New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_bme_pgi	19797 =	NA (NA)	53 (1.180)	39/288	0.2	94.7%	intergenic (+177/+14)	nhaR/insB1	transcriptional activator of nhaA/IS1 transposase B
	?	NC_000913_3_bme_pgi	61481 =	3 (0.070)					coding (1784/2907 nt)	rapA	RNA polymerase remodeling/recycling factor ATPase; RNA polymerase‑associated, ATP‑dependent RNA translocase

GAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACc‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_bme_pgi/19944‑19797 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CCAATACGCTGCTCCAGTAGATCCGGGTTGAATGGCAGGTCAAACATCACCATGTGGCTGGCGAACTGGAAGTTACGTCCTTCAGAACCGATTTCTGAGCACAGCAGTACCTGTGCGCCGGTGTCTTCTTCGGCAAACCAGGCGGCA  >  NC_000913_3_bme_pgi/61481‑61627                                                                                                                                                                                                                                                                                                         GAATTGAGCGGCATAACCTGAATCTGAGGCAGCACGTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCGCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTGGGAGTCATTACC                                                                                                                                                    <  2:432156/149‑1     TGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACTGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCAAT                                                                                                                                                <  2:410578/149‑1                 CCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGATACGCTGCTCCAG                                                                                                                                    >  1:335792/1‑149                 CCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTATCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCACTACGCTGCTCCAG                                                                                                                                    >  1:115908/1‑149                  CTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCAATACGCTGCTCCAGT                                                                                                                                   >  2:69104/1‑149                   TGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCAATACGCTGCTCCAGTA                                                                                                                                  >  1:46517/1‑149                          GAGGCAGTACGTGGGACGGGTGGTACGGAAGTCGTTGTCGTACTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAATATATCACACTATCAATAAGTTGGAGTCATTACCCAATACGCTGCTCCAGTAGATCCGG                                                                                                                           <  2:244739/149‑1                             GCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCAATACGCTGCTCCAGTAGATCCGGGTT                                                                                                                        >  2:134380/1‑149                             GCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCAATACGCTGCTCCAGTAGATCCGGGTT                                                                                                                        >  1:597516/1‑149                                gaaaCTGGCACGGCGGGGACGGAAGTCGCTGTCGTTTTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCAAGACGCTGCTCCAGTAGAGCCGGGTTGAA                                                                                                                     <  2:356579/145‑1                                  ACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCAATACGCTGCTCCAGTAGATCCGGGTTGAATG                                                                                                                   <  1:421113/149‑1                                       gcagcGCTGGGACGGAAGTCGCTTGCGTGCTCAAAATCGGTGGAGCTGAATGACAAAGTCATCGGGCATTATCTGCACATAAAACCCTATCAATAAGTTGGAGTCATTACCCAATACGCTGCTCCAGTAGATCCGGGTTGAATGGCAGG                                                                                                              <  2:466862/144‑1                                       GCACGGCTGGGACGGAAGTCGCTGTGGTTCTCAAAAGCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCAATACGCTGCTCCAGTAGATCCGGGTTGAATGGCAGG                                                                                                              <  2:150441/149‑1                                       GCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAACTCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCAATACGCTGCTCCAGTAGATCCGGGTTGAA                                                                                                                     >  1:320588/1‑142                                       GCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCAATACGCTGCTCCAGTAGATCCGGGTTGAA                                                                                                                     >  1:721469/1‑142                                       GCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCAATACGCTGCTCCAGTAGATCCGGGTTGAA                                                                                                                     <  2:721469/142‑1                                       GCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCAATACGCTGCTCCAGTAGATCCGGGTTGAA                                                                                                                     <  2:320588/142‑1                                                    GGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCAATACGCTGCTCCAGTAGATCCGGGTTGAATGGCAGGTCAAACATCACCA                                                                                                 <  1:69104/149‑1                                                            CTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCAATACGCTGCTCCAGTAGATCCGGGTTGAATGGCAGGACAAACATCACCATGTGGCTG                                                                                         >  2:378995/1‑149                                                                 GTTCCCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCAATACGCTGCTCCAGTCGCTCCGGTGTGAATGGCAGGTCAAACATCACCATGTGGCTGGCGAA                                                                                    <  1:593399/149‑1                                                                       AAAATCGTTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCAATACGCTGCTCCAGTAGATCCGGGTTGAATGGCAGGTCAAACATCACCATGTGGCTGGCGAACTGGAA                                                                              <  1:413955/149‑1                                                                       AAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCAATACGCTGCTCCAGTAGATCCGGGTTGAATGGCAGGTCAAACATCACCATGTGGCTGGCGAACTGGAA                                                                              <  1:138328/149‑1                                                                       AAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCAATACGCTGCTCCAGTAGATCCGGGTTGAATGGCAGGTCAAACATCACCATGTGGCTGGCGAACTGGAA                                                                              <  2:55244/149‑1                                                                       AAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCAATACGCTGCTCCAGTAGATCCGGGTTGAATGGCAGGTCAAACATCACCATGTGGCTGGCGAACTGGAA                                                                              <  1:37912/149‑1                                                                       AAAAGCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCAATACGCTGCTCCAGTAGATCCGGGTTGAATGGCAGGTCAAACATCACCATGTGGCTGGCGAACTGGAA                                                                              <  1:659777/149‑1                                                                        AAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCAATACGCTGCTCCAGTAGATCCGGGTTGAATGGCAGGTCAAACATCACCATGTGGCTGGCGAACTGGAAG                                                                             >  2:43189/1‑149                                                                           gCGGTGGAGCTGGATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCTAATACGCTGCTCCAGTAGATCCGGGTTGAATGGCAGGTCAAACATCACCATGTGGCTGGCGAACTGGAAGTTA                                                                          <  1:392672/148‑1                                                                            CGGGGGAGCTGCATGACAAAGCCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCAATACGCTGCTCCAGTAGATCCGGGTTGAATGGCAGGTCAAACATCACCATGTGGCTGGCGAACTGGAAGTTAC                                                                         <  1:331083/149‑1                                                                              GTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAAGAAGTTGGAGTCATTACCCAAGACGCTGCTCCAGTAGATCCGGGTTGAATGGCAGGTCACAGGTTATCAGGTGGCTGGCGAACTGGAAGTTACGT                                                                       <  1:191831/149‑1                                                                                   gcgGCATGACAAAGTCATCGGGCATTATCTGAACATAACACACTATCAATAAGTTGGAGTCATTACCCAATACGCTGCTCCAGTAGATCCGGGTTGAATGGCAGGTCAAACATCACCATGTGGCTGGCGAACTGGAAGTTACGTCCTTC                                                                  <  2:75128/146‑1                                                                                   GCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCAATACGCTGCTCCAGTAGATCCGGGTTGAATGGCAGGT                                                                                                             <  1:679863/106‑1                                                                                   GCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCAATACGCTGCTCCAGTAGATCCGGGTTGAATGGCAGGT                                                                                                             >  2:679863/1‑106                                                                                    CTGCATGACAAAGTCATCGGGCATTATCTGAACATAGAACACTATCAATAAGTTGGAGTCATTACCCAATACGCTGCTCCAGTAGATCCGGGTTGAATGGCAGGTCAAACATCACCATGTGGCTGGCGAACTGGAAGTTACGTCCTTCA                                                                 <  1:647589/149‑1                                                                                       caaGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGCGTCATTACCCAATACGCTGCTCCAGTAGATCCGGGTTGAATGGCAGGTCAAACATCACCATGTGGCTGGCGAACTGGAAGTTACGTCCTTCAGAA                                                              <  1:667922/146‑1                                                                                        ataACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGAGGGAGTCATTCCCCAATACGCTGCTCCAGTAGATCCCGGGTGAATGGCAGGTCAAACATCCCCATGTGGCTGACGAACGGGACGTTGCGTCCTTCAGAAC                                                             >  2:211664/4‑149                                                                                         TGACAATGTTATCGTGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCAATACGCTGCGCCAGTAGATCCGGGTTGAATGGCAGGTCAAACATCACCATGTGGCTGGCGAACTGGAAGTTACGTCCTTCAGAACC                                                            <  2:745446/149‑1                                                                                            CAAAGTCATCGGGCATTATCTGAACATAAAACACTGTCCAGAAGTTGGATTCATTAGCCAATACGCTGCTCCAGTAGATCCGGGTTGAATGGCAGGTCAAACATCACCATGTGGCTGGCGAACTGGAAGTTACGTCCTTCAGAACCGAT                                                         <  1:766835/149‑1                                                                                            CAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCAATACGCTGCTCCAGTAGATCCGGGTTGAATGGCAGGTCAAACATCACCATGTGGCTGGCGAACTGGAAGTTACGTCCTTCAGAACCGAT                                                         >  2:770250/1‑149                                                                                            CAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCAATACGCTGCTCCAGTAGATCCGGGTTGAATGGCAGGTCAAACATCACCATATGGCTGGCGAACTGGAAGTTACGTCCTTCAGAACCGAT                                                         >  2:378625/1‑149                                                                                                      GGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCAATACGCTGCTCCAGTAGATCCGGGTTGAATGGCAGGTCAACCATCACCAGGTGGCTGGCGAACTGTAAGTTACGTCCTGCAGAACCAATTTCTGATCAC                                               >  1:324223/1‑149                                                                                                          ATTATCTGACCATAAGACACTATCAATAAGTTGGAGTCATTACCCAATACGCTGCTCCAGTAGATCCGGGTTGAATGGCAGGTCAAACATCACCATGTGGCTGGCGAACTGGAAGTTACGTCCTTCAGAACCGATTTCTGAGCACAGCA                                           >  2:495332/1‑149                                                                                                             ATCTGAACATAAAACACTATCAATAAGTTGGATTCATTACCCAATACGCTGCTCCAGTAGATCCGGGTTGAATGGCAGGTCAAACACCACCATGTGGCTGGCGAACTGGAAGTTACGTCCTTCAGAACCGATTGCTGAGCACAGCAGTA                                        <  2:38955/149‑1                                                                                                              TCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCAATACGCTGCTCCAGTAGATCCGGGTTGAATGGCAGGTCAAACATCACCATGTGGCTGGCGAACTGGAAGTTACGTCCTTCAGAACCGATTTCTGAGCACAGCAGTAC                                       <  1:375011/149‑1                                                                                                                  AACATAAAACACTATCAATAAGTTGGAGTCATTACCCAATACGCTGCTCCAGTAGATCCGGGTTGAATGGCAGGTCAAACATCACCATGTGGCTGGCGAACTGGAA                                                                              >  2:347091/1‑106                                                                                                                  AACATAAAACACTATCAATAAGTTGGAGTCATTACCCAATACGCTGCTCCAGTAGATCCGGGTTGAATGGCAGGTCAAACATCACCATGTGGCTGGCGAACTGGAA                                                                              <  1:347091/106‑1                                                                                                                      TAAAACACTATCAATAAGGTGGAGTCATTACCCAATACGCTGCTCCAGTAGATCCGGGTTGAATGGCAGGTCAAACATCACCATGTGGCTGGCGAACTGGAAGTTACGTCCTTCAGAACCGATTTCTGAGCACAGCAGTACCTGTGCGC                               <  2:509218/149‑1                                                                                                                          tCACTATCAATAAGTTGGAGTCATTACCCAATACGCTGCTCCAGTAGATCCGGGTTGAATGGCAGGTCAAACATCACCATGTGGCTGGCGAACTGGAAGTTACGTCCTTCAGAACCGATTTCTGAGCACAGCAGTACCTGTGCGCCGGT                           <  1:345634/148‑1                                                                                                                               ATCAATAAGTTAGAGTCATTACCCAATACGCTGCTCCAGTAGATCCGGGTTGAATGGCAGGTCAAACATCACCATGTGGCTGGCGAACTGGAAGTTACGTCCTTCAGAACCGATTTCTGAGCACAGCAGTACCTGTGCGCCGGTGTCTT                      >  1:501727/1‑149                                                                                                                                  aagtAGTTGGGGGCATTCCCCAATACGCTGCTCCAGTAGATCCGGGTAGAATGGCAGGTCAAGCATCACCATGTGGCTGGCGAACTGGAAGTTACGTCGTTCAGTAACGATTTCTGAGCACAGCAGTACCTGTGCGCCGGTGTCTTCTT                   <  2:412372/145‑1                                                                                                                                   ATAATTTGGACGCATGACCCAATACGCTGCTCCAGTAGATCCGGGTTGAATGGCAGGTCAAACATCACCATGTGGCTGGCGAACTTGAAGTTACGTCCTTCAGAACCGATTTCTGAGCACAGCAGTACCTGTGCGCCGGTGTCTTCTTC                  <  2:55340/149‑1                                                                                                                                   ATAAGATGGCGTCATTACCCAATACTCTGCTCCAGTAGCTCCGGGTTGAATGGCAGGTCAAACATCACCATGTGGCTGGCGAACTGGAAGTTACGTCCTTCAGAACCGATTTCTGAGCACTGCAGTACCTGTGCGCCGGTGTCTTCTTC                  <  2:451572/149‑1                                                                                                                                    cAAGTTGGAGTCATTACCCAATACGCTGCTCCAGTAGATCCGGGTTGAATGGCAGGTCAAACATCACCATGTGGCTGGCGAACTGGAAGTTACGTCCTTCAGAACCGATTTCTGAGCACAGCAGTACCTGTGCGCCGGTGTCTTCTTCG                 <  1:134187/148‑1                                                                                                                                               cagTACCCAATACGCTGCTCCAGTAGATCCGGGTTGCATGGCAGGTCAAACATCACCATGTGGCTGGCGAACTGGAAGTTACGTCCTTCAGAACCGATTTCTGAGCACAGCAGTACCTGTGCGCCGGTGTCTTCTTCGGCAAACCAGGC      <  2:56032/146‑1                                                                                                                                                   ACCCAATACGCTGCTCCAGTAGATCCGGGTTGAATGGCAGGTCAAACATCACCATGTGGCTGGCGAACTGGAAGTTACGTCCTTCAGAACCGATTTCTGAGCACAGCAGTACCTGTGCGCCGGTGTCTTCTTCGGCAAACCAGGCGGCA  <  2:597516/149‑1                                                                                                                                                                                                                                                                                                         GAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACc‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_bme_pgi/19944‑19797 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CCAATACGCTGCTCCAGTAGATCCGGGTTGAATGGCAGGTCAAACATCACCATGTGGCTGGCGAACTGGAAGTTACGTCCTTCAGAACCGATTTCTGAGCACAGCAGTACCTGTGCGCCGGTGTCTTCTTCGGCAAACCAGGCGGCA  >  NC_000913_3_bme_pgi/61481‑61627

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ 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.