New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_010473	285519 =	67 (1.750)	46 (1.200)	41/398	0.1	40.7%	intergenic (‑74/+1)	ecpA/ecpR	common pilus major fimbrillin subunit EcpA/ECP biosynthesis operon DNA‑binding transcriptional regulator EcpR
	?	NC_010473	319815 =	NA (NA)					coding (28/444 nt)	ECDH10B_RS01610	transferase

TCCAGACGATGATTACTGGTACGTACTTGTGCGCCTAAATATGCCTGGTTTGCAACTACCGAGTCGGCAATAAAACATTGCGGACCAATCGTTGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGT‑GCCAGGACGAATAAACGCATAATTACT‑‑AGACTGGCCCCCTGAATC‑TCCA‑GACAACCAATAT‑CACTTAAATAAGTGATAGTCTTAATACT‑A‑GTTTTTAGACT‑AGTCATTGGAGAACAGATGATTGA‑TGTCTT‑AGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCGCAATTGTTCAGCAGAGCTTTGAACCGGGGATGACGGTCTCCCTC  >  NC_010473/319625‑320007                                                                                                                                                                                                |                                                                                                                                                                                                           tCCAGACGATGATTACTGGTACGTACTTGTGCGCCTAAATATGCCTGGTTTGCAACTACCGAGTCGGCAATAAAACATTGCGGACCAATCGTTGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGT‑GCCAGGACGAATAAAAGCATAATTACT‑‑AGACTGGcc                                                                                                                                                                                                 >  1:1139S31/1‑200 (MQ=255)  ccAGACGATGATTACTGGTACGTACTTGTGCGCCTAAATATGCCTGGTTTGCAACTACCGAGTCGGCAATAAAACATTGCGGACCAATCGTTGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGT‑GCCAGGACGAATAAACGCATAATTACT‑‑AGACTGGccc                                                                                                                                                                                                >  1:14167S103/1‑200 (MQ=255)         atgatTACTGGTACGTACTTGTGCGCCTAAATATGCCTGGTTTGCAACTACCGAGTCGGCAATAAAACATTGCGGACCAATCGTTGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGT‑GCCAGGACGAATAAACGCATAATTACT‑‑AGACTGGCCCCCTGAAt                                                                                                                                                                                         <  1:19047S6/200‑1 (MQ=255)          tgatTACTGGTACGTACTTGTGCGCCTAAATATGCCTGGTTTGCAACTACCGAATCGGCAATAAAACATTGCGGACCAATCGTTGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGT‑GCCAGGACGAATAAACGCATAATTACT‑‑AGACTGGCCCCCTGAAtc                                                                                                                                                                                        <  1:19952S2/200‑1 (MQ=255)               aCTGGTACGTACTTGTGCGCCTAAATATGCCTGGTTTGCAACGACCCAGTCGGCAATAAAACATTGCGGACCAATCGTTGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGT‑GCCAGGACGAATAAACGCATAATTACT‑‑‑GACCGGCCCC‑‑GAATC‑TCCA‑GACa                                                                                                                                                                              <  1:31494S55/200‑1 (MQ=255)                  ggTACGTACTTGTGCGCCTAAATATGCCTGGTTTGCAACTACCGAGTCGGCAATAAAACATTGCGGACCAATCGTTGCTCCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTGCTGTTGCCAGGACGAATAAACGCATAATTACT‑‑AGACTGGCCCCCTGAATC‑TCCA‑GAc                                                                                                                                                                               >  1:29146S17/1‑200 (MQ=255)                  ggTACGTACTTGTGCGCCTAAATATGCCTGGTTTGCAACTACCGAGTCGGCAATAAAACATTGCGGACCAATAGTTACTTC‑‑CTTCAATGACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGT‑GCCAGGACGAATAAACGCATAATTACT‑‑AGACTGGCCCCCTGAATC‑TCCA‑GACAAc                                                                                                                                                                            >  1:29546S13/1‑200 (MQ=255)                                  ccTAAATATGCCTGGTTTGCAACTACCGAGTCGGCAATAAAACATTGCGGACCAATCGTTGCTTCCGCTTCAATGACCG‑‑‑‑‑TTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGT‑GCCAGGACGAATAAACGCATAATTACT‑‑AGACTGGCCCCCTGAATC‑TCCA‑GACAACCAATAT‑CACTTAAATAAGt                                                                                                                                                        >  1:20622S109/1‑200 (MQ=39)                                              tGGTTTGCAACTACCGAGTCGGCAATAAAACATTGCGGACCAATCGTTGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTCATTATTGT‑GCCAGGACGAATAAACGCATAATTACT‑‑AGACCGGCCCC‑‑GAATC‑TCCA‑GACAACCAATAT‑CACTTAAATAAGTGATAGTCtt                                                                                                                                               <  1:28102S7/200‑1 (MQ=255)                                                 tttGCAACTACCGAGTCGGCAATAAAACATTGCGGACCAATCGTTGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGT‑GCCAGGACGAATAAACGCATAATTACT‑‑AGACTGGCCCCCTGAATC‑TCCA‑GACAACCAATAT‑CACTTAAATAAGTGATAGTCTTa                                                                                                                                              >  1:22399S16/1‑200 (MQ=40)                                                 tttGCAACTACCGAGTCGGCAATAAAACATTGCGGACCAATCGTTGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGT‑GCCAGGACGAATAAACGCATAATTACT‑‑AGACTGGCCCC‑‑‑ACTC‑TCCA‑GACAACCAATAT‑CACTTAAATAAGTGATAGTCTTAATa                                                                                                                                           <  1:1153S65/200‑1 (MQ=255)                                                       aCTACCGAGTCGGCAATAAAACATTGCGGACCAATCGTTGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGT‑GCCAGGACGAATAAACGCATAATTACT‑‑AGACTGGCCCCCTGAATC‑TCCA‑GACAACCAATAT‑CACTTAAATAAGTGATAGTCTTAATACT‑a                                                                                                                                       >  1:10419S17/1‑200 (MQ=39)                                                           ccGAGTCGGCAATAAAACATTGCGGACCAATCGTTGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGT‑GCCAGGACGAATAAACGCATAATTACT‑‑AGACTGGCCCCCTGAATC‑TCCA‑GACAACCAATAT‑CACTTAAATAAGTGATAGT‑ATAATACT‑A‑Gtttt                                                                                                                                 >  1:11383S16/1‑200 (MQ=39)                                                               gTCGGCAATAAAACATTGCGGACCAATCGTTGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGT‑GCCAGGACGAATAAACGCATAATTACT‑‑AGACTGGCCCCCTGAATC‑TCCA‑GACAACCAATAT‑CACTTAAATAAGTGATAGTCTTAATACT‑A‑GTTTTTAg                                                                                                                              >  1:3548S30/1‑200 (MQ=39)                                                               gTCGGCAATAAAACATTGCGGACCAATCGTTGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGT‑GCCAGGACGAATAAACGCATAATTACT‑‑AGACTGGCCCCCTGAATC‑TCCA‑GACAACCAATAT‑CACTTAAATAAGTGATAGTCTTAATACT‑A‑GTTTTTAg                                                                                                                              <  1:24163S60/200‑1 (MQ=39)                                                                     aaTAAAGCATTGCGGACCAATCGTTGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGT‑GCCAGGACGAATAAACGCATAATTACT‑‑AGACTGGCCCCCTGAATC‑TCCA‑GACAACCAATAT‑CACTTAAATAAGTGATAGTCTTAATACT‑A‑GTTTTTAGACT‑AGt                                                                                                                       <  1:16100S222/200‑1 (MQ=38)                                                                        aaaaCATTGCGGACCAATCGTTGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGT‑GCCAGGACGAATAAACGCATAATTACT‑‑AGACTGGCCCCCTGAATC‑TCCA‑GACAACCAATAT‑CACTTAAATAAGTGATAGTCTTAATACT‑A‑GTTTTTAGACT‑AGTCAt                                                                                                                    <  1:11700S1/200‑1 (MQ=38)                                                                            cATTGCGGACCAATCGTTGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGT‑GCCAGGACGAATAAACGCATAATTACT‑‑AGACTGGCCCCCTGAATC‑TCCA‑GACAACCAATAT‑CACTTAAATAAGTGATAGTCTTAATACT‑A‑GTTTTTAGACT‑AGTCATTGga                                                                                                                <  1:19872S60/200‑1 (MQ=38)                                                                                 cGGACCAATCGTTGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGT‑GCCAGGACGAATAAACGCATAATTACT‑‑AGACTGGCCCCCTGAATC‑TCCA‑GACAACCAATAT‑CACTTAAATAAGTGATAGTCTTAATACT‑A‑GTTTTTAGACT‑AGTCATTGGAGAACa                                                                                                           <  1:27060S19/200‑1 (MQ=38)                                                                                  ggACCAATCGTTGCTTCCGCTCGAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGT‑GCCAGGACGAATAAACGCATAATTACT‑‑AGACTGGCCCCCTGAATC‑TCCA‑GACAACCAATAT‑CACTTAAATAAGTGATAGTCTTAATACT‑A‑GTTTTTAGACT‑AGTCATTGGAGAACAg                                                                                                          >  1:27771S11/1‑200 (MQ=37)                                                                                    aCCAATCGTTGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGT‑GCCAGGACGAATAAACGCATAATTACT‑‑AGACTGGCCCCCTGAATC‑TCCA‑GACAACCAATAT‑CACTTAAATAAGTGATAGTCTTAATACT‑A‑GTTTTTAGACT‑AGTCATTGGAGAACAgat                                                                                                        <  1:16495S19/200‑1 (MQ=37)                                                                                       aaTCGTTGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGT‑GCCAGGACGAATAAACGCATAATTACT‑‑AGACTGGCCCCCTGAATC‑TCCA‑GACAACCAATAT‑CACTTAAATAAGTGATAGTCTTAATACT‑A‑GTTTTTAGACT‑AGTCATTGGAGAACAgatgat                                                                                                     <  1:22621S36/200‑1 (MQ=37)                                                                                          cGTTGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGT‑GCCAGGACGAATAAACGCATAATTACT‑‑AGACTGGCCCCC‑GTATCCTCCA‑GACAACCAATAT‑CACTTAAATAAGTGATAGTCTTAATACT‑A‑GTTTTTAGACT‑AGTCATTGGAGAACAGAtgattga                                                                                                  <  1:24923S134/200‑1 (MQ=37)                                                                                               cTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGT‑GCCAGGACGAATAAACGCATAATTACT‑‑AGACTGGCCCCCTGAATC‑TCCA‑GACAACCAATAT‑CACTTAAATAAGTGATAGTCTTAATACT‑A‑GTTTTTAGACT‑AGTCATTGGAGAACAGATGATTGA‑TGTCt                                                                                            <  1:19014S18/200‑1 (MQ=37)                                                                                                 tCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGT‑GCCAGGACGAATAAACGCATAATTACT‑‑AGACTGGCCCCCTGAATC‑TCCA‑GACAACCAATAT‑CACTTAAATAAGTGATAGTCTTAATATTTA‑GTTTTTAGACT‑AGTCATTGGAGAACAGATGATTGA‑TGTCtt                                                                                           >  1:23365S10/1‑200 (MQ=25)                                                                                                  ccGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGT‑GCCAGGACGAATAAACACATAATTACT‑‑AGACTGGCCCCCTGAATC‑TCCA‑GACAACCAATAT‑CACTTAAATAAGTGATAGTCTTAATACT‑A‑GTTTTTAGACT‑AGTCATTGGAGAACAGATGATTGA‑TGTCTT‑Ag                                                                                        >  1:30354S108/1‑200 (MQ=25)                                                                                                           tAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGT‑GCCAGGACGAATAAACGCATAATTACT‑‑AGACTGGCCCCCTGAATC‑TCCA‑GACAACCAATAT‑CACTTAAATAAGTGATAGTCTTAATACT‑A‑GTTTTTAGACT‑AGTCATTGGAGAACAGATGATTGA‑TGTCTT‑AGGGCCGgaga                                                                               <  1:12864S9/200‑1 (MQ=35)                                                                                                              ccGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGT‑GCCAGGACGAATAAACGCATAATTACT‑‑AGACTGGCCCCCTGAATC‑TCCA‑GACAACCAATAT‑CACTTAAATAAGTGATAGTCTTAATACT‑AAGATTTT‑GACTTAGTCATTGGAGAACAGATGATTGA‑TGTCTT‑AGGGCCGGAGaaa                                                                             >  1:5362S65/1‑200 (MQ=25)                                                                                                                 cATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGT‑GCCAGGACGAATAAACGCATAATTGCTACAGACTGGCCCCCTGAATC‑TCCA‑GACAACCAATATTCACTTAAATAAGTGATAGTCTTAATACT‑A‑GTTTTTAGACT‑AGTCATTGGAGAACAGATGATTGA‑TGTCT‑‑‑GGGCCGGAGAAACGc                                                                          >  1:8970S26/1‑200 (MQ=21)                                                                                                                          tctcGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGT‑GCCAGGACGAATAAACGCATAATTACT‑‑AGACTGGCCCCCTGAATC‑TCCA‑GACAACCAATAT‑CACTTAAATAAGTGATAGTCTTAATACT‑A‑GTTTTTAGACT‑AGTCATTGGAGAACAGATGATTGA‑TGTCTT‑AGGGCCGGAGAAACGCAGACGGCGTa                                                                >  1:27039S18/1‑200 (MQ=34)                                                                                                                             cGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGT‑GCCAGGACGAATAAACGCATAATTACT‑‑AGACTGGCCCCCTGAATC‑TCCA‑GACAACCAATAT‑CACTTAAATAAGTGATAGTCTTAATACT‑A‑CGTTTCAGACT‑AGTCATTGGAGAACAGATGATTGA‑TGTCTT‑AGGGCCGGAGAAACGCAGACGGCGTACca                                                             >  1:15384S2/1‑200 (MQ=21)                                                                                                                              ggTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGT‑GCCAGGACGAATATACGCATAATTACT‑‑AGACTGGCCCCCTGAATC‑TCCA‑GACAACCAATAT‑CACTAAAATAAGTGATAGTCTTAATACT‑A‑GTTTTTAGACT‑AGTCATTGGAGAACAGATGATTGA‑TGTCTT‑AGGGCCGGAGAAACGCAGACGGCGTACcac                                                            <  1:23371S46/200‑1 (MQ=18)                                                                                                                              ggTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGT‑GCCAGGACGAATAAACGCATAATTACT‑‑AGACTGGCCCCCTGAATC‑TCCA‑GACAACCAATAT‑CACTTAAATAAGTGATAGTCTTAATACT‑A‑GTTTTTAGACT‑AGTCATTGGAGAACAGATGATTGA‑TGTCTT‑AGGGCCGGAGAAACGCAGACGGCGTACcac                                                            >  1:13923S17/1‑200 (MQ=34)                                                                                                                                     aaaCCAATTTTTACGCCATTGCTGATTATTG‑‑GC‑GCGACCAATAAACGCATAATTACT‑‑AGACTGGCCCCCTGAATC‑TCCA‑GACAACCAATAT‑CACTTAAATAAGTGATAGTCTTAATACT‑A‑GTTTTTAGACT‑AGTCATTGGAGAACAGATGATTGA‑TGTCTT‑AGGGCCGGAGAAACGCAGACGGCGTACCACACAGGaaaa                                                   <  1:512S27/200‑1 (MQ=17)                                                                                                                                                tACGCCATTGCTGATTATTGT‑GCCAGGACGAATAAACGCATAATTACT‑‑AGACTGGCCCCCTGAATC‑TCCAATACAACCAATAT‑CACTTAAATAAGTGATAGTCTTAATACT‑A‑GTTTTTAGACT‑AGTCATTGGAGAACAGATGATTGAGTTGCTCCAGGCCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCGc                                             <  1:3689S27/200‑1 (MQ=17)                                                                                                                                                      aTTGCTGATTATTGT‑GCCAGGACGAATAAACGCATAATTACT‑‑AGACTGGCCCCCTGA‑TC‑TCCA‑GACAACCAATAT‑CACTTAAATAAGTGATAGTCTTAATGCT‑C‑GTTTC‑AGAC‑‑‑‑TCAGTG‑‑GAACAGATGATTGA‑TGTCTT‑AGGGC‑‑‑A‑AAACGCAGACGGCGTACCACACAGGAAAAGATCGCAATTGTTCAGCAGAGCTTTg                         >  1:22284S130/1‑200 (MQ=17)                                                                                                                                                           tGATTATTGT‑GCCAGGACGAATAAACGCATAATTACT‑‑TTACTGGCCCCCTGAATC‑TCCA‑GACAACCAATAT‑CACTTAAATAAGTGATAGTCTTAATACT‑A‑GTTTTTAGACT‑AGTCATTGGAGAACAGATGATTGA‑TGTCTT‑AGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATTGCAATTGTTCAGCaga                               <  1:31135S13/200‑1 (MQ=17)                                                                                                                                                                           gACGAATAAACGCATAATTACT‑‑AGACTGGCCCCCTGAATC‑TCCA‑GACAACCAATAT‑CACTTAAATAAGTGATAGTCTTAATACT‑A‑GTTTTTAGACT‑AGTCATTGGAGAACAGATGATTGA‑TGTCTT‑AGGGCCGGAGAAACGCAGACGGCGTACCACACAG‑AAAAGATCGCAATTGTTCAGCAGAGCTTTGAACCGGGGAt               <  1:23822S9/200‑1 (MQ=14)                                                                                                                                                                             ccaaTAAACGCATAATTACT‑‑AGACTGGCCCCCTGAATC‑TCCA‑GACAACCAATAT‑CACTTAAATAAGTGATAGTCTTAATACT‑A‑GTTTTTAGACT‑AGTCATTGGAGAACAGATGATTGA‑TGTCTT‑AGGGC‑GGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCGCAATTGTTCAGCAGAGCTTTGAACCGGGGATGa             <  1:22586S5/198‑1 (MQ=11)                                                                                                                                                                                      gCATAATTACT‑‑AGACTGGCCCCCTGAATC‑TCCA‑GACAACCAATAT‑CACTTAAATAAGTGATAGTCTTAATACT‑A‑GTTTTTAGACT‑AGTCATTGGAGAACAGATGATTGA‑TGTCTT‑AGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCGCAATTGTTCAGCAGAGCTTTGAACCGGGGATGACGGTCTcc     >  1:5210S5/1‑200 (MQ=11)                                                                                                                                                                                         tAATTACT‑‑AGACTGGCCCCCTGAATC‑TCCA‑GACAACCAATAT‑CACTTAAATAAGTGATAGTCTTAATACT‑A‑GTTTTTAGACT‑AGTCATTGGAGAACAGATGATTGA‑TGTCTT‑AGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCGCAATTGTTCAGCAGAGCTTTGAACCGGGGacgacgattctcgtt  <  1:2689S38/200‑10 (MQ=11)                                                                                                                                                                                                |                                                                                                                                                                                                           TCCAGACGATGATTACTGGTACGTACTTGTGCGCCTAAATATGCCTGGTTTGCAACTACCGAGTCGGCAATAAAACATTGCGGACCAATCGTTGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATTGT‑GCCAGGACGAATAAACGCATAATTACT‑‑AGACTGGCCCCCTGAATC‑TCCA‑GACAACCAATAT‑CACTTAAATAAGTGATAGTCTTAATACT‑A‑GTTTTTAGACT‑AGTCATTGGAGAACAGATGATTGA‑TGTCTT‑AGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCGCAATTGTTCAGCAGAGCTTTGAACCGGGGATGACGGTCTCCCTC  >  NC_010473/319625‑320007

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 50 ≤ 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.