New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 5241748	61 (1.410)	5 (0.120)	5/244	NT	8.4%	coding (172/633 nt)	hmgC	maleylacetoacetate isomerase
	?	NC_002947	= 5241781	51 (1.230)					coding (139/633 nt)	hmgC	maleylacetoacetate isomerase

CCCCGAACCCTGGCCCGTGCCTCGGCGGTGGCCGGCAGCAACGCAGGCTGTGGATAAACCTCTTCCAGGTACTCGATGATCGCCGGCGACTGCACCAGCACCTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACGCTGCTCACCCTGCAGCAGGTTGACCGGCAGGGACTGGTAAGCCAGCCCCTTCAGTGCCAGGGCAATGCGCACCCGGTAGGACGAGGTGGAACGGTAATAGGTGTACAGCTCCATACCCCT  >  NC_002947/5241636‑5241925                                                                                                                                                  |                                                                                                                                                 tcccgAACCCTGGCCCGTGCCTCGGCGGTGGCCGGCAGCAACGCAGGCTGTGGATAAACCTCTCCCAGGTACTCGATGATCGCCGGCGACTGCACCAGCACCTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTgacg                                                                                                                                              <  2:461259‑M2/149‑5 (MQ=255)        cccTGGCCCGTGCCTCGGCGGTGGCCGGCAGCAACGCAGGCTGTGGATAAACCTCTTCCAGGTACTCGATGATCGCCGGCGACTGCACCAGCACCTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTGACGGCTACac                                                                                                                                       <  1:1128954/150‑2 (MQ=255)         ccTGGCCCGTGCCTCGGCGGTGGCCGGCAGCAACGCAGGCTGTGGATAAACCTCTTCCAGGTACTCGATGATCGCCGGCGACTGCACCAGCACCTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTGACGGCTACATa                                                                                                                                      >  2:176611/1‑150 (MQ=255)         ccTGGCCCGTGCCTCGGCGGTGGCCGGCAGCAACGCAGGCTGTGGATAAACCTCTTCCAGGTACTCGATGATCGCCGGCGACTGCACCAGCACCTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTGACGGCTACATa                                                                                                                                      <  1:1118794/150‑1 (MQ=255)         ccTGGCCCGTGCCTCGGCGGTGGCCGGCAGCAACGCAGGCTGTGGATAAACCTCTTCCAGGTACTCGATGATCGCCGGCGACTGCACCAGCACCTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTGACGGCTACATa                                                                                                                                      >  2:732520/1‑150 (MQ=255)             gCCCGTGCCTCGGCGGTGGCCGGCAGCAACGCAGGCTGTGGATAAACCTCTTCCAGGTACTCGATGATCGCCGGCGACTGCACCAGCACCTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTGACGGCTACATAGccc                                                                                                                                  >  2:921467/1‑150 (MQ=255)                     cTCGGCGGTGGCCGGCAGCAACGCAGGCTGTGGATAAACCTCTTCCAGGTACTCGATGATCGCCGGCGACTGCACCAGCACCTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACg                                                                                                                          >  1:377817/1‑150 (MQ=255)                      tCGGCGGTGGCCGGCAGCAACGCAGGCTGTGGATAAACCTCTTCCAGGTACTCGATGATCGCCGGCGACTGCACCAGCACCTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACgc                                                                                                                         >  2:1065986/1‑150 (MQ=255)                                    cagcaACGCAGGCTGTGGATAAACCTCTTCCAGGTACTCGATGATCGCCGGCGACTGCACCAGCACCTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACGCTGCTCACCCTgcag                                                                                                           >  1:575619/1‑150 (MQ=255)                                       caACGCAGGCTGTGGATAAACCTCTTCCAGGTACTCGATGATCGCCGGCGACTGCACCAGCACCTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACCCTGCGCACCCTGcagcag                                                                                                        <  2:542538/150‑1 (MQ=255)                                          cGCAGGCTGTGGATAAACCTCTTCCAGGTACTCGATGATCGCCGGCGACTGCACCAGCACCTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACGCTGCTCACCCTGCAGCAGGtt                                                                                                     <  1:312651/150‑1 (MQ=255)                                          cGCAGGCTGTGGATAAACCTCTTCCAGGTACTCGATGATCGCCGGCGACTGCACCAGCACCTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACGCTGCTCACCCTGCAGCAGGtt                                                                                                     <  1:176611/150‑1 (MQ=255)                                          cGCAGGCTGTGGATAAACCTCTTCCAGGTACTCGATGATCGCCGGCGACTGCACCAGCACCTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACGCTGCTCACCCTGCAGCAGGtt                                                                                                     <  1:732520/150‑1 (MQ=255)                                              ggCCGTGGATAAACCCCCTCCAGGTACTCGACGATCGCCGGCGACTACACCATCAGCTCACCGCCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACGCTGCTCACCCTGCAGCAGGTTGAcc                                                                                                 <  2:799375/150‑1 (MQ=255)                                                cTGTGGATAAACCTCTTCCAGGTACTCGATGATCGCCGGCGACTGCACCAGCACCTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACGCTGCTCACCCTGCAGCAGGTTGACCgg                                                                                               <  1:901575/150‑1 (MQ=255)                                                   tgGATAAACCTCTTCCAGGTACTCGATGATCGCCGGCGACTGCACCAGCACCTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACGCTGCTCACCCTGCAGCAGGTTGACCGGCAg                                                                                            <  2:462020/150‑1 (MQ=255)                                                   tgGATAAACCTCTTCCAGGTACTCGATGATCGCCGGCGACTGCACCAGCACCTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACGCTGCTCACCCTGCAGCAGGTTGACCGGCAg                                                                                            <  2:847651/150‑1 (MQ=255)                                                   tgGATAAACCTCTTCCAGGTACTCGATGATCGCCGGCGACTGCACCAGCACCTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACGCTGCTCACCCTGCAGCAGGTTGACCGGCAg                                                                                            <  2:311924/150‑1 (MQ=255)                                                    ggATAAACCTCTTCCAGGTACTCGATGATCGCCGGCGACTGCACCAGCACCTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACGCTGCTCACCCTGCAGCAGGTTGACCGGCAgg                                                                                           <  1:1105618/150‑1 (MQ=255)                                                        aaaCCTCGTCCAGGTACTCGATGAGCGCCGGCGACTGCACCAGCACCTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACGCTGCTCACCCTGCAGCAGGTTGACCGGCAGGGACt                                                                                       <  2:110106/150‑1 (MQ=255)                                                         aaCCTCCTCATGTTACTCGATGATCGCCGGCGACTGCACCAGCACCTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACGCTGCTCACCCTGCAGCAGGTTGACCGGCAGGGACTg                                                                                      <  1:597613/150‑1 (MQ=255)                                                           ccTCTTCCAGGTACTCGATGATCGCCGGCGACTGCACCAGCACCTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCACTGCGGGTTGACGGCTACATAGCCCTCGCCACGCTGCACACACTGCAGCAGGTTTAGCGGCAGGGACTGGt                                                                                    >  1:516157/1‑150 (MQ=255)                                                            ctctTCCAGGTACTCGATGATCGCCGGCGACTGCACCAGCACCTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACGCTGCTCACCCTGCAGCAGGTTGACCGGCAGGGACTGGTa                                                                                   <  2:377817/150‑1 (MQ=255)                                                            ctctTCCAGGTACTCGATGATCGCCGGCGACTGCACCAGCACCTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACGCTGCTCACCCTGCAGCAGGTTGACCGGCAGGGACTGGTa                                                                                   <  1:921467/150‑1 (MQ=255)                                                             tctTCCAGGTACTCGATGATCGCCGGCGACTGCACCAGCACCTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACGCTGCTCACCCTGCAGCAGGTTGACCGGCAgg                                                                                           >  2:352403/1‑141 (MQ=255)                                                             tctTCCAGGTACTCGATGATCGCCGGCGACTGCACCAGCACCTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACGCTGCTCACCCTGCAGCAGGTTGACCGGCAgg                                                                                           <  1:352403/141‑1 (MQ=255)                                                               ttCCAGGTACTCGATGATCGCCGGCGACTGCACCAGCACCTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACGCTGCTCACCCTGCAGCAGGTTGACCGGCAGGGACTGGTAagc                                                                                >  2:151375/1‑150 (MQ=255)                                                               ttCCAGGTACTCGAGGAGCGCCGGCGACTGCACCAGCACCTCACCACCGTCGGTGCGCAAGGCCAGTACGCGGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACGCGGCTCACCCTGCAGCAGGTTGACCGGCAGGGACTGGTAagc                                                                                <  1:921485/150‑1 (MQ=255)                                                                  cAGGTACTCGATGATCGCCGGCGACTGCACCAGCACCTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACGCACTCCAGTCTGCAGCAGGTTGACCGGCAGGGACTGGTAagccag                                                                             >  1:11293/1‑150 (MQ=255)                                                                         tCGATGATCGCCGGCGACTGCACCAGCACCTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACGCTGCTCACCCTGCAGCAGGTTGACCGGCAGGGACTGGTAAGCCAGCCCCTTc                                                                      >  1:1087470/1‑150 (MQ=255)                                                                          cGATGATCGCCGGCGACTGCACCAGCACCTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTGACGGCTACATAGCCCTCACCACGCTGCTCACCCTGCAGCAGGTTGACCGGCAGGGACTGGTAAGCCAGCCCCTTCa                                                                     <  2:575619/150‑1 (MQ=255)                                                                                         aCTGCACCAGCACCTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTGACTGCTACATAGCCCTCGCCACGCTGCTCACCCTGCAGCAGGTTGACCGGCAGGGACTGGTAAGCCAGCCCCTTCAGTGCCAGGGCAATgc                                                      <  2:1099422/150‑1 (MQ=255)                                                                                         aCTGCACCAGCACCTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACGCTGCTCACCCTGCAGCAGGTTGACCGGCAGGGACTGGTAAGCCAGCCCCTTCAGTGCCAGGGCAATgc                                                      <  1:461259/150‑1 (MQ=255)                                                                                           tGCACCAGCACCTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACGCTGCTCACCCTGCAGCAGGTTGACCGGCAGGGACTGGTAAGCCAGCCCCTTCAGTGCCAGGGCAATgcgc                                                    >  2:645420/1‑150 (MQ=255)                                                                                           tGCACCAGCACCTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACGCTGCTCACCCTGCAGCAGGTTGACCGGCAGGGACTGGTAAGCCAGCCCCTTCAGTGCCAGGGCAATgcgc                                                    >  2:387001/1‑150 (MQ=255)                                                                                           tGCACCAGCACCTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACGCTGCTCACCCTGCAGCAGGTTGACCGGCAGGGACTGGTAAGCCAGCCCCTTCAGTGCCAGGGCAATgcgc                                                    >  2:215757/1‑150 (MQ=255)                                                                                              aCCAGCACCTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACGCTGCTCACCCTGCAGCAGGTTGACCGGCGGGGACTGGTAAGCCAGCCCCTTCAGTGCCAGGGCAATGCGCAcc                                                 >  2:358215/1‑150 (MQ=255)                                                                                                   cACCTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACGCTGCTCACCCTGCAGCAGGTTGACCGGCAGGGACTGGTAAGCCAGCCCCTTCAGTGCCAGGGCAATGCGCACCCGGTa                                            <  1:632100/150‑1 (MQ=255)                                                                                                    aCCTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTgacggtggtgaggtgctggtgcagtcgccggcgatcatcgagtacctggaagaggtttatccacagcctgcgttgctgccggccaccgccgaggcacgg                                               <  1:540184‑M2/146‑100 (MQ=255)                                                                                                    aCCTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTgacggtggtgaggtgctggtgcagtcgccggcgatcatcgagtacctggaagaggtttatccacagcctgcgttgctgccggccaccgccgaggcacgg                                               >  2:540184‑M2/1‑47 (MQ=255)                                                                                                    aCCTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACGCTGCTCACCCTGCAGCAGGTTGACCGGCAGGGACTGGTAAGCCAGCCCCTTCAGTGCCAGGGCAATGCGCACCCGGTAg                                           >  2:504762/1‑150 (MQ=255)                                                                                                     ccTNACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTgacggtggtgaggtgctggtgcagtcgccggcgatcatcgagtacctggaagaggtttatccacagcctgcgttgctgccggccaccgccgaggcacgggccag                                          <  2:700459‑M2/150‑105 (MQ=255)                                                                                                      cTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACGCTGCTCACCCTGCAGCAGGTTGACCGGCAGGGACTGGTAAGCCAGCCCCTTCAGTGCCAGGGCAATGCGCACCCGGTAGGa                                         <  2:433763/150‑1 (MQ=255)                                                                                                       tCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACGCTGCTCACCCTGCAGCAGGTTGACCGGCAGGGACTGGTAAGCCAGCCCCTTCAGTGCCAGGGCAATGCGCACCCGGTAGGAc                                        >  1:816458/1‑150 (MQ=255)                                                                                                                   gTGCGCAAGGCCGGTACGCGGCCCTGCGCACCgacggtggtgaggtgctggtgcagtcgccggcgatcatcgagtacctggaagaggtttatccacagcctgcgttgctgccggccaccgccgaggcacgggccagggttcggggggtgg                            <  2:538836‑M2/150‑119 (MQ=255)                                                                                                                    tGCGCAAGGCCGGTACGCGGCCCTGCGCACCgacggtggtgaggtgctggtgcagtcgccggcgatcatcgagtacctggaagaggtttatccacagcctgcgttgctgccggccaccgccgaggcacgggccagggttcggggggtggc                           <  1:420213‑M2/150‑120 (MQ=255)                                                                                                                       gcAAGGCCGGTACGCGGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACGCTGCTCACCCTGCAGCAGGTTGACCGGCAGGGACTGGTAAGCCAGCCCCTTCAGTGCCAGGGCAATGCGCACCCGGTAGGACGAGGTGGAACGGTAAt                        <  1:1106590/150‑1 (MQ=255)                                                                                                                        cAAGGCCGGTACGCGGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACGCTGCTCACCCTGCAGCAGGTTGACCGGCAGGGACTGGTAAGCCAGCCCCTTCAGTGCCAGGGCAATGCGCACCCGGTAGGACGAGGTGTAACGGTAATa                       <  1:151375/150‑1 (MQ=255)                                                                                                                           ggCCGGTACGCGGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACGCTGCTCACCCTGCAGCAGGTTGACCGGCAGGGACTGGTAAGCCAGCCCCTTCAGTGCCAGGGCAATGCGCACCCGGTAGGACGAGGTGGAACGGTAATAGgt                    <  1:504762/150‑1 (MQ=255)                                                                                                                                 tACGCGGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACGCTGCTCACCCTGCAGCAGGTTGACCGGCAGGGACTGGTAAGCCAGCCCCTTCAGTGCCAGGGCAATGCGCACCCGGTAGGAAGAGGCGGTACGTCAATGTGTGTACAg              <  2:1123023/150‑1 (MQ=255)                                                                                                                                    gcgGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACGCTGCTCACCCTGCAGCAGGTTGACCGGCAGGGACTGGTAAGCCAGCCCCTTCAGTGCTAGGGCAATGCGCACCCGGTAGGACGAGGTGGAACGGTAATAGGTGTACAGCTc           <  2:1065716/150‑1 (MQ=255)                                                                                                                                    gcgGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACGCTGCTCACCCTGCAGCAGGTTGACCGGCAGGGACTGGTAAGCCAGCCCCTTCAGTGCCAGGGCAATGCGCACCCGGTAGGACGAgg                                    >  2:661392/1‑125 (MQ=255)                                                                                                                                    gcgGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACGCTGCTCACCCTGCAGCAGGTTGACCGGCAGGGACTGGTAAGCCAGCCCCTTCAGTGCCAGGGCAATGCGCACCCGGTAGGACGAgg                                    <  1:661392/125‑1 (MQ=255)                                                                                                                                    gcgGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACGCTGCTCACCCTGCAGCAGGTTGACCGGCAGGGACTGGTAAGCCAGCCCCTTCAGTGCCAGGGCAATGCGCACCCGGTAGGACGAGGTGGAACGGTAATAg                      >  2:1007959/1‑139 (MQ=255)                                                                                                                                    gcgGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACGCTGCTCACCCTGCAGCAGGTTGACCGGCAGGGACTGGTAAGCCAGCCCCTTCAGTGCCAGGGCAATGCGCACCCGGTAGGACGAGGTGGAACGGTAATAg                      <  1:1007959/139‑1 (MQ=255)                                                                                                                                          cTGCGGGTTGACGGCTACATAGCCCTCGCCACGCTGCTCACCCTGCAGCAGGTTGACCGGCAGGGACTGGTAAGCCAGCCCCTTCAGTGCCAGGGCAATGCGCACCCGGTAGGACGAGGTGGAACgg                            >  1:936334/1‑127 (MQ=255)                                                                                                                                          cTGCGGGTTGACGGCTACATAGCCCTCGCCACGCTGCTCACCCTGCAGCAGGTTGACCGGCAGGGACTGGTAAGCCAGCCCCTTCAGTGCCAGGGCAATGCGCACCCGGTAGGACGAGGTGGAACgg                            <  2:936334/127‑1 (MQ=255)                                                                                                                                             cGGGGTGACGGCTACATAGCCCGCGCGACGCTGCTCACCCTGCAGTAGGTTGACCGGCAGGGACTGGTAAGCCAGCCCCGTCAGTGCCAGGGCAATGCGCACCCGGTAGGACGAGGTGGAACGGTAATAGGTGTACAGCTCCATAccccg  <  2:3797/150‑2 (MQ=255)                                                                                                                                                  |                                                                                                                                                 CCCCGAACCCTGGCCCGTGCCTCGGCGGTGGCCGGCAGCAACGCAGGCTGTGGATAAACCTCTTCCAGGTACTCGATGATCGCCGGCGACTGCACCAGCACCTCACCACCGTCGGTGCGCAAGGCCGGTACGCGGCCCTGCGGGTTGACGGCTACATAGCCCTCGCCACGCTGCTCACCCTGCAGCAGGTTGACCGGCAGGGACTGGTAAGCCAGCCCCTTCAGTGCCAGGGCAATGCGCACCCGGTAGGACGAGGTGGAACGGTAATAGGTGTACAGCTCCATACCCCT  >  NC_002947/5241636‑5241925

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.