New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 5040496	50 (0.960)	4 (0.080)	4/248	NT	8.8%	coding (8/1122 nt)	PP_4446	group II intron‑encoding maturase
	?	NC_002947	= 5040543	36 (0.740)					intergenic (‑40/‑81)	PP_4446/PP_5680	group II intron‑encoding maturase/Cro/CI family transcriptional regulator

CTGTACGATCTTGTCCTCCAGAGAGGCAATGCCCAGCGGACGCTGCCTGCCGTCGGCTTTGGGAATGTAGACCCGCCGCGATGGCGTTGCCCGATATCTCAAAGATGTGCTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGATCGGGCAATTGCTGCCGCATCAGTGGGGTGCCAGCCTGACTTACGCAAGGTGAGTTCGCCGGACGCTTACCTCCGAGCGGTGAAGGGTGTGAGCCAGGCGGAGTTGCCTGCAGACCGCAAGCACCTCTACAAGCTCGAA  >  NC_002947/5040402‑5040683                                                                                                                                               |                                                                                                                                             ctgTACGATCTTGTCCTCCAGAGAGGCAATGCCCAGCGGACGCTGCCTGCCGTCGGCTTTGGGAATGTAGACCCGCCGCGATGGCGTTGCCCGATATCTCAAAGATGTGCTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGatcggg                                                                                                                                        >  1:46579‑M2/1‑142 (MQ=255) ctgTACGATCTTGTCCTCCAGAGAGGCAATGCCCAGCGGACGCTGCCTGCCGTCGGCTTTGGGAATGTAGACCCGCCGCGATGGCGTTGCCCGATATCTCAAAGATGTGCTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGatcggg                                                                                                                                        >  5:99954‑M2/1‑142 (MQ=255) ctgTACGATCTTGTCCTCCAGAGAGGCAATGCCCAGCGGACGCTGCCTGCCGTCGGCTTTGGGAATGTAGACCCGCCGCGATGGCGTTGCCCGATATCTCAAAGATGTGCTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGatcgg                                                                                                                                         >  3:205807‑M2/1‑142 (MQ=255)  tgTACGATCTTGTCCTCCAGAGAGGCAATGCCCAGCGGACGCTGCCTGCCGTCGGCTTTGGGAATGTAGACCCGCCGCGATGGCGTTGCCCGATATCTCAAAGATGTGCTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGatcgggc                                                                                                                                       <  4:216629‑M2/148‑8 (MQ=255)   gTACGATCTTGTCCTCCAGAGAGGCAATGCCCAGCGGACGCTGCCTGCCGTCGGCTTTGGGAATGTAGACCCGCCGCGATGGCGTTGCCCGATATCTCAAAGATGTGCTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGatcgggcaa                                                                                                                                     <  5:295181‑M2/149‑10 (MQ=255)    tACGATCTTGTCCTCCAGAGAGGCAATGCCCAGCGGACGCTGCCTGCCGTCGGCTTTGGGAATGTAGACCCGCCGCGATGGCGTTGCCCGATATCTCAAATATGTGCTGCCGCGGC‑TGCCGACGCAGCGGGCCAGTGACATCGGGCAAt                                                                                                                                    >  4:182619/1‑149 (MQ=255)     aCGATCTTGTCCTCCAGAGAGGCAATGCCCAGCGGACGCTGCCTGCCGTCGGCTTTGGGAATGTAGACCCGCCGCGATGGCGTTGCCCGATATCTCAAAGATGTGCTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGATCGGGCAAtt                                                                                                                                   >  7:29289/1‑149 (MQ=255)      cGATCTTGTCCTCCAGAGAGGCAATGCCCAGCGGACGCTGCCTGCCGTCGGCTTTGGGAATGTAGACCCGCCGCGATGGCGTTGCCCGATATCTCAAAGATGTGCTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGATCGGGCAATtg                                                                                                                                  <  6:295181/149‑1 (MQ=255)             gTCCTCCAGAGAGGCAATGCCCAGCGGACGCTGCCTGCCGTCGGCTTTGGGAATGTAGACCCGCCGCGATGGCGTTGCCCGATATCTCAAAGATGTGCTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGATCGGGCAATtgctg                                                                                                                               <  3:216629/145‑1 (MQ=255)                 tccAGAGAGGCAATGCCCAGCGGACGCTGCCTGCCGTCGGCTTTGGGAATGTAGACCCGCCGCGATGGCGTTGCCCGATATCTCAAAGATGTGCTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGATCGGGCAATTGCTGCCGCAt                                                                                                                         >  7:156432/1‑147 (MQ=255)                 tccAGAGAGGCAATGCCCAGCGGACGCTGCCTGCCGTCGACTTTGGGAATGTAGACCCGCCGCGATGGCGTTGCCCGATATCTCAAAGATGTGCTGACGCGGC‑TGCCGCCGCAGCGGGCCAGTGAGATCGGGCAATTGCTGCCGCAt                                                                                                                         >  4:81551/1‑147 (MQ=255)                   cAGAGAGGCAATGCCCAGCGGACGCTGCCTGCCGTCGGCTTTGGGAATGTAGACCCGCCGCGATGGCGTTGCCCGATATCTCAAAGATGTGCTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGATCGGGCAATTGCTGCCGCATCAGt                                                                                                                     >  5:304741/1‑149 (MQ=255)                    agagagGCAATGCCCAGCGGACGCTGCCTGCCGTCGGCTTTGGGAATGTAGACCCGCCGCGATGGCGTTGCCCGATATCTCAAAGATGTGCTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGATCGGGCAATTGCTGCCGCATCAGTg                                                                                                                    <  7:235617/149‑1 (MQ=255)                     gagagGCAATGCCCAGCGGACGCTGCCTGCCGTCGGCTTTGGGAATGTAGACCCGCCGCGATGGCGTTGCCCGATATCTCAAAGATGTGCTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGATCGGGCAATTGCTGCCGCATCAGTgg                                                                                                                   <  4:50741/149‑1 (MQ=255)                       gagGCAATGCCCAGCGGACGCTGCCTGCCGTCGGCTTTGGGAATGTAGACCCGCCGCGATGGCGTTGCCCGATATCTCAAAGATGTGCTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGATCGGGCAATTGCTGCCGCATCAGTgggg                                                                                                                 <  8:29289/149‑1 (MQ=255)                            aaTGCCCAGCGGACGCTGCCTGCCGTCGGCTTTGGGAATGTAGACCCGCCGCGATGGCGTTGCCCGATATCTCAAAGATGTGCTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGATCGGGCAATTGCTGCCGCATCAGTGGGGTGc                                                                                                              >  7:27789/1‑147 (MQ=255)                                cccAGGGGACGCTGCCTGCCGTCGGCTTTGGGAATGTAGACCCGCCGCGATGGCGTTGCCCGATATCTCAAAGATGTGCTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGATCGGGCAATTGCTGCCGCATCAGTGGGGTGCCAGCCt                                                                                                        <  3:298806/149‑1 (MQ=255)                                cccAGCGGACGCTGCCTGCCGTCGGCTTTGGGAATGTAGACCCGCCGCGATGGCGTTGCCCGATATCTCAAAGATGTGCTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGATCGGGCAATTGCTGCCGCATCAGTGGGGTGCCAGCCt                                                                                                        >  7:138538/1‑149 (MQ=255)                                cccAGCGGACGCTGCCTGCCGTCGGCTTTGGGAATGTAGACCCGCCGCGATGGCGTTGCCCGATATCTCAAAGATGTGCTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGATCGGGCAATTGCTGCCGCATCAGTGGGGTGCCAGCCt                                                                                                        >  4:278391/1‑149 (MQ=255)                                  cAGCGGACGCTGCCTGCCGTCGGCTTTGGGAATGTAGACCCGCCGCGATGGCGTTGCCCGATATCTCAAAGATGTGCTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGATCGGGCAATTGCTGCCGCATCAGTGGGGTGCCAGCCTGa                                                                                                      >  6:246560/1‑149 (MQ=255)                                  cAGCGGACGCTGCCTGCCGTCGGCTTTGGGAATGTAGACCCGCCGCGATGGCGTTGCCCGATATCTCAAAGATGTGCTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGATCGGGCAATTGCTGCCGCATCAGTGGGGTGCCAGCCTGa                                                                                                      <  2:243547/149‑1 (MQ=255)                                     cGGACGCTGCCTGCCGTCGGCTTTGGGAATGTAGACCCGCCGCGATGGTGTTGCCCGATATCTCAAAGATGTGCTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGATCGGGCAATTGCTGCCGCATCAGTGGGGTGCCAGCCTGACt                                                                                                    >  3:91759/1‑148 (MQ=255)                                                     tCGGCTTTGGGAATGTAGACCCGCCGCGATGGCGTTGCCCGATATCTCAAAGATGTGCTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGATCGGGCAATTGCTGCCGCATCAGTGGGGTGCCAGCCTGACTTACGCAAGGt                                                                                          <  6:229295/142‑1 (MQ=255)                                                     tCGGCTTTGGGAATGTAGACCCGCCGCGATGGCGTTGCCCGATATCTCAAAGATGTGCTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGATCGGGCAATTGCTGCCGCATCAGTGGGGTGCCAGCCTGACTTACGCAAGGt                                                                                          >  5:229295/1‑142 (MQ=255)                                                     tCGGCTTTGGGAATGTAGACCCGCCGCGATGGCGTTGCCCGATATCTCAAAGATGTGCTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGATCGGGCAATTGCTGCCGCATCAGTGGGGTGCCAGCCTGACTTACGCAAGGTGAGTTCg                                                                                   >  1:20810/1‑149 (MQ=255)                                                          tttGGGAATGTAGACCCGCCGCGATGGCGTTGCCCGATATCTCAAAGATGTGCTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGATCGGGCAATTGCTGCCGCATCAGTGGGGTGCCAGCCTGACTTAc                                                                                                 >  2:313812/1‑130 (MQ=255)                                                          tttGGGAATGTAGACCCGCCGCGATGGCGTTGCCCGATATCTCAAAGATGTGCTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGATCGGGCAATTGCTGCCGCATCAGTGGGGTGCCAGCCTGACTTAc                                                                                                 <  1:313812/130‑1 (MQ=255)                                                          tttGGGAATGTAGACCCGCCGCGATGGCGTTGCCCGATATCTCAAAGATGTGCTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGATCGGGCAATTGCTGCCGCATCAGTGGGGTGCCAGCCTGACTTACGCAAGGTGAGTTCGCCGGa                                                                              >  6:73213/1‑149 (MQ=255)                                                             gggAATGTAGACCCGCCGCGATGGCGTTGCCCGATATCTCAAAGATGTGCTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGATCGGGCAATTGCTGCCGCATCAGTGGGGTGCCAGCCTGACTTACGCAAGGTGAGTTCGCCGGACg                                                                            <  6:304741/148‑1 (MQ=255)                                                               gAATGTAGACCCGCCGCGATGGCGTTGCCCGATATCTCAAAGATGTGCTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGATCGGGCAATTGCTGCCGCATCAGTGGGGTGCCAGCCTGACTTACGCAAGGTGAGTTCGCCGGACGCtt                                                                         <  8:187388/149‑1 (MQ=255)                                                               gAATGTAGACCCGCCGCGATGGCGTTGCCCGATATCTCAAAGATGTGCTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGATCGGGCAATTGCTGCCGCATCAGTGGGGTGCCAGCCTGACTTACGCAAGGTGAGTTCGCCGGACGCtt                                                                         <  7:12365/149‑1 (MQ=255)                                                                 aTGTAGACCCGCCGCGATGGCGTTGCCCGATATCTCAAAGATGTGCTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGATCTGGCAATTGCTGCCGCATCAGTGGGGTGCCAGCCTGACTTACTCAAGGTGAGTTCGCCGGACGCTTAc                                                                       <  8:138538/149‑1 (MQ=255)                                                                         ccgccgCGATGGCGTTGCCCGATATCTCAAAGATGTGCTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGATCGGGCAATTGCTGCCGCATCAGTGGGGTGCCAGCCTGACTTACGCAAGGTGAGTTCGCCGGACGCTTACCTCCGAGc                                                               >  4:74637/1‑149 (MQ=255)                                                                         ccgccgCGATGGCGTTGCCCGATATCTCAAAGATGTGCTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGATCGGGCAATTGCTGCCGCATCAGTGGGGTGCCAGCCTGACTTACGCAAGGTGAGTTCGCCGGACGCTTACCTCCGAGc                                                               >  3:165941/1‑149 (MQ=255)                                                                           gccgcGATGGCGTTGCCCGATATCTCAAAGATGTGCTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGATCGGGCAATTGCTGCCGCATCAGTGGGGTGCCAGCCTGACTTACGCAAGGTGAGTTCGCCGGACGCTTACCTCCGAGCgg                                                             <  5:246560/149‑1 (MQ=255)                                                                               cgATGGCGTTGCCCGATATCTCAAAGATGTGCTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGATCGGGCAATTGCTGCCGCATCAGTGGGGTGCCAGCCTGACTTACGCAAGGTGAGTTCGCCGGACGCTTACCTCCGAGCGGTGaa                                                         <  5:73213/149‑1 (MQ=255)                                                                                    gCGTTGCCCTATATCTCAAAGATGTGGTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGATCGGGCAATTGCTGCCGCATCAGTGGGGTGCCAGCCTGACTTACGCAAGGTGAGTTCGCCGGACGCTTACCTCCGAGCGGTGAAGGgt                                                     <  3:182619/148‑1 (MQ=255)                                                                                      gTTGCCCGATATCTCAAAGATGTGCTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGATCGGGCAATTGCTGCCGCATCAGTGGGGTGCCAGCCTGACTTACGCAAGGTGAGTTCGCCGGACGCTTACCTCCGAGCGGTGAAGGgtgt                                                   >  8:88657/1‑148 (MQ=255)                                                                                       ttGCCCGATATCTCAAAGATGTGCTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGatcgggcaacgccatcgcggcgggtctacattcccaaagccgacggcaggcagcgtccgctgggcattgcctctctggag                                                              <  2:272996‑M2/136‑81 (MQ=255)                                                                                       ttGCCCGATATCTCAAAGATGTGCTGACGCCGC‑TGCCGACGCAGCGGGCCAGTGAGatcgggcaacgccatcgcggcgggtctacattcccaaagccgacggcaggcagcgtccgctgggcattgcctctctggag                                                              >  1:272996‑M2/1‑56 (MQ=255)                                                                                          cccGATATCTCAAAGATGTGCTGACGCGGCGTGCCGACGCAGCGGGCCAGTGAGATCGGGCAATTGCTGCCGCATCAGTGGGGTGCCAGCCTGACTTACGCAAGGTGAGTTCGCCGGACGCTTACCTCCGAGCGGTGAAGGGTGTGAGc                                               >  1:29355/1‑149 (MQ=255)                                                                                          cccGATATCTCAAAGATGTGCTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGatcgggcaacgccatcgcggcgggtctacattcccaaagccgacggcaggcagcgtccgctgggcattgcctctctggaggacaagatcgtacag                                               <  4:220321‑M2/148‑96 (MQ=255)                                                                                            cGATATCTCAAAGATGTGCTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGATCGGGCAATTGCTGCCGCATCAGTGGGGTGCCAGCCTGACTTACGCAAGGTGAGTTCGCCGGACGCTTACCTCCGAGCGGTGAAGCGTGTGAGCCAg                                            >  3:266522/1‑149 (MQ=255)                                                                                                   tcAAAGATGTGCTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGATCGGGCAATTGCTGCCGCATCAGTGGGGTGCCAGCCTGACTTACGCAAGGTGAGTTCGCCGGACGCTTACCTCCGAGCGGTGAAGGGTGTGAGCCAGGCGGAGt                                     >  3:78389/1‑149 (MQ=255)                                                                                                                             gACGCAGCGGGCCAGTGAGATCGGGCAATTGCTGCCGCATCAGTGGGGTGCCAGCCTGACTTACGCAAGGTGAGTTCGCCGGACGCTTACCTCCGAGCGGTGAAGGGTGTGAGCCAGGCGGAGTTGCCTGCAGACCGCAAGCACCTCTa            >  7:102288/1‑149 (MQ=255)                                                                                                                               cGCAGCGTGCCAGTGAGATCGGGCAATTGCTGCCGCATCAGTGGGGTGCCATCCTGACTTACGCAAGGTGAGTTCGCCGGACGCTTACCTCCGAGCGGTGAAGGGTGTGAGCCAGGCGGAGTTGCCTGCAGACCGCAAGCACCTCTACa          <  8:156432/149‑1 (MQ=255)                                                                                                                                      ggCCAGTGAGATCGGGCAATTGCTGCCGCATCAGTGGGGTGCCAGCCTGACTTACGCAAGGTGAGTTCGCCGGACGCTTACCTCCGAGCGGTGAAGGGTGTGAGCCAGGCGGAGTTGCCTGCAGACCGCAAGCACCTCTACAAGCTCg    >  4:153424/1‑148 (MQ=255)                                                                                                                                       gCCAGTGAGatcgggcaacgccatcgcggcgggtctacattcccaaagccgacggcaggcagcgtccgctgggcattgcctctctggaggacaagatcgtacagcaggcagtcgttaccgttctgaatgcgatttatgaagaggacttt  >  3:220321‑M2/1‑9 (MQ=255)                                                                                                                                               |                                                                                                                                             CTGTACGATCTTGTCCTCCAGAGAGGCAATGCCCAGCGGACGCTGCCTGCCGTCGGCTTTGGGAATGTAGACCCGCCGCGATGGCGTTGCCCGATATCTCAAAGATGTGCTGACGCGGC‑TGCCGACGCAGCGGGCCAGTGAGATCGGGCAATTGCTGCCGCATCAGTGGGGTGCCAGCCTGACTTACGCAAGGTGAGTTCGCCGGACGCTTACCTCCGAGCGGTGAAGGGTGTGAGCCAGGCGGAGTTGCCTGCAGACCGCAAGCACCTCTACAAGCTCGAA  >  NC_002947/5040402‑5040683

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.