New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1286708 =	53 (0.830)	45 (0.890)	19/160	1.5	62.1%	intergenic (+182/+358)	narI/rttR	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
	?	NC_000913	= 1287241	13 (0.260)					intergenic (‑5/+3)	rttR/tyrV	rtT sRNA, processed from tyrT transcript/tRNA‑Tyr

GAGAAGCTTCGACCAAGGTTCGACTTGAGCGCCAGCGAGAGAGCGTTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/1286818‑1286708 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aatccttcccccaccaccatcACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCGCAATTAAATATTCTGCCCATGCGGGGAAGGATGAGAAGCTTCGACCAAGGTTCGACTCGAGCGCCAGCGAGAGAGCGTTGCCGCAGGCAACGACCCGA  <  NC_000913/1287241‑1287109                                                                                                                                                                                                                                                      GAGAAGCTTCGATTAAGGTTCGGCTCGAGCGCCAGCGAGAGAGCGTTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACCTTCAAAAGTCCCTGAACTTCCCAAC                                                                                                           <  1:102174/139‑1        TTCGATTAAGGTTCGGCTCGAGCGCCAGCGAGAGAGCGTTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCG                                                                                                    <  2:1390208/139‑1         tcgattAAGGTTCGGCTCGAGCGCCAGCGAGAGAGCGTTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCGC                                                                                                   >  2:436285/7‑139         tcgattAAGGTTCGGCTCGAGCGCCAGCGAGAGAGCGTTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCGC                                                                                                   >  1:1221679/7‑139         tcgattAAGGTTCGGCTCGAGCGCCAGCGAGAGAGCGTTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCGC                                                                                                   >  1:1121581/7‑139              tAAGGTTCGGCTCGAGCGCCAGCGAGAGAGCGTTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCGCAATTA                                                                                              <  1:436285/138‑1               AAGGTTCGGCTCGAGCGCCAGCGAGAGAGCGTTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCGCAATTAA                                                                                             <  2:1121581/139‑1                AGGTTCGGCTCGAGCGCCAGCGAGAGAGCGTTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCGCAATTAAA                                                                                            <  2:1221679/139‑1                 GGTTCGGCTCGAGCGCCAGCGAGAGAGCGTTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCGCAATTAAAT                                                                                           >  1:1425911/1‑139                      ggctcGAGCGCCAGCGAGAGAGCGTTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATC                                                                                                      <  1:20435/118‑1                      ggctcGAGCGCCAGCGAGAGAGCGTTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATC                                                                                                      >  2:20435/6‑123                        ctcGAGCGCCAGCGAGAGAGCGTTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACTTTCAAACGTCCCTGAACTTCCCAACGAATCCGCAATTAAATATTCTGC                                                                                    <  1:589178/136‑1                          cGAGCGCCAGCGAGAGAGCGTTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCGCAATTAAATATTCTGCCC                                                                                  <  1:1634670/138‑1                            AGCGCCAGCGAGAGAGCGTTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCGCAATTAAATATTCTGCCCAT                                                                                <  2:990998/139‑1                            AGCGCCAGCGAGAGAGCGTTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCGCAATTAAATATTCTGCCCAT                                                                                >  1:990998/1‑139                            AGCGCCAGCGAGAGAGCGTTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCGCAATTAAATATTCTGCCCAT                                                                                <  2:1425911/139‑1                            AGCGCCAGCGAGAGAGCGTTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATC                                                                                                      <  2:56045/117‑1                            AGCGCCAGCGAGAGAGCGTTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATC                                                                                                      >  1:56045/1‑117                            AGCGCCAGCGAGAGAGCGTTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACTTTCAAAAGTCCCTGAACTT                                                                                                                 >  1:1199584/1‑106                            AGCGCCAGCGAGAGAGCGTTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAATAATCCTTCCCCCACCACCATCACTTTCAAAAGTCCCTGAACTT                                                                                                                 <  2:1199584/106‑1                             GCGCCAGCGAGAGAGCGTTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCGCA                                                                                                  <  1:526408/120‑1                             GCGCCAGCGAGAGAGCGTTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCGCA                                                                                                  >  2:526408/1‑120                             GCGCCAGCGAGAGAGCGTTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCG                                                                                                    >  1:1470929/1‑118                             GCGCCAGCGAGAGAGCGTTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCG                                                                                                    <  2:1470929/118‑1                             GCGCCAGCGAGAGAGCGTTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCAC                                                                                                                                              >  2:1069562/1‑76                             GCGCCAGCGAGAGAGCGTTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCAC                                                                                                                                              <  1:1069562/76‑1                                            CGTTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCT                                                                                                                                                      >  1:238483/1‑53                                            CGTTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCT                                                                                                                                                      <  2:238483/53‑1                                             GTTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACTTTCAAAAGTCCCTG                                                                                                                      >  1:315668/1‑84                                             GTTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACTTTCAAAAGTCCCTG                                                                                                                      <  2:315668/84‑1                                             GTTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACC                                                                                                                                             >  1:1628751/1‑61                                             GTTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACC                                                                                                                                             <  2:1628751/61‑1                                              TTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCG                                                                                                    <  2:769307/101‑1                                              TTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCG                                                                                                    >  1:769307/1‑101                                              TTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACTTTCAAA                                                                                                                              <  1:61199/75‑1                                              TTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACTTTCAAA                                                                                                                              >  2:61199/1‑75                                              TTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACTTTCA                                                                                                                                <  1:1079564/73‑1                                              TTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACTTTCA                                                                                                                                >  2:1079564/1‑73                                              TTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTA                                                                                                                                                           <  2:494304/46‑1                                              TTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTA                                                                                                                                                           >  1:494304/1‑46                                                 CCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCGCAATTAAATATTCTGCCCATGCGGGGAAGGATGAGAAGCTT                                                           >  2:246811/1‑139                                                 CCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCGCAATTAAATATTCTGCCCAT                                                                                >  2:213179/1‑118                                                 CCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCGCAATTAAATATTCTGCCCAT                                                                                <  1:213179/118‑1                                                    CAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACTTTCAAA                                                                                                                              <  2:1093716/69‑1                                                    CAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACTTTCAAA                                                                                                                              >  1:1093716/1‑69                                                              CCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATC                                                                                                                                       <  2:77135/50‑1                                                              CCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATC                                                                                                                                       >  1:77135/1‑50                                                                 GAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCGCAATTAAATATTCTGCC                                                                                   >  1:1605484/1‑99                                                                 GAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCGCAATTAAATATTCTGCC                                                                                   <  2:1605484/99‑1                                                                 GAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACTTTCAAAAGTCCCTGAAC                                                                                                                   >  2:9357/1‑67                                                                 GAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACTTTCAAAAGTCCCTGAAC                                                                                                                   <  1:9357/67‑1                                                                            CGCGCAGCGCTGAGTAATCCTTCCCCCACCACCAT                                                                                                                                        >  1:174385/1‑35                                                                            CGCGCAGCGCTGAGTAATCCTTCCCCCACCACCAT                                                                                                                                        <  2:174385/35‑1                                                                              CGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACTTTCAAA                                                                                                                              <  2:763392/43‑1                                                                              CGCAGCGCTGAGTAATCCTTCCCCCACCACCATCACTTTCAAA                                                                                                                              >  1:763392/1‑43                                                                                        cGTAATCCTTCCCCCACCACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCGCAATTAAATATTCTGCCC                                                                                  <  2:1213824/76‑1                                                                                        AGTAATCCTTCCCCCACCACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCGCAATTAAATATTCTGCCC                                                                                  >  1:1213824/1‑77                                                                                                  CCCCCACCACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCGCAATTAAATATTCTGCCCATGCGGGGAAGGATGAGAAGCTTCGATTAAGGTTCGGCTCGAGCGTCAGCCAGAGAGCGTTGCCGCAGGCAA          >  1:994650/1‑139                                                                                                  CCCCCACCACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCGCAATTAAATATTCTGCCCATGCGGGGAAGGATGAGAAGC                                                             <  2:184549/88‑1                                                                                                  CCCCCACCACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCGCAATTAAATATTCTGCCCATGCGGGGAAGGATGAGAAGC                                                             >  2:343251/1‑88                                                                                                  CCCCCACCACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCGCAATTAAATATTCTGCCCATGCGGGGAAGGATGAGAAGC                                                             >  1:184549/1‑88                                                                                                  CCCCCACCACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCGCAATTAAATATTCTGCCCATGCGGGGAAGGATGAGAAGC                                                             <  1:343251/88‑1                                                                                                  CCCCCACCACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCGCAATTAAATATTCTGCCCA                                                                                 >  2:701129/1‑68                                                                                                  CCCCCACCACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCGCAATTAAATATTCTGCCCA                                                                                 <  1:701129/68‑1                                                                                                  CCCCCACCACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCGCAATTAAATATTCTGCC                                                                                   <  1:1083818/66‑1                                                                                                  CCCCCACCACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCGCAATTAAATATTCTGCC                                                                                   >  2:1083818/1‑66                                                                                                      ctCCACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCGCAATTAAATATTTTGCCCATGCGGGGAAGGATGAGAAGCTTCGATTAAGGTTCGGCTCGAGCGTCAGCGAGAGAGCGTTGCCGCAGGCAACGAC      <  2:994650/137‑1                                                                                                      CACCACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCGCAATTAAATATTCTGCCCATGCGGGGAAGGATGAGAAGCTTCAATTAAGGTTCGGCTCGAGCGTCAGCGAGAGAGCGTTGCCGCAGGCAACGAC      <  1:246811/139‑1                                                                                                        CCACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCGCAATTAAATATTCTGCCCATGCGGGGAAGGATGAGAAGCTTCGATTAAGGTTCGGCTCGAGCGTCAGCGAGAGAGCGTTGCCGCAGGCAACGACCC    >  1:1193558/1‑139                                                                                                          ACCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCGCAATTAAATATTCTGCCCATGCGGGGAAGGATGAGAAGCTTCGATTAAGGTTCGGCTCGAGCGTCAGCGAGAGAGCGTTGCCGCAGGCAACGACCCGA  <  2:1193558/139‑1                                                                                                           CCATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCGCAATTAAATATTCTGCCCATGCGGGGAAGGATGAGAAGCTTCGAtt                                                      >  1:1213330/1‑84                                                                                                           CCATCACTTGCAAAAGTCCCTGAACTTCCCAACGAATCCGCAATTAAATATTCTGCCCATGCGGGGAAGGATGAGAAGCTTCGAtt                                                      <  2:1213330/86‑3                                                                                                            CATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCGCAATTAAATATTCTGCCCATGCGGGGAAGGATGAGAAGCTTCGATTAAGGTTCGGCTCGAGCGt                                    >  1:811396/1‑102                                                                                                            CATCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCGCAATTAAATATTCTGCCCATGCGGGGAAGGATGAGAAGCTTCGATTAAGGTTCGGCTCGAGCGt                                    <  2:811396/103‑2                                                                                                              TCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCGCAATTAAATATTCTGCCCATGCGGGGAAGGATGAGAAGCTTCGATTAAGGTTCGGCTCGAGCGTCAGCGAG                             >  1:711505/1‑108                                                                                                              TCACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCGCAATTAAATATTCTGCCCATGCGGGGAAGGATGAGAAGCTTCGATTAAGGTTCGGCTCGAGCGTCAGCGAG                             <  2:711505/108‑1                                                                                                                                                                                                                                                      GAGAAGCTTCGACCAAGGTTCGACTTGAGCGCCAGCGAGAGAGCGTTGCCGCAGGCAACGACCCGAAGGGCGAAGCGCGCAGCGCTGAGTAATCCTTCCCCCACCACCATC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/1286818‑1286708 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aatccttcccccaccaccatcACTTTCAAAAGTCCCTGAACTTCCCAACGAATCCGCAATTAAATATTCTGCCCATGCGGGGAAGGATGAGAAGCTTCGACCAAGGTTCGACTCGAGCGCCAGCGAGAGAGCGTTGCCGCAGGCAACGACCCGA  <  NC_000913/1287241‑1287109

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ 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.