New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 3903097	40 (0.890)	4 (0.090)	4/240	NT	9.4%	intergenic (+18/+97)	PP_3445/ilvA‑I	hypothetical protein/threonine deaminase
	?	NC_002947	= 3903142	38 (0.870)					intergenic (+63/+52)	PP_3445/ilvA‑I	hypothetical protein/threonine deaminase

CGAGAACTTCAAGCGCTACGCCGACTTCAAAAGCCTGGAAACGTTCCGCAAGTTCGTTGCCGGCTTTTTCATGCGCGAGCGTTGAAATTGGCTCGCGCAGTTCCCTGCAGGAGATCGCCCT‑GCCCTTCGGGCGGGGCGGTCACGCAGCGAACACAGGCGGCAGGCGGCTAGACAGGCGTGCATTGGCCGCACAGGCGCGTCAGCCCAGGAACAGCTTGTACGCCGGGTTGTCAGTCTCGTCCCAGTACCGGTACCCCATCTCGTCCAGCGTCGACGGCAAGCCCGCCAAC  >  NC_002947/3902995‑3903284                                                                                                                                                     |                                                                                                                                               cGAGAACTTCAAGCGCTACGCCGACTTCAAAAGCCTGGAAACGTTCCGCAAGTTCGTTGCCGGCTTTTTCATGCGCGAGCGTTGAAATTGGCTCGCGCAGTTCCCTGCAGGAGATCGCCCT‑GCCCTTCGGGCGGGGCGGTCACGCAGCga                                                                                                                                              <  2:883320‑M2/150‑3 (MQ=255)  gagaACTTCAAGCGCTACGCCGACTTCAAAAGCCTGGAAACGTTCCTCAAGTTCGTTGCCGGCTTTTTCATGCGCGAGCGTTGAAATTGGCTCGCGCAGTTCCCTGCAGGA‑ATCGTCGTTGCCCTTCGGGCGGGGCGGTCACGCAGCgaa                                                                                                                                             >  1:1188858‑M2/1‑147 (MQ=255)  gagaACTTCAAGCGCTACGCCGACTTCAAAAGCCTGGAAACGTTCCGCAAGTTCGTTGCCGGCTTTTTCATGCGCGAGCGTTGAAATGGGCTCGCGCAGTTCCCTGCAGGAGATCGCCCT‑GCCCTTCGGGCGGGGCGGTCACGCAGCgaa                                                                                                                                             >  2:418356‑M2/1‑147 (MQ=255)       cTTCAAGCGCTACGCCGACTTCAAAAGCCTGGAAACGTTCCGCAAGTTCGTTGCCGGCTTTTTCATGCGCGAGCGTTGAAATTGGCTCGCGCAGTTCCCTGCAGGAGATCGCCCT‑GCCCTTCGGGCGGGGCGGTCACGCAGCGAACAcag                                                                                                                                        <  1:883320/150‑1 (MQ=255)        ttCAAGCGCTACGCCGACTTCAAAAGCCTGGAAACGTTCCGCAAGTTCGTTGCCGGCTTTTTCATGCGCGAGCGTTGAAATTGGCTCGCGCAGTTCCCTGCAGGAGATCGCCCT‑GCCCTTCGGGCGGGGCGGTCACGCAGCGAACAcagg                                                                                                                                       >  1:864048/1‑150 (MQ=255)        ttCAAGCGCTACGCCGACTTCAAAAGCCTGGAAACGTTCCGCAAGTTCGTTGCCGGCTTTTTCATGCGCGAGCGTTGAAATTGGCTCGCGCAGTTCCCTGCAGGAGATCGCCCT‑GCCCTTCGGGCGGGGCGGTCACGCAGCGAACAcagg                                                                                                                                       <  2:1192919/150‑1 (MQ=255)                cTACGCCGACTTCAAAAGCCTGGAAACGTTCCGCAAGTTCGTTGCCGGCTTTTTCATGCGCGAGCGTTGAAATTGGCTCGCGCAGTTCCCTGCAGGAGATCGCCCT‑GCCCTTCGGGCGGGGCGGTCACGCAGCGAACAcaggcggcaggc                                                                                                                               <  2:1056213/150‑1 (MQ=255)                   cGCCGACTTCAAAAGCCTGGAAACGTTCCGCAAGTTCGTTGCCGGCTTTTTCATGCGCGAGCGTTGAAATTGGCTCGCGCAGTTCCCTGCAGGAGATCGCCCT‑GCGCTTCGGGCGGGGCGGTCACGCAGCGAACACaggcggcaggcggc                                                                                                                            >  2:869867/1‑150 (MQ=255)                          ttCAAAAGCCTGGAAACGTTCCGCAAGTTCGTTGCCGGCTTTTTCATGCGCGAGCGTTGAAATTGGCTCGCGCAGTTCCCTGCAGGAGATCGCCCT‑GCCCTTCGGGCGGGGCGGTCACGCAGCgaa                                                                                                                                             >  1:587746‑M2/1‑123 (MQ=255)                          ttCAAAAGCCTGGAAACGTTCCGCAAGTTCGTTGCCGGCTTTTTCATGCGCGAGCGTTGAAATTGGCTCGCGCAGTTCCCTGCAGGAGATCGCCCT‑GCCCTTCGGGCGGGGCGGTCACGCAGCgaa                                                                                                                                             <  2:587746‑M2/126‑4 (MQ=255)                          ttCAAAAGCCTGGAAACGTTCCGCAAGTTCGTTGCCGGCTTTTTCATGCGCGAGCGTTGAAATTGGCTCGCGCAGTTCCCTGCAGGAGATCGCCCT‑GCCCTTCGGGCGGGGCGGTCACGCAGCGAACACAGGCGGCAGGCGGCTAGACAg                                                                                                                     >  1:1161001/1‑150 (MQ=255)                          ttCAAAAGCCTGGAAACGTTCCGCAAGTTCGTTGCCGGCTTTTTCATGCGCGAGCGTTGAAATTGGCTCGCGCAGTTCCCTGCAGGAGATCGCCCT‑GCCCTTCGGGCGGGGCGGTCACGCAGCGAACACAGGCGGCAGGCGGCTAGACAg                                                                                                                     <  2:1104730/150‑1 (MQ=255)                                       aaaCGTTCCGCAAGTTCGTTGCCGGCTTTTTCATGCGCGAGCGTTGAAATTGGCTCGCGCAGTTCCCTGCAGGAGATCGCCCT‑GCCCTTCGGGCGGGGCGGTCACGCAGCGAACACAGGCGGCAGGCGGCTAGACAGGCGTGCATTGGcc                                                                                                        <  1:1092554/150‑1 (MQ=255)                                                  aaGTTCGTTGCCGGCTTTTTCATGCGCGAGCGTTGAAATTGGCTCGCGCAGTTCCCTGCAGGAGATCGCCCT‑GCCCTTCGGGCGGGGCGGTCACGCAGCGAACACAGGCGGCAGGCGGCTAGACAg                                                                                                                     >  2:1109980/1‑126 (MQ=255)                                                  aaGTTCGTTGCCGGCTTTTTCATGCGCGAGCGTTGAAATTGGCTCGCGCAGTTCCCTGCAGGAGATCGCCCT‑GCCCTTCGGGCGGGGCGGTCACGCAGCGAACACAGGCGGCAGGCGGCTAGACAg                                                                                                                     <  1:1109980/126‑1 (MQ=255)                                                          tGCCGGCTTTTTCATGCGCGAGCGTTGAAATTGGCTCGCGCAGTTCCCTGCAGGAGATCGCCCT‑GCCCTTCGGGCGGGGCGGTCACGCAGCGAACACAGGCGGCAGGCGGCTAGACAGGCGTGCATTGGCCGCACAGGCGCGTCAGCCCa                                                                                     <  1:68653/150‑1 (MQ=255)                                                          tGCCGGCTTTTTCATGCGCGAGCGTTGAAATTGGCTCGCGCAGTTCCCTGCAGGAGATCGCCCT‑GCCCTTCGGGCGGGGCGGTCACGCAGCGAACACAGGCGGCAGGCGGCGAGACAGGCGTGCATTGGCCGCACAGGCGCGTCAGCCCa                                                                                     <  2:53526/150‑1 (MQ=255)                                                              ggCTTTTTCATGCGCGAGCGTTGAAATTGGCTCGCGCAGTTCCCTGCAGGAGATCGCCCT‑GCCCTTCGGGCGGGGCGGTCACGCAGCGAACACAGGCGGCAGGCGGCTAGACa                                                                                                                      <  1:1122329/113‑1 (MQ=255)                                                              ggCTTTTTCATGCGCGAGCGTTGAAATTGGCTCGCGCAGTTCCCTGCAGGAGATCGCCCT‑GCCCTTCGGGCGGGGCGGTCACGCAGCGAACACAGGCGGCAGGCGGCTAGACa                                                                                                                      >  2:1122329/1‑113 (MQ=255)                                                              ggCTTTTTCATGCGCGAGCGTTGAAATTGGCTCGCGCAGTTCCCTGCAGGAGATCGCCCT‑GCCCTTCGGGCGGGGCGGTCACGCAGCGAACACAGGCGGCAGGCGGCTAGACAGGCGTGCATTGGcc                                                                                                        >  2:460425/1‑127 (MQ=255)                                                              ggCTTTTTCATGCGCGAGCGTTGAAATTGGCTCGCGCAGTTCCCTGCAGGAGATCGCCCT‑GCCCTTCGGGCGGGGCGGTCACGCAGCGAACACAGGCGGCAGGCGGCTAGACAGGCGTGCATTGGcc                                                                                                        <  1:460425/127‑1 (MQ=255)                                                                        tGCGCGAGCGTTGAAATTGGCTCGCGCAGTTCCCTGCAGGAGATCGCCCT‑GCCCTTCGGGCGGGGCGGTCACGCAGCGAACACAGGCGGCAGGCGGCTAGACAGGCGTGCATTGGCCGCACAGGCGCGTCAGCCCAGGAACAGCTTGTAc                                                                       <  1:156331/150‑1 (MQ=255)                                                                             gtgCGTTGACATTGTCTCGAGCGATTCCGTGACCGCGATGACCCA‑GACGTTCGAGCGGGGGCTTTCCGCAGCGGACGCAGGCCGCAGGCGGCTCAGCAGGCGTGCATTGGCCGGACAGGCGCGTCAGCCCAGGAACAGCTTGTACGCCgg                                                                  <  2:211528/148‑1 (MQ=255)                                                                                     aaaTTGGCTCGCGCAGTTCCCTGCAGGAGATCGCCCT‑GCCCTTCGGGCGGGGCGGTCACGCAGCGAACACAGGCGGCAGGCGGCTAGACAGGCGTGCATTGGCCGCACAGGCGCGTCAGCCCAGGAACAGCTTGTACGCCGGGTTGTCAg                                                          >  1:189808/1‑150 (MQ=255)                                                                                         tGGCTCGCGCAGTTCCCTGCAGGAGATCGCCCT‑GCCCTTCGGGCGGGGCGGTCACGCAGCGAACACAGGCGGCAGGCGGCTAGACAGGCGTGCATTGGCCGCACAGGCGCGTCAGCCCAGGAACAGCTTGTACGCCGGGTTGTCAGtctc                                                      <  1:906350/150‑1 (MQ=255)                                                                                         tGGCTCGCGCAGTTCCCTGCAGGAGATCGCCCT‑GCCCTTCGGGCGGGGCGGTCACGCAGCGAACACAGGCGGCAGGCGGCTAGACAGGCGTGCATTGGCCGCACAGGCGCGTCAGCCCAGGAACAGCTTGTACGCCGGGTTGTCAGtctc                                                      <  1:869867/150‑1 (MQ=255)                                                                                            tttgtccAGTTACCTGCATAAGATCGCCCT‑GTCCGTCGGGCGGGGCGGTCACGCAGCGAACACAGGCGGCAGGCGGCTAGACAGGCGTGCATTGGCCGCACAGGCGCGTCAGCCCAGGAACAGCTTGTACGCCGGGTTGTCAGTCTCGTc                                                   <  2:672018/144‑1 (MQ=255)                                                                                             tCGCGCAGTTCCCTGCAGGAGATCGCCCT‑GCCCTTCGGGCGGGGCGGTCACGCAGCGAACACAGGCGGCAGGCGGCTAGACAGGCGTGCATTGGCCGCACAGGCGCGTCAGCCCAGGAACAGCTTGTACGCCGGGTTGTCAGTCTCGTcc                                                  >  1:1065861/1‑150 (MQ=255)                                                                                                 gcAGTTCCCTGCAGGAGATCGCCCT‑GCCCTTCGGGCGGGGCGGTCACGCAGCGAACACAGGCGGCAGGCGGCTAGACAGGCGTGCATTGGCCGCACAGGCGCGTCAGccc                                                                                      >  1:489425/1‑110 (MQ=255)                                                                                                 gcAGTTCCCTGCAGGAGATCGCCCT‑GCCCTTCGGGCGGGGCGGTCACGCAGCGAACACAGGCGGCAGGCGGCTAGACAGGCGTGCATTGGCCGCACAGGCGCGTCAGccc                                                                                      <  2:489425/110‑1 (MQ=255)                                                                                                   aGTTCCCTGCAGGAGATCGCCCT‑GCCCTTCGGGCGGGGCGGTCACGCAGCgaactgcgcgagccaatttcaacgctcgcgcatgaaaaagccggcaacgaacttgcggaacgtttccaggcttttgaagtcggcgtagcgcttgaagttc                                            <  2:872880‑M2/150‑101 (MQ=255)                                                                                                     ttCCCTGCAGGAGATCGCCCT‑GCCCTTCGGGCGGGGCGGTCACGCAGCgaactgcgcgagccaatttcaacgctcgcgcatgaaaaagcc                                                                                                      <  1:524048‑M2/90‑43 (MQ=255)                                                                                                     ttCCCTGCAGGAGATCGCCCT‑GCCCTTCGGGCGGGGCGGTCACGCAGCgaactgcgcgagccaatttcaacgctcgcgcatgaaaaagcc                                                                                                      >  2:524048‑M2/1‑48 (MQ=255)                                                                                                         cTGCAGGAGATCGCCCT‑GCCCTTCGGGCGGGGCGGTCACGCAGCGAACACAGGCGGCAGGCGGCTAGACAGGCGTGCATTGGc                                                                                                         <  2:752428/83‑1 (MQ=255)                                                                                                         cTGCAGGAGATCGCCCT‑GCCCTTCGGGCGGGGCGGTCACGCAGCGAACACAGGCGGCAGGCGGCTAGACAGGCGTGCATTGGc                                                                                                         >  1:752428/1‑83 (MQ=255)                                                                                                          tGCAGGAGATCGCCCT‑GCCCTTCGGGCGGGGCGGTCACGCAGCGATCACAGGCGGCAGGCGGCTAGACAGGCGTGCATTGGCCGCACAGGCGCGTCAGCCCAGGAACAGCTTGTAc                                                                       >  1:281649/1‑116 (MQ=255)                                                                                                          tGCAGGAGATCGCCCT‑GCCCTTCGGGCGGGGCGGTCACGCAGCGAACACAGGCGGCAGGCGGCTAGACAGGCGTGCATTGGCCGCACAGGCGCGTCAGCCCAGGAACAGCTTGTAc                                                                       <  2:281649/116‑1 (MQ=255)                                                                                                                     gccct‑gccctTCGGGCGGGGCGGTCACGCAGCGAACACAGGCGGCAGGCGGCTAGACAGGCGTGCATTGGCCGCACAGGCGCGTCAGCCCAGGAACAGCTTGTACGCCGGGTTGTCAGTCTCGTCCCAGTACCGGTACCCCATCTCGTcc                          <  1:706217/150‑1 (MQ=255)                                                                                                                            ccctTCGGGCGGGGCGGTCACGCAGCGAACACAGGCGGCAGGCGGCTAGACAGGCGTGCATTGGCCGCACAGgc                                                                                                >  2:33112/1‑74 (MQ=255)                                                                                                                            ccctTCGGGCGGGGCGGTCACGCAGCGAACACAGGCGGCAGGCGGCTAGACAGGCGTGCATTGGCCGCACAGgc                                                                                                <  1:33112/74‑1 (MQ=255)                                                                                                                             ccgaagggcagggcgGTCACGCAGCGAACACAGGCGGCAGGCGGCTAGACAGGCGTGCATTGGCCGCACAGGCGCGTCAGCCCAGGAACAGCTTGTACGCCGGGTTGTc                                                            <  2:17153/104‑1 (MQ=255)                                                                                                                             ccgaagggcagggcgGTCACGCAGCGAACACAGGCGGCAGGCGGCTAGACAGGCGTGCATTGGCCGCACAGGCGCGTCAGCCCAGGAACAGCTTGTACGCCGGGTTGTc                                                            >  1:17153/6‑109 (MQ=255)                                                                                                                                  gggcggggcgGTCACGCAGCGAACACAGGCGGCAGGCGGCTAGACAGGc                                                                                                                   <  2:450586/49‑1 (MQ=255)                                                                                                                                  gggcggggcgGTCACGCAGCGAACACAGGCGGCAGGCGGCTAGACAGGc                                                                                                                   >  1:450586/1‑49 (MQ=255)                                                                                                                                    gcggggcggTCACGCAGCGAACACAGGCGGCAGGCGGCTAGACAGGCGTGCATTGGCCGCACAGGCGCGTCAGCCCAGGAACAGCTTGTACGCCGGGTTGTCAGTCTCGTCCCAGTACCGGTACCCCATCTCGTCCAGCGTCGACGGCaa            >  2:409440/1‑150 (MQ=255)                                                                                                                                         gcggTCACGCAGCgaactgcgcgagccaatttcaacgctcgcgcatgaaaaagccggcaacgaacttgcggaacgtttccaggcttttgaagtcggcgtagcgcttgaagttctcggtatccggctcggggccgatgggctgttccagca       >  1:872880‑M2/1‑13 (MQ=255)                                                                                                                                           tgTCACCCAGCTAACACAGGCGGCAGGCGGCTAGACAGGCGTGCATTGGCCGCACAGGCGCGTCAGCCCAGGAACAGCTTGTACGCCGGGTTGTCAGTCTCGTCCCAGTACCGGTACCCCATCTCGTCCAGCGTCGACGGCAAGCCCGcc     <  2:1161001/149‑1 (MQ=255)                                                                                                                                             tCACGCAGCGAACACAGGCGGCAGGCGGCTAGACAGGCGTGCATTGGCCGCACAGGCGCGTCAGCCCAGGAACAGCTTGTAc                                                                       <  2:1036232/82‑1 (MQ=255)                                                                                                                                             tCACGCAGCGAACACAGGCGGCAGGCGGCTAGACAGGCGTGCATTGGCCGCACAGGCGCGTCAGCCCAGGAACAGCTTGTAc                                                                       >  1:1036232/1‑82 (MQ=255)                                                                                                                                              cACGCAGCGAACACAGGCGGCAGGCGGCTAGACAGGCGTGCATTGGCCGCACAGGCGCGTCAGCCCAGGAACAGCTTGTACGCCGGGTTGTCAGTCTCGTCCCAGTACCGGTACCCCATCTCGTCCAGCGTCGACGGCAAGCCCGCCAAc  <  1:409440/150‑1 (MQ=255)                                                                                                                                                 gCAGCGAACACAGGCGGCAGGCGGCTAGACAGGCGTGCATTGGCCGCACAGGCGCGTCAGCCCAGGAACAGCtt                                                                           <  2:777267/74‑1 (MQ=255)                                                                                                                                                 gCAGCGAACACAGGCGGCAGGCGGCTAGACAGGCGTGCATTGGCCGCACAGGCGCGTCAGCCCAGGAACAGCtt                                                                           >  1:777267/1‑74 (MQ=255)                                                                                                                                                    gCGAACACAGGCGGCAGGCGGCTAGACAGGCGTGCATTGGCCGCACAGGCGCGTCAGCCCAGGaa                                                                                 <  1:283367/65‑1 (MQ=255)                                                                                                                                                    gCGAACACAGGCGGCAGGCGGCTAGACAGGCGTGCATTGGCCGCACAGGCGCGTCAGCCCAGGaa                                                                                 >  2:283367/1‑65 (MQ=255)                                                                                                                                                     |                                                                                                                                               CGAGAACTTCAAGCGCTACGCCGACTTCAAAAGCCTGGAAACGTTCCGCAAGTTCGTTGCCGGCTTTTTCATGCGCGAGCGTTGAAATTGGCTCGCGCAGTTCCCTGCAGGAGATCGCCCT‑GCCCTTCGGGCGGGGCGGTCACGCAGCGAACACAGGCGGCAGGCGGCTAGACAGGCGTGCATTGGCCGCACAGGCGCGTCAGCCCAGGAACAGCTTGTACGCCGGGTTGTCAGTCTCGTCCCAGTACCGGTACCCCATCTCGTCCAGCGTCGACGGCAAGCCCGCCAAC  >  NC_002947/3902995‑3903284

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.