New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	4021060 =	19 (0.760)	5 (0.210)	5/254	2.4	21.1%	coding (1727/2067 nt)	PP_3546	two‑component system sensor histidine kinase/response regulator
	?	NC_002947	4021082 =	19 (0.790)					coding (1749/2067 nt)	PP_3546	two‑component system sensor histidine kinase/response regulator

GGGTACCCGCATCGAGCTGCTGTTACCCCGCCACCACGAGCAAGCCCAGGCGCCAATCAGCAAACCTCCGCGCACGCTCTTGCAAAGAAGCAGCGAGGCTGCAAAACGCATTCTGTTGGTTGAAGACCAGACGGCCTTGC‑GCCTGGTGATTGGCGAAGTGTTGGAAGAGCTGGGCTATCGGGTGGACGCCTTCGAGAACGGTCCGTCTGCCCTCACCCACCTGCAAAGCGGCGAACGGCCAGACTTGCTGCTGAGCGATGTCGGCCTGCCTGGCGGCCTGAATGGCCGCC  >  NC_002947/4020935‑4021224                                                                                                                                                     |                                                                                                                                               caggcaggccgacatcgctcagcagcaagtctggccgttcgccgctttgcaggtgggtgagggcagacggaccgttctcgaaggcgtccacccgatagcccagctcttccaacacttcgccaatcACCAGACGGCCTTGC‑GCCTGGTGAt                                                                                                                                              >  1:368481‑M1/126‑150 (MQ=255)    tACCCGCATCGAGCTGCCGTTACCCCGCCACCACGAGCAAGCCCAGGCGCCAATCAGCGAGACACTGATCAGCCTCTTGCAAAGAAGCAGCGAGGCTGCAACACGCATTCTGGTGGTTGAAGACCAGACGGCCTTGC‑GCCTGGTGATTgg                                                                                                                                           <  1:143688/150‑1 (MQ=255)      cccGCATCGAGCTGCTGTTACCCCGCCACCACGAGCAAGCCCAGGCGCCAATCAGCAAACCTCCGCGCACGCTCTTGCAAAGAAGCAGCGAGGCTGCAAAACGCATTCTGTTGGTTGAAGACCAGACGGCCTTGC‑GCCTGGTGATTGGCg                                                                                                                                         <  1:87248/150‑1 (MQ=255)                         agcaagtctggccgttcgccgctttgcaggtgggtgagggcagacggaccgttctcgaaggcgtccacccgatagcccagctcttccaacacttcgccaatcaccagacggccttgcgcctggtGATTGGCGAAGTGTTGGAAGAGCTgg                                                                                                                       <  2:360560‑M2/26‑1 (MQ=255)                                  ccacGAGCAAGCCCAGGCGCCAATCAGCAAACCTCCGCGCACGCTCTTGCAAAGAAGCAGCGAGGCTGCAAAACGCATTCTGTTGGTTGAAGACCAGACGGCCTTGC‑GCCTGGTGATTGGCGAAGTGTTGGAAGAGCTGGGCTATCGGGt                                                                                                             <  1:292315/150‑1 (MQ=255)                                  ccacGAGCAAGCCCAGGCGCCAATCAGCAAACCTCCGCGCACGCTCTTGCAAAGAAGCAGCGAGGCTGCAAAACGCATTCTGTTGGTTGAAGACCAGACGGCCTTGC‑GCCTGGTGATTGGCGAAGTGTTGGAAGAGCTGGGCTATCGGGt                                                                                                             >  1:204021/1‑150 (MQ=255)                                  ccacGAGCAAGCCCAGGCGCCAATCAGCAAACCTCCGCGCACGCTCTTGCAAAGAAGCAGCGAGGCTGCAAAACGCATTCTGTTGGTTGAAGACCAGACGGCCTTGC‑GCCTGGTGATTGGCGAAGTGTTGGAAGAGCTGGGCTATCGGGt                                                                                                             >  1:361789/1‑150 (MQ=255)                                        gCAAGCCCAGGCGCTAATCAGCAAACCTCCGCGCACGCTCTTGCAAAGAAGCAGCGAGGCTGCAAAACGCATTCTGTTGGTTGAAGACCAGACGGCCTTGC‑GCCTGGTGATTGGCGAAGTGTTGGAAGAGCTGGGCTATCGGGTGGACGc                                                                                                       >  2:8698/1‑150 (MQ=255)                                            gCCCAGGCGCCAATCAGCAAACCTCCGCGCACGCTCTTGCAAAGAAGCAGCGAGGCTGCAAAACGCATTCTGTTGGTTGAAGACCAGACGGCCTTGC‑GCCTGGTGATTGGCGAAGTGTTGGAAGAGCTGGGCTATCGGGTGGACGCCTTc                                                                                                   >  1:622622/1‑150 (MQ=255)                                              ccAGGCGCCAATCAGCAAACCTCCGCGCACGCTCTTGCAAAGAAGCAGCGAGGCTGCAAAACGCATTCTGTTGGTTGAAGACCAGACGGCCTTGC‑GCCTGGTGATTGGCGAAGTGTTGGAAGAGCTGGGCTATCGGGTGGACGCCTTCga                                                                                                 <  2:365465/150‑1 (MQ=255)                                                aGGCGCCAATCAGCAAACCTCCGCGCACGCTCTTGCAAAGAAGCAGCGAGGCTGCAAAACGCATTCTGTTGGTTGAAGACCAGACGGCCTTGC‑GCCTGGTGATTGGCGAAGTGTTGGAAGAGCTGGGCTATCGGGTGGACGCCTTCgaga                                                                                               >  1:104247/1‑150 (MQ=255)                                                              aaaCCTCCGCGCACGCTCTTGCAAAGAAGCAGCGAGGCTGCAAAACGCATTCTGTTGGTTGAAGACCAGACGGCCTTGC‑GCCTGGTGATTGGCGAAGTGTTGGAAGAGCTGGGCTATCGGGTg                                                                                                            >  1:193464/1‑123 (MQ=255)                                                              aaaCCTCCGCGCACGCTCTTGCAAAGAAGCAGCGAGGCTGCAAAACGCATTCTGTTGGTTGAAGACCAGACGGCCTTGC‑GCCTGGTGATTGGCGAAGTGTTGGAAGAGCTGGGCTATCGGGTg                                                                                                            <  2:193464/123‑1 (MQ=255)                                                              aaaCCTCCGCGCACGCTCTTGCAAAGAAGCAGCGAGGCTGCAAAACGCATTCTGTTGGTTGAAGACCAGACGGCCTTGC‑GCCTGGTGATTGGCGAAGTGTTGGAAGAGCTGGGCTATCGGGTGTACTCCTTCGAGAGCGGTCCgggcggc                                                                                 <  2:166662/150‑7 (MQ=255)                                                                          gttctcgaaggcgtccacccgatagcccagctcttccaacacttcgccaatcACCAGACGGCCTTGC‑GCCTGGTg                                                                                                                                                <  2:316992‑M1/23‑1 (MQ=255)                                                                          gctctcgaaggcgtccacccgatagcccagctcttccaacacttcgccaatcACCAGACGGCCTTGC‑GCCTGGTg                                                                                                                                                >  1:316992‑M1/53‑75 (MQ=255)                                                                                  gCAAAGAAGCAGCGAGGCTGCAAAACGCATTCTGTTGGTTGAAGACCAGACGGCCTTGC‑GCCTGGTGATTGGCGAAGTGTTGGAAGAGCTGGGCTATCGGGTGGACGCCTTCGAGAACGGTCCGTCTGCCCTCAACCACCTTCAAAgcgg                                                             <  2:24105/150‑1 (MQ=255)                                                                                       gaagCAGCGAGGCTGCAAAACGCATTCTGTTGGTTGAAGACCAGACGGCCTTGC‑GCCTGGTGATTGGCGAAGTGTTGGAAGAGCTGGGCTATCGGGTGGACGCCTTCGAGAACGGTCCGTCTGCCCTCACCCACCTGCAAAGCGGCGAAc                                                        <  1:8698/150‑1 (MQ=255)                                                                                                  gCTGCAAAACGCATTCTGTTGGTTGAAGACCAGACGGCCTTGC‑GCCTGGTGATTGGCGAAGTGTTGGAAGAGCTGGGCTATCGGGTGGACGCCTTCGAGAACGGTCCGTCTGCCCTCACCCACCTGCAAAGCGGCGAACGGCCAGACTtg                                             <  2:204021/150‑1 (MQ=255)                                                                                                    ccagctcttccaacacttcgccaatcACCAGGCG‑CAAGGCCGTCTGGTGATTGGCGAAGTGTTGGAAGAGCTGGGCTATCGGGTGGACGCCTTCGAGAACGGTCCGTCTGCCCTCACCCACCTGCAAAGCGGCGAACGGCCAGACTtgct                                           <  2:360560‑M1/124‑1 (MQ=255)                                                                                                         aaCGCATTCTGTTGGTTGAAGACCAGACGGCCTTGC‑GCCTGGTGATTGGCGAAGTGTTGGAAGAGCTGGGCTATCGGGTGGACGCCTTCGAGAACGGTCCGTCTGCCCTCACCCACCTGCAAAGCGGCGAACGGCCAGACTTGCTGCTGa                                      >  2:570053/1‑150 (MQ=255)                                                                                                             cATTCTGTTGGTTGAAGACCAGACGGCCTTGC‑GCCTGGTGATTGGCGAAGTGTTGGAAGAGCTGGGCTATCGGGTGGACGCCTTCGAGAACGGTCCGTCTGCCCTCACCCACCTGCAAAGCGGCGAACGGCCAGACTTGCTGCTGAGCGa                                  <  1:570053/150‑1 (MQ=255)                                                                                                                          gAAGACCAGACGGCCTTGC‑GCCTGGTGATTGGCGAAGTGTTGGAAGAGCTGGGCTATCGGGTGGACGCCTTCGAGAACGGTCCGTCTGCCCTCACCCACCTGCAAAGCGGCGAACGGCCAGACTTGCTGCTGAGCGATGTCGgcctgcct                     <  2:622622/150‑1 (MQ=255)                                                                                                                            atcaccaggcgcaaggccgtctggtGATTGGCGAAGTGTTGGAAGAGCTGGGCTATCGGGTGGACGCCTTCGAGAACGGTCCGTCTGCCCTCACCCACCTGCAAAGCGGCGAACGGCCAGACTTGCTGCTGAGCGATGTCGGcctgcctg                    >  1:368481‑M2/26‑150 (MQ=255)                                                                                                                              caccaggcgcaaggccgtctggtGATTGGCGAAGTGTTGGAAGAGCTGGGCTATCGGGTGGACGCCTtcgagagc                                                                                             >  1:316992‑M2/24‑73 (MQ=255)                                                                                                                              caccaggcgcaaggccgtctggtGATTGGCGAAGTGTTGGAAGAGCTGGGCTATCGGGTGGACGCCTTCGAGAAc                                                                                             <  2:316992‑M2/52‑1 (MQ=255)                                                                                                                                     ggCCTTGC‑GCCTGGTGATTGGCGAAGTGTTGGAAGAGCTGGGCTATCGGGTGGACGCCTTCGAGAACGGTCCGTCTGCCCTCACCCACCTGCAAAGCGGCGAACGGCCAGACTTGCTGCTGAGCGATGTCGGCCTGCCTGGCGGCCTGaa          <  2:104247/150‑1 (MQ=255)                                                                                                                                              gtctggtGATTGGCGAAGTGTTGGAAGAGCTGGGCTATCGGGTGGACGCCTTCGAGAACGGTCCGTCTGCCCTCACCCACCTGCAAAGCGGCGAACGGCCAGACTTGCTGCTGAGCGATGTCGGCCTGCCTGGCGGCCTGAATGgccgcc  <  1:360560‑M2/143‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                               GGGTACCCGCATCGAGCTGCTGTTACCCCGCCACCACGAGCAAGCCCAGGCGCCAATCAGCAAACCTCCGCGCACGCTCTTGCAAAGAAGCAGCGAGGCTGCAAAACGCATTCTGTTGGTTGAAGACCAGACGGCCTTGC‑GCCTGGTGATTGGCGAAGTGTTGGAAGAGCTGGGCTATCGGGTGGACGCCTTCGAGAACGGTCCGTCTGCCCTCACCCACCTGCAAAGCGGCGAACGGCCAGACTTGCTGCTGAGCGATGTCGGCCTGCCTGGCGGCCTGAATGGCCGCC  >  NC_002947/4020935‑4021224

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ 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.