Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC	NC_000913	1,977,451	(CTGGAAAGTTGCAG)1→2	coding (394/579 nt)	flhC ←	DNA‑binding transcriptional dual regulator FlhC

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1977430 =	2 (0.060)	19 (0.560)	19/474	0.7	92.8%	coding (415/579 nt)	flhC	DNA‑binding transcriptional dual regulator FlhC
	?	NC_000913	= 1977443	1 (0.030)					coding (402/579 nt)	flhC	DNA‑binding transcriptional dual regulator FlhC

CGATTGGGGCAAAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAGCCTGTACTCTCTGTTCATCCAGCAGTTGTGGGATAATATCGGCAGGATTCTGGGAAAGTTTACGTCTTTTTACTGCCCGGGATGGCGGTTGACATAAGCTGCAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATTGCCGCCGCAGCAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCGCACCAATGTCCAGGCACGGGTTAATGCCAGCAGTGGTCCTTCTTCTGCTTGTGGGCACTGTTCAAGGTATAAACGGTAGGCTTTGATCACCGCATCGACGCCATTACACAAACCGGTTTTCAGTAAAAACTGCCATGCATTACAGAACATCGAAGCATGAACGTTTTGTTCCCAGGTCATAAACCAGTCGGTTGAGAATGGCAGCATGCCTTTCGGCGGTG  >  NC_000913/1977198‑1977693                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                           aaaagcagcggtacgtcgttaccgctgctggaatgttgcgcctcaccgtatcagttaaacagcctgtactctctgttcatccagcagttgtgggataatatcggcaggattctgggaaagtttacgtctttttactgcccgggatggcggttgacataagctgcaggcaaagctgccaacaggctggtgagcgtgggtaataaaattgccgccgcagcagttgcagctggaaagttgcagctggaaagttg                                                                                                                                                                                                                                                       >  1:355698‑M1/233‑251 (MQ=255) aaaagcagcggtacgacctaaccgctgccggcctgatgcgcctcaccgtatcagtcaaacagcctgtactctctgttcatccagcagttgtgggataatatcggcaggattctgggaaagtttacgtctttttactgcccgggatggcggttgacataagctgaaggcaaagctgccaacaggctggtgagcgtgggtaataaaattgacgccgcagcagttgcagctggaaagttgcagctggaaaggtg                                                                                                                                                                                                                                                       <  2:174936‑M1/19‑4 (MQ=255)        ggCAAAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAGCCTGTACTCTCTGTTCATCCAGCAGTTGTGGGATAATATCGGCAGGATTCTGGGAAAGTTTACGTCTTTTTACTGCCCGGGATGGCGGTTGACATAAGCTGCAGGCAAAGCTGCCAACAGGCGGGTGAGCGGGGGTAATAAAAGTGCCGCCTCAGCAGTTGCAGCTGTAAagttgcagctgg                                                                                                                                                                                                                                                >  2:144246‑M2/1‑239 (MQ=255)             ccgtcgttaccgctgctggaatgttgcgcctcaccgtatcagttaaacagcctgtactctctgttcatccagcagttgtgggataatatcggcaggattctgggaaagtttacgtctttttactgcccgggatggcggttgacataagctgcaggcaaagctgccaacaggctggtgagcgtgggtaataaaattgccgccgcagcagttgcagctggaaAGTTGCAGCTGGAAAGTTGCAGTAATCCACt                                                                                                                                                                                                                                           >  2:334311‑M1/221‑251 (MQ=255)               aaaaGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAGCCTGTACTCTCTGTTCATCCAGCAGTTGTGGGATAATATCGGCAGGATTCTGGGAAAGTTTACGTCTTTTTACTGCCCGGGATGGCGGTTGACATAAGCTGCAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATTGCCGCCGCAGCAGTTGCAGCTGGAAagttgcagctggaaagttg                                                                                                                                                                                                                                         >  1:355698‑M2/1‑232 (MQ=255)               aaaaGCAGCGGTACGACCTAACCGCTGCCGGCCTGATGCGCCTCACCGTATCAGTCAAACAGCCTGTACTCTCTGTTCATCCAGCAGTTGTGGGATAATATCGGCAGGATTCTGGGAAAGTTTACGTCTTTTTACTGCCCGGGATGGCGGTTGACATAAGCTGAAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATTGACGCCGCAGCAGTTGCAGCTGGAAagttgcagctggaaaggtg                                                                                                                                                                                                                                         <  2:174936‑M2/251‑20 (MQ=255)                       cgctgctggaatgttgcgcctcaccgtatcagttaaacagcctgtactctctgttcatccagcagttgtgggataatatcggcaggattctgggaaagtttacgtctttttactgcccgggatggcggttgacataagctgcaggcaaagctgccaacaggctggtgagcgtgggtaataaaattgccgccgcagcagttgcagctggaaAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAAc                                                                                                                                                                                                                                 >  2:99579‑M1/211‑251 (MQ=255)                           ccgtcgttACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAGCCTGTACTCTCTGTTCATCCAGCAGTTGTGGGATAATATCGGCAGGATTCTGGGAAAGTTTACGTCTTTTTACTGCCCGGGATGGCGGTTGACATAAGCTGCAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATTGCCGCCGCAGCAGTTGCAGCTGGAAagttgcagctggaaagttgcagtaatccact                                                                                                                                                                                                                             >  2:334311‑M2/2‑220 (MQ=255)                             tggaatgttgcgcctcaccgtatcagttaaacagcctgtactctctgttcatccagcagttgtgggataatatcggcaggcttctgggaaagtttacgtctttttactgcccgggatggcggttgacataagctgcaggcaaagctgccaacaggctggtgagcgtgggtaataaaattgccgccgcagcagttgcagctggaaAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAAccgcccc                                                                                                                                                                                                                           <  2:356568‑M1/47‑4 (MQ=255)                                     cGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAGCCTGTACTCTCTGTTCATCCAGCAGTTGTGGGATAATATCGGCAGGATTCTGGGAAAGTTTACGTCTTTTTACTGCCCGGGATGGCGGTTGACATAAGCTGCAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATTGCCGCCGCAGCAGTTGCAGCTGGAAagttgcagctggaaagttgcagtaatccactttcaacaaac                                                                                                                                                                                                                   >  2:99579‑M2/1‑210 (MQ=255)                                        gcctcaccgtatcagttaaacagcctgtactctctgttcatccagcagttgtgggctaatatcggcaggattctgggaaagtttacgtctttttactgcccgggatggcggttgacataagctgcaggcaaagctgccaacaggctggtgagcgggggtaataaaattgccgccgcagcagttgcagctggaaAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCGCACCAATGTCCAGGc                                                                                                                                                                                                                <  1:47566‑M1/58‑1 (MQ=255)                                           tgGAATGTTGCGCCTCACCGTATCAGTTAAACAGCCTGTACTCTCTGTTCATCCAGCAGTTGTGGGATAATATCGGCAGGCTTCTGGGAAAGTTTACGTCTTTTTACTGCCCGGGATGGCGGTTGACATAAGCTGCAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATTGCCGCCGCAGCAGTTGCAGCTGGAAagttgcagctggaaagttgcagtaatccactttcaacaaaccgcccc                                                                                                                                                                                                             <  2:356568‑M2/251‑48 (MQ=255)                                            caccgtatcagttaaacagcctgtactctctgttcatccagcagttgtgggataatatcggcaggattctgggaaagtttacgtctttttactgcccgggatggcggttgacataagctgcaggcaaagctgccaacaggctggtgagcgtgggtaataaaattgccgccgcagcagttgcagctggaaAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCGCACCAATGTCCAGGCAc                                                                                                                                                                                                              >  1:148011‑M1/190‑249 (MQ=255)                                                      gcCTCACCGTATCAGTTAAACAGCCTGTACTCTCTGTTCATCCAGCAGTTGTGGGCTAATATCGGCAGGATTCTGGGAAAGTTTACGTCTTTTTACTGCCCGGGATGGCGGTTGACATAAGCTGCAGGCAAAGCTGCCAACAGGCTGGTGAGCGGGGGTAATAAAATTGCCGCCGCAGCAGTTGCAGCTGGAAagttgcagctggaaagttgcagtaatccactttcaacaaaccgcaccaatgtccaggc                                                                                                                                                                                                  <  1:47566‑M2/251‑59 (MQ=255)                                                          cACCGTATCAGTTAAACAGCCTGTACTCTCTGTTCATCCAGCAGTTGTGGGATAATATCGGCAGGATTCTGGGAAAGTTTACGTCTTTTTACTGCCCGGGATGGCGGTTGACATAAGCTGCAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATTGCCGCCGCAGCAGTTGCAGCTGGAAagttgcagctggaaagttgcagtaatccactttcaacaaaccgcaccaatgtccaggcac                                                                                                                                                                                                >  1:148011‑M2/1‑189 (MQ=255)                                                                                                    atcggcaggattctgggaaagtttacgtctttttactgcccgggatggcggttgacataagctgcaggcaaagctgccaacaggctggtgagcgtgggtaataaaattgccgccgcagcagttgcagctggaaAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCGCACCAATGTCCAGGCACGGGTTAATGCCAGCAGTGGTCCGTCTTCTGCTTGTGGGCACTGTTCAAGGTATAAAc                                                                                                                                                     >  2:154244‑M1/134‑250 (MQ=255)                                                                                                               tctgggaaagtttacgtctttttactgcccgggatggcggttgacataagctgcaggcaaagctgccaacaggctggtgagcgtgggtaataaaattgccgccgcagcagttgcagctggaaAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCGCACCAATGTCCAGGCACGGGTTAATGCCAGCAGTGGTCCTTCTTCTTCTTGTGGGCACTGTTCAAGGTATAAACGGTAGGCTTTg                                                                                                                                          >  1:217925‑M1/123‑250 (MQ=255)                                                                                                                  atCGGCAGGATTCTGGGAAAGTTTACGTCTTTTTACTGCCCGGGATGGCGGTTGACATAAGCTGCAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATTGCCGCCGCAGCAGTTGCAGCTGGAAagttgcagctggaaagttgcagtaatccactttcaacaaaccgcaccaatgtccaggcacgggttaatgccagcagtggtccgtcttctgcttgtgggcactgttcaaggtataaac                                                                                                                                       >  2:154244‑M2/1‑133 (MQ=255)                                                                                                                          ttacgtctttttactgcccgggatggcggttgacataagctgcaggcaaagctgccaacaggctggtgagcgtgggtaataaaattgccgccgcagcagttgcagctggaaAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCGCACCAATGTCCAGGCACGGGTTAATGCCAGCAGTGGTCCTTCTTCTGCTTGTGGGCACTGTTCAAGGTATAAACGGTAGGCTTTGATCACCGCATc                                                                                                                               >  1:356568‑M1/112‑250 (MQ=255)                                                                                                                             tCTGGGAAAGTTTACGTCTTTTTACTGCCCGGGATGGCGGTTGACATAAGCTGCAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATTGCCGCCGCAGCAGTTGCAGCTGGAAagttgcagctggaaagttgcagtaatccactttcaacaaaccgcaccaatgtccaggcacgggttaatgccagcagtggtccttcttcttcttgtgggcactgttcaaggtataaacggtaggctttg                                                                                                                            >  1:217925‑M2/1‑122 (MQ=255)                                                                                                                                  ttttactgcccgggatggcggttgacataagctgcaggcaaagctgccaacaggctggtgagcgtgggtaataaaattgccgccgcagcagttgcagctggaaAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCGCACCAATGTCCAGGCACGGGTTAATGCCAGCAGTGGTCCTTCTTCTGCTTGTGGGCACTGTTCAAGGTATAAACGGTAGGCTTTGATCACCGCATCGACGcc                                                                                                                         >  1:100777‑M1/104‑248 (MQ=255)                                                                                                                                       ctgcccgggatggcggttgacataagctgcaggcaaagctgccaacaggctggtgagcgtgggtaataaaattgccgccgcagcagttgcagctggaaAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCGCACCAATGTCCAGGCACGGGTTAATGCCAGCAGTGGTCCTTCTTCTGCTTGTGGGCACTGTTCAAGGTATAAACGGTAGGCTTTGATCACCGCATCGACGCCATTacac                                                                                                                  <  2:163011‑M1/152‑1 (MQ=255)                                                                                                                                        ttACGTCTTTTTACTGCCCGGGATGGCGGTTGACATAAGCTGCAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATTGCCGCCGCAGCAGTTGCAGCTGGAAagttgcagctggaaagttgcagtaatccactttcaacaaaccgcaccaatgtccaggcacgggttaatgccagcagtggtccttcttctgcttgtgggcactgttcaaggtataaacggtaggctttgatcaccgcatc                                                                                                                 >  1:356568‑M2/1‑111 (MQ=255)                                                                                                                                                ttttACTGCCCGGGATGGCGGTTGACATAAGCTGCAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATTGCCGCCGCAGCAGTTGCAGCTGGAAagttgcagctggaaagttgcagtaatccactttcaacaaaccgcaccaatgtccaggcacgggttaatgccagcagtggtccttcttctgcttgtgggcactgttcaaggtataaacggtaggctttgatcaccgcatcgacgcc                                                                                                           >  1:100777‑M2/1‑103 (MQ=255)                                                                                                                                                     cTGCCCGGGATGGCGGTTGACATAAGCTGCAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATTGCCGCCGCAGCAGTTGCAGCTGGAAagttgcagctggaaagttgcagtaatccactttcaacaaaccgcaccaatgtccaggcacgggttaatgccagcagtggtccttcttctgcttgtgggcactgttcaaggtataaacggtaggctttgatcaccgcatcgacgccattacac                                                                                                    <  2:163011‑M2/250‑153 (MQ=255)                                                                                                                                                                          aagctgccaacaggctggtgagcgtgggaaataaaattgccgccgcagcagttgcagctggaaAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCGCACCAATGTCCAGGCACGGGTTAATGCCAGCAGTGGTCCTTCTTCTGCTTGTGGGCACTGTTCAAGGTATAAACGGTAGGCTTTGATCACCGCATCGACGCCATTACACAAACCGGTTTTCAGTAAAAACTGCCATGCATTAc                                                                                <  2:156332‑M1/186‑1 (MQ=255)                                                                                                                                                                                        aaGCTGCCAACAGGCTGGTGAGCGTGGGAAATAAAATTGCCGCCGCAGCAGTTGCAGCTGGAAagttgcagctggaaagttgcagtaatccactttcaacaaaccgcaccaatgtccaggcacgggttaatgccagcagtggtccttcttctgcttgtgggcactgttcaaggtataaacggtaggctttgatcaccgcatcgacgccattacacaaaccggttttcagtaaaaactgccatgcattac                                                                  <  2:156332‑M2/249‑187 (MQ=255)                                                                                                                                                                                                                      gcagcagttgcagctggaaAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCGCACCAATGTCCAGGCACGGGTTAATGCCAGCAGTGGTCCTTCTTCTGCTTGTGGGCACTGTTCAAGGTATAAACGGTAGGCTTTGATCACCGCATCGACGCCATTACACAAACCGGTTTTCAGTAAAAACTGCCATGCATTACAGAACATCGAAGCATGAACGTTTTGTTCCCAGGTCATAAACCAGTc                                  >  2:47566‑M1/20‑251 (MQ=255)                                                                                                                                                                                                                            gttgcagctggaaAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCGCACCAATGTCCAGGCACGGGTTAATGCCAGCAGTGGTCCTTCTTCTGCTTGTGGGCACTGTTCAAGGTATAAACGGTAGGCTTTGATCACCGCATCGACGCCATTACACAAACCGGTTTTCAGTAAAAACTGcc                                                                                         >  1:120805‑M1/14‑190 (MQ=255)                                                                                                                                                                                                                            gttgcagctggaaAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCGCACCAATGTCCAGGCACGGGTTAATGCCAGCAGTGGTCCTTCTTCTGCTTGTGGGCACTGTTCAAGGTATAAACGGTAGGCTTTGATCACCGCATCGACGCCATTACACAAACCGGTTTTCAGTAAAAACTGcc                                                                                         <  2:120805‑M1/177‑1 (MQ=255)                                                                                                                                                                                                                                    gcagcaGTTGCAGCTGGAAagttgcagctggaaagttgcagtaatccactttcaacaaaccgcaccaatgtccaggcacgggttaatgccagcagtggtccttcttctgcttgtgggcactgttcaaggtataaacggtaggctttgatcaccgcatcgacgccattacacaaaccggttttcagtaaaaactgccatgcattacagaacatcgaagcatgaacgttttgttcccaggtcataaaccagtc                    >  2:47566‑M2/1‑19 (MQ=255)                                                                                                                                                                                                                                     ggaaAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCTACAAACCGCACCAATGTCCAGGCACGGGTTAATGCCAGCAAGGGTCCTTCTTCTGCGTGTGGGCACTGTTCAAGGTATAAACGGTAGGCTTTGATCACCGCATCGACCCCAGTACGCAAACCGGTTTTCAGTAAAAACTGCCATGCAGTTCAGAAGATGGAAGCATGAACTTTTTGTTCCCAAATCATAGACCAGTCGATTGATAATGgc                     >  2:30777‑M1/5‑249 (MQ=255)                                                                                                                                                                                                                                        aAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCGCACCAATGTCCAGGCACGGGTTAATGCCAGCAGTGGTCCTTCTTCTGCTTGTGGGCACTGTTCAAGGTATAAACGGTAGGCTTTGATCACCGCATCGACGCCATTACACAAACCGGTTTTCAGTAAAAACTGCCATGCATTACAGAACATCGAAGCATGAACGTTTTGTTCCCAGGTCATAAACCAGTCGGTTGAGAATGGCAGCAt                >  1:304644‑M1/2‑251 (MQ=255)                                                                                                                                                                                                                                          gttgcagctggaaagttgcagctggaaagttgcagtaatccactttcaacaaaccgcaccaatgtccaggcacgggttaatgccagcagtggtccttcttctgcttgtgggcactgttcaaggtataaacggtaggctttgatcaccgcatcgacgccattacacaaaccggttttcagtaaaaactgcc                                                                           >  1:120805‑M2/1‑13 (MQ=255)                                                                                                                                                                                                                                          gttgcagctggaaagttgcagctggaaagttgcagtaatccactttcaacaaaccgcaccaatgtccaggcacgggttaatgccagcagtggtccttcttctgcttgtgggcactgttcaaggtataaacggtaggctttgatcaccgcatcgacgccattacacaaaccggttttcagtaaaaactgcc                                                                           <  2:120805‑M2/190‑178 (MQ=255)                                                                                                                                                                                                                                             gCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCGCACCAATGTCCAGGCACGGGTTAATGCCAGCAGTGGTCCTTCTTCTGCTTGTGGGCACTGTTCAAGGTATAAACGGTAGGCTTTGATCACCGCATCGACGCCATTACACAAACCGGTTTTCAGTAAAAACTGCCATGCATTACAGAACATCGAAGCATGAACGTTTTGTTCCCAGGTCATAAACCAGTCGGTTGAGAATGGCAGCATGCCtt           <  2:95959/251‑1 (MQ=255)                                                                                                                                                                                                                                                   ggaaagttgcagctggaaagttgcagtaatccactttctacaaaccgcaccaatgtccaggcacgggttaatgccagcaagggtccttcttctgcgtgtgggcactgttcaaggtataaacggtaggctttgatcaccgcatcgaccccagtacgcaaaccggttttcagtaaaaactgccatgcagttcagaagatggaagcatgaactttttgttcccaaatcatagaccagtcgattgataatggc       >  2:30777‑M2/1‑4 (MQ=255)                                                                                                                                                                                                                                                      aagttgcagctggaaagttgcagtaatccactttcaacaaaccgcaccaatgtccaggcacgggttaatgccagcagtggtccttcttctgcttgtgggcactgttcaaggtataaacggtaggctttgatcaccgcatcgacgccattacacaaaccggttttcagtaaaaactgccatgcattacagaacatcgaagcatgaacgttttgttcccaggtcataaaccagtcggttgagaatggcagcat  >  1:304644‑M2/1‑1 (MQ=255)                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                           CGATTGGGGCAAAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTCACCGTATCAGTTAAACAGCCTGTACTCTCTGTTCATCCAGCAGTTGTGGGATAATATCGGCAGGATTCTGGGAAAGTTTACGTCTTTTTACTGCCCGGGATGGCGGTTGACATAAGCTGCAGGCAAAGCTGCCAACAGGCTGGTGAGCGTGGGTAATAAAATTGCCGCCGCAGCAGTTGCAGCTGGAAAGTTGCAGTAATCCACTTTCAACAAACCGCACCAATGTCCAGGCACGGGTTAATGCCAGCAGTGGTCCTTCTTCTGCTTGTGGGCACTGTTCAAGGTATAAACGGTAGGCTTTGATCACCGCATCGACGCCATTACACAAACCGGTTTTCAGTAAAAACTGCCATGCATTACAGAACATCGAAGCATGAACGTTTTGTTCCCAGGTCATAAACCAGTCGGTTGAGAATGGCAGCATGCCTTTCGGCGGTG  >  NC_000913/1977198‑1977693

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ 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.