New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_bme_pgi	= 20563	NA (NA)	40 (0.880)	34/290	0.4	88.9%	intergenic (‑55/+252)	insA/rpsT	IS1 repressor TnpA/30S ribosomal subunit protein S20
	?	NC_000913_3_bme_pgi	= 61489	5 (0.110)					coding (1776/2907 nt)	rapA	RNA polymerase remodeling/recycling factor ATPase; RNA polymerase‑associated, ATP‑dependent RNA translocase

CGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913_3_bme_pgi/20423‑20563 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GCGTATTGGTCGTCTGGATCGTATCGGCCAGGCGCACGATATTCAGATCCATGTGCCTTATCTGGAGAAAACCGCTCAGTCGGTGCTGGTGCGCTGGTATCACGAAGGTCTGGATGCATTTGAGCACACCTGCCCGACC  <  NC_000913_3_bme_pgi/61489‑61351                                                                                                                                                                                                                                                                                          CGCAGATGTCCGGCGGTGCTTCTGCCGTTACGGACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGCGTATTG                                                                                                                                     <  2:449629/149‑1    TGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGCGTATTGGTC                                                                                                                                  <  1:246787/149‑1                   CTTTTGCCGTTACGCACCACCCCGTCAGTAACTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAACTCAATAAGTTGGCAGCATCACCGCGTATCGCTCGTCTGGATCGTATCG                                                                                                                   >  2:753176/1‑149                          CGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGCGTATTGGTCGTCTGGATCGTATCGGCCAGGC                                                                                                            >  2:93813/1‑149                              ACGCACCACCCCGTCAGTAGGTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGCGTATTGGTCGTCTGGATCGTATCGGCCAGGCGCAC                                                                                                        <  2:305698/149‑1                                  ACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAACCAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGCGTATTGGTCGTCTGGATCGTCGCGGCCAGGCGCCCGATA                                                                                                    >  2:398129/1‑149                                   CCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAACAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGCGTATTGGTCGTCTGGGTCGTATCGGCCAGGCGCACGATAT                                                                                                   >  1:670069/1‑149                                        CCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGCGTATTGGTCGTCTGGATCGTATCGGCCAGGCGCACGATATTCAGA                                                                                              <  1:371754/149‑1                                                  CTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGCGTATTGGTCGTCTGGATCGTATCGGCCAGGCGCACGATATTCAGATCCATGTGCC                                                                                    >  1:113407/1‑149                                                        AGGAGGGACAGCTGATAAAAACAGAAGCCACTGGAGCATCTCAAAAACACCATCATACACTAAATTAGTAAGTTGGCAGCATCACCGCGTATTGGTCGTTTGGATCGTATCGGCCAGGCGCACGCTATTGCGATTCATGTTCGTTATCT                                                                              <  2:675635/149‑1                                                        AGGAGGGAAAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGTGTATTGGTCGTCTGGATCGTATCGGCCAGGCGCACGATATTCAGATCCATGTGCCTTATCT                                                                              <  2:700783/149‑1                                                         GGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGCGTATTGGTCGTCTGGATCGTATCGGCCAGGCGCACGATATTCAGATCCATGTGCCTTATCTG                                                                             <  2:56651/149‑1                                                         GGAGGGACAGCTCAAAGAAACAGAAGCCACTGGAGCACCTCAAAAACATCATCATACCCTAAATCAGTAAGTTGGCAGCATCACCGCGTATTGGTCGTCTGGATCGTATCGGCCAGGCGCACGATATTCAGATCCATGTGCCTTATCTG                                                                             <  2:59134/149‑1                                                             GGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGCGTATTGGTCGTCTGGATCGTATCGGCCAGGCGCACGATATTCAGATCCATGTGCCTTATCTGGAGA                                                                         >  2:773915/1‑149                                                                   CTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGCGTATTGGTCGTCTGGATCGAATCGGCCAGGCGCACGATATTCAGATCCATGTGCCTTAACTGGAGAAAACCG                                                                   >  1:452618/1‑149                                                                    TGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGCGTATTGGTCGTCTGGATCGTATCGGCCAGGCGCACGATATTCAGATCCATGTGCCTTATCTGGAGAAAACCGC                                                                  <  1:93813/149‑1                                                                     GATAGAAACAGAAGCCACGGGAGCACCTCAAAAACATCAGCATACACTAAATCAGTAAGTTGGCAGCATCACCGCGTATTGGTCGTCTGGATCGTATCGGCCAGGCGCACGATATTCAGATCCATGTGCCTTATCTGGAGAAAACCGCT                                                                 <  2:124392/149‑1                                                                      ATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGCGTATTGGTCGTCTGGATCGTATCGGCCAGGCGCACGATATTCAGATCCATGTGCCTTATCTGGAGAAAACCGCTC                                                                >  1:275615/1‑149                                                                              AGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGAAGCATCACCGCGTATTGGTCGTCTGCATCGTATCGGCCAGGCGCACGATATTCAGATCCATGTGCCTTATCTGGAGCAAACCGCCCAGCCGGgg                                                        >  2:441088/1‑147                                                                                     ACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCATCGCGTATTGGTCAGCTGGGTCGTATCGGCCAGGCGCACGATATTCAGATCCATGTGCCTTATCTGGAGAAAACCGCTCCGTCGGTGCTGGTGC                                                 >  2:208955/1‑149                                                                                        GGAGCACCTCAAAAACACCATCAGTCACTAAATCAGTAAGTTGGCAGCATCACCGGGTATTGGTCGTCTGGATCGTATCGGCCAGGCGCACGATATTCAGATCCATGTGCCTTATCTGGAGAAAACCGCTCAGTCGGTGCTGGTGCGCT                                              <  2:751416/149‑1                                                                                               CTCAAAAACCCCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGCGTATTGGTCGTCTGGATCGTATCGGCCAGGCGCACGATATTCAGATCCATGTGCCTTATCTGGAGAAAACCGCTCAGTCGGTGCTGGTGCGCTGGTATCA                                       <  1:695877/149‑1                                                                                                  AAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGCGTATTGGTCGTCTGGATCGTATCGGCCAGGCGCACGATGTTCAGATCCATGTGCCTTATCTGGAGAATACCGCTCGGTCGGTGCTGGTGCGCTGGTATgtgta                                    >  1:165734/1‑144                                                                                                   AAAACACCATCACACACTAAATCAGTAAGTTGGCAGCATCACCGCGTATTGGTCGTCTGGATCGTATCGGCCAGGCGCACGATATTCAGATCCATGTGCCTTATCTGGAGAAAACCGCTCAGTCGGTGCTGGTGCGCTGGTATCACGAA                                   <  1:532327/149‑1                                                                                                   AAAACACCAGCATACAGTAAATCAGTAAGTTGGCAGCATCACCGCGTATTGGTCGTCTGGATCGTATCGGCCAGGCGCACGATATTCAGATCCATGTGCCTTATCTGGAGAAAACCGCTCAGTCGGTGCTGGTGCGCTGGTATCACGAA                                   <  2:670069/149‑1                                                                                                    AAACACCATCGTACACTAAATCAGTATGTTGGCAGCTTTACCGCGTATTGGTCGTCTGGATCGTATCGGCCAGGCGCACGATCTTCAGCTCCATGTGAATTATCTGGCGAGACGCGCTCAGTCGGTGCTCGTGCGCTGGTATCATGAAG                                  <  2:674483/149‑1                                                                                                    AAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGCGTATTGGTCGTCTGGATCGTATCGGCCAGGCGCACGATATTCAGATCCATGTGCCTTATCTGGAGAAAACCGCTCAGTCGGTGCTGGTGCGCTGGTATCACGAAG                                  <  1:652329/149‑1                                                                                                           ATCATACACTAAATCAGTAAGTTGGCAGCATCACCGCGTATTGGTCGTCTGGATCGTATCGGCCAGGCGCACGATATTCAGATCCATGTGCCTTATCTGGAGAAAACCGCTCAGTCGGTGCTGGTGCGCTGGTATCACGAAGGTCTGGA                           <  1:356630/149‑1                                                                                                                 CACTAAATCAGTAAGTTGGCAGCATCACCGCGTATTGGTCGTCTGGATCGTATCGGCCAGGCGCACGATATTCAGATCCATGTGCCTTATCTGGAGAAAACCGCTCAGTCGGTGCTGGTGCGCTGGTCTCACGAAGGTCTGGATGCATT                     >  2:286897/1‑149                                                                                                                  ACTAAATCAGTAAGTTGGCAGCATCACCGCGTATTGGTCGTCTGGATCGTATCGGCCAGGCGCACGATATTCAGATCCATGTGCCTTATCTGGAGAAAACCGCTCAGTCGGTGCTGGTGCGCTGGTATCACGAAGGTCTGGATGCATTT                    <  1:773915/149‑1                                                                                                                    TAACTCAGTAAGTTGGCAGCATCACCGCGTATTGGTCGTCTGGATCGTATCGGCCAGGCGCACGATATTCAGATCCATGTGCCTTATCTGGAGAAAACCGCTCAGTCGGTGCTGGTGCGCTGGTATCACGAAGGTCTGGATGCATTTGA                  <  1:491062/149‑1                                                                                                                     gaagCAGTAAGTTGGGAGCAACACCGCGTATTGGTCGTCTGGATCGTATCGGCCAGGCGCACGATATTCAGATCCATGTGCCTTATCTGGAGAAAACCGCTCAGTCGGTGCTGGTGCGCTGGTATCACGAAGGTCTGGATGCATTTGAG                 <  2:458472/145‑1                                                                                                                           GTAAGTTGGCAGCATCACCGCGTATTGGTCGTCTGGATCGTATCGGCCAGGCGCACGATATTCAGATCCATGTGCCTTATCTGGAGAAAACCGCTCAGTCGGTGCTGGTGCGCTGGTATCACGAAGGTCTGGATGCATTTGAGCACACC           >  1:678657/1‑149                                                                                                                           GTAAGTTGGCAGCATCACCGCGTATTGGTCGTCTGGATCGTATCGGCCAGGCGCACGATATTCAGATCCATGTGCCTTATCTGGAGAAAACCGCTCAGTCGGTGCTGGTGCGCTGGTATCACGAAGGTCTGGATGCATTTGAGCACACC           >  1:701158/1‑149                                                                                                                            TAAGTTGGCAGCATCACCGCGTATTGGTCGTCTGGATCGTATCGGCCAGGCGCACGATATTCAGATCCATGTGCCTTATCTGGAGAAAACCGCTCAGTCGGTGCTGGTGCGCTGGTATCACGAAG                                  <  2:354597/125‑1                                                                                                                            TAAGTTGGCAGCATCACCGCGTATTGGTCGTCTGGATCGTATCGGCCAGGCGCACGATATTCAGATCCATGTGCCTTATCTGGAGAAAACCGCTCAGTCGGTGCTGGTGCGCTGGTATCACGAAG                                  >  1:354597/1‑125                                                                                                                                  GGCAGCATCACCGCGTATTGGTCGTCTGGATCGTATCGGCCAGGCGCACGATATTCAGATCCATGTGCCTTATCTGAAGAAAACCGCTCAGTCGGTGCTGGTGCACTGGTATCACGAAGGTCTGGCTGCATCTGAGCACACCTGCCCGA    >  2:481484/1‑149                                                                                                                                   GCACCATCACCGCGTATTGGTCGTCTGGACCGTATCGGCCAGGCGCACGATATTCAGATCCATGTGCCTTATCTGGAGAAAACCGCTCAGTCGGTGCTGGTGCTCTGGTATCACGAAGGTCTGGATGCATTTGAGCACACCTGTCCGAC   <  2:316964/149‑1                                                                                                                                    catccTCACCGCGTATTGGTCGTCTGGATCGTATCGGCCAGGCGCACGATATTCAGATCCATGTGCCTTATCTGGAGAAAACCGCTCAGTCGGTGCTGGTGCGCTGGTATCACGAAGGTCTGGATGCATTTGAGCACACCTGCCCGACC  <  1:687130/144‑1                                                                                                                                    CAGCATCACCGCGTATTGGTCGTCTGGATCGTATCGGCCAGGCGCACGATATTCAGATCCATGTGCCTTATCTGGAGAAAACCGCTCAGTCGGTGCTGGTGCGCTGGTATCACGAAGGTCTGGATGCATTTGAGCACACCTGCCCGACC  >  1:423155/1‑149                                                                                                                                                                                                                                                                                          CGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913_3_bme_pgi/20423‑20563 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GCGTATTGGTCGTCTGGATCGTATCGGCCAGGCGCACGATATTCAGATCCATGTGCCTTATCTGGAGAAAACCGCTCAGTCGGTGCTGGTGCGCTGGTATCACGAAGGTCTGGATGCATTTGAGCACACCTGCCCGACC  <  NC_000913_3_bme_pgi/61489‑61351

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ 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.