTTCTACGTAGCGCGCCAGCGGCATGCCCGGCA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGGAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCa                                                            >  1:262522/1‑149 (MQ=255)                                                               cGGAAGATCGAAGTCCTCTACGTAGCGCGCCAGCGGCATGCCCGGCA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGcccc                                                              <  4:260053/147‑1 (MQ=255)                                                                ggAAGATCGAAGTCTTCTACGTAGCGCGCCAGCGGCATGCCCGGCA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAg                                                           <  6:301047/149‑1 (MQ=255)                                                                    gATCGAAGTCTTCTACGTAGCGCGCCAGCGGCATCACCGGCA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGcgca                                                       >  5:184071/1‑146 (MQ=255)                                                                          aGTCTTCTACGTAGCGCGCCAGCGGCATGCCCGGCA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTc                                                 <  3:112439/149‑1 (MQ=255)                                                                              ttctACGTAGCGCGCCAGCGGCATGCCCGGCA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTgccgc                                                                                                   <  4:37977/95‑1 (MQ=255)                                                                              ttctACGTAGCGCGCCAGCGGCATGCCCGGCA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTgccgc                                                                                                   >  3:37977/1‑95 (MQ=255)                                                                              ttctACGTAGCGCGCCAGCGGCATGCCCGGCA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGtcgat                                                                                         <  4:219859/105‑1 (MQ=255)                                                                              ttctACGTAGCGCGCCAGCGGCATGCCCGGCA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGtcgat                                                                                         >  3:219859/1‑105 (MQ=255)                                                                              ttctACGTAGCGCGCCAGCGGCATGCCCGGCA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGtcga                                                                                          >  8:26822/1‑104 (MQ=255)                                                                              ttctACGTAGCGCGCCAGCGGCATGCCCGGCA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGtcga                                                                                          <  7:26822/104‑1 (MQ=255)                                                                              ttctACGTAGCGCGCCAGCGGCATGCCCGGCA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCt                                             >  5:295357/1‑149 (MQ=255)                                                                                 tACGTAGCGCGCCAGCGGCATGCCCGGCA‑‑CCTCATCAACCCGCAGCCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCa                                          >  1:228871/1‑149 (MQ=255)                                                                                   cGTAGCGCGCCAGCGGCATGCCCGGCA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCAt                                         <  2:92977/148‑1 (MQ=255)                                                                                    gTAGCGCGCCAGCGGCATGCCCGGCA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAg                                                           >  6:42853/1‑129 (MQ=255)                                                                                          cgcCAGCGGCATGCCCGGCA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCg                                   >  4:222061/1‑147 (MQ=255)                                                                                          cgcCAGCGGCATGCCCGGCA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCg                                   <  3:222061/147‑1 (MQ=255)                                                                                            ccAGCGGCATGCCCGGCA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGACCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTGAGCTCCTTGAGCCGGCGt                               >  5:47009/1‑149 (MQ=255)                                                                                              aGCGGCATGCCCGGCA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTc                             >  5:46281/1‑149 (MQ=255)                                                                                              aGCGGCATGCCCGGCA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTc                             <  3:50144/149‑1 (MQ=255)                                                                                                   cATGCCCGGCA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTCGCTgg                        <  2:262522/149‑1 (MQ=255)                                                                                                            cA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTCGCTGGGCATCAGGc               >  5:282480/1‑149 (MQ=255)                                                                                                                  tcatcaACCCGCACGCCAAGCAACTGCGCGGCTGCACggttgatgaggtgccgggcatgccgctggcgcgctacgtagaagacttcgatcttccggagttggtgcgggccaacaagtcgcgcatcaacggcttgcg                        >  6:111416‑M2/1‑37 (MQ=255)                                                                                                                  tcatcaACCCGCACGCCAAGCAACTGCGCGGCTGCACggttgatgaggtgccgggcatgccgctggcgcgctacgtagaagacttcgatcttccggagttggtgcgggccaacaagtcgcgcatcaacggcttgcg                        <  5:111416‑M2/136‑100 (MQ=255)                                                                                                                    atcaACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTCGCTGGGCATCAGGCCcaca          <  6:282480/148‑1 (MQ=255)                                                                                                                    atcaACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTCGCTGGGCATCAGGCCcac           <  6:254966/147‑1 (MQ=255)                                                                                                                     tcaACCCGCACGCCAAGCAACTGCCCGGCTGCACggttgatgaggtgccgggcatgccgctgccgcgctacgtagaagacttcgatcttccggagttggtgcgggccaacaagtcgcgcatcaacggcttgcgcatcaaagtcaaaggt        <  5:114573‑M2/149‑116 (MQ=255)                                                                                                                         cccGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTCGCTGGGCATCAGGCCCACACGCTTa    <  6:295357/149‑1 (MQ=255)                                                                                                                            gCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTCGCTGGGCATCa                  >  6:45573/1‑132 (MQ=255)                                                                                                                            gCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTCGCTGGGCATCa                  <  5:45573/132‑1 (MQ=255)                                                                                                                                         cTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTCGCTGGGCATCAGGCCCACACGCTTAAc  <  6:189436/135‑1 (MQ=255)                                                                                                                                         cTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTCGCTGGGCATCAGGCCCACACGCTTAAc  >  5:189436/1‑135 (MQ=255)                                                                                                                                                      |                                                                                                                          ACATCACCTTTGACTTTGATGCGCAAGCCGTTGATGCGCGACTTGTTGGCCCGCACCAACTCCGGAAGATCGAAGTCTTCTACGTAGCGCGCCAGCGGCATGCCCGGCA‑‑CCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTCGCTGGGCATCAGGCCCACACGCTTAAC  >  NC_002947/5101154‑5101422

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.