Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC JC	NC_000913	1,673,883	IS5 (–) +4 bp	intergenic (‑382/‑27)	mdtJ ← / → tqsA	multidrug efflux system transporter/pheromone AI‑2 transporter

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1673883 =	0 (0.000)	46 (0.780)	42/298	0.8	100%	intergenic (‑382/‑30)	mdtJ/tqsA	multidrug efflux system transporter/pheromone AI‑2 transporter
	?	NC_000913	= 2290113	NA (NA)					noncoding (1/1195 nt)	IS5	repeat region
*	?	NC_000913	= 1673886	0 (0.000)	51 (0.860)	45/298	0.6	100%	intergenic (‑385/‑27)	mdtJ/tqsA	multidrug efflux system transporter/pheromone AI‑2 transporter
	?	NC_000913	2101749 =	NA (NA)					noncoding (1195/1195 nt)	IS5	repeat region

TCGTCATCGCGGATGATAATTGTCCTCGGTAGTTGAACACGCCTGATTTGTATCATAGCTTAAGAATTAACTCAAAATATTTTCACTTCTTTACCTGAGCGGTTTGATTTTCGTTATGATGACGGAGCGAAAAAGACATTATTATTAG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/1673739‑1673886 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCAGTTT  >  NC_000913/2101749‑2101894                                                                                                                                                                                                                                                                                                        TCGTCATCGCGGATGATAATTGTCCTCGGTAGTTGAACACGCCTGATTTGTATCATAGCTTAAGAATTAACTCAAAATATTTTCACTTCTTTACCTGAGCGGTTTGATTTTCGTTATGATGACGGAGCGAAAAAGACATTATTATTAGGG                                                                                                                                                  >  2:821210/1‑150   GTCATCGCGGATGATAATTGTCCTCGGTAGTTGAACACGCCTGATTTGTATCATAGCTTAAGAATTAACTCAAAATATTTTCACTTCTTTACCTGAGCGGTTTGATTTTCGTTATGATGACGGAGCGAAAAAGACATTATTATTAGGGAAG                                                                                                                                               <  1:719643/151‑1    TCATCGCGGATGATAATTGTCCTCGGTAGTTGAACACGCCTGATTTGTATCATAGCTTAAGAATTAACTCAAAATATTTTCACTTCTTTACCTGAGCGGTTTGATTTTCGTTATGATGACGGAGCGAAAAAGACATTATTATTAGGGAAGG                                                                                                                                              >  2:661429/1‑151           GGATGATAATTGTCCTCGGTAGTTGAACACGCCTGATTTGTATCATAGCTTAAGAATTAACTCAAAATATTTTCACTTCTTTACCTGAGCGGTTTGATTTTCGTTATGATGACGGAGCGAAAAAGACATTATTATTAGGGAAGGTGCGAAT                                                                                                                                       >  1:258788/1‑151           GGATGATAATTGTCCTCGGTAGTTGAACACGCCTGATTTGTATCATAGCTTAAGAATTAACTCAAAATATTTTCACTTCTTTACCTGAGCGGTTTGATTTTCGTTATGATGACGGAGCGAAAAAGACATTATTATTAGGGAAGGTGCGAAT                                                                                                                                       <  2:714877/151‑1             ATGATAATTGTCCTCGGTAGTTGAACACGCCTGATTTGTATCATAGCTTAAGAATTAACTCAAAATATTTTCACTTCTTTACCTGAGCGGTTTGATTTTCGTTATGATGACGGAGCGAAAAAGACATTATTATTAGGGAAGGTGCGAATAA                                                                                                                                     <  2:322585/151‑1              TGATAATTGTCCTCGGTAGTTGAACACGCCTGATTTGTATCATAGCTTAAGAATTAACTCAAAATATTTTCACTTCTTTACCTGAGCGGTTTGATTTTCGTTATGATGACGGAGCGAAAAAGACATTATTATTAGGGAAGGTGCGAATA                                                                                                                                      >  1:518061/1‑149                   ATTGTCCTCGGTAGTTGAACACGCCTGATTTGTATCATAGCTTAAGAATTAACTCAAAATATTTTCACTTCTTTACCTGAGCGGTTTGATTTTCGTTATGATGACGGAGCGAAAAAGACATTATTATTAGGGAAGGTGCGAATAAGCGGGG                                                                                                                               >  2:80153/1‑151                            GGTAGTTGAACACGCCTGATTTGTATCATAGCTTAAGAATTAACTCAAAATATTTTCACTTCTTTACCTGAGCGGTTTGATTTTCGTTATGATGACGGAGCGAAAAAGACATTATTATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTC                                                                                                                      >  1:614219/1‑151                               AGTTGAACACGCCTGATTTGTATCATAGCTTAAGAATTAACTCAAAATATTTTCACTTCTTTACCTGAGCGGTTTGATTTTCGTTATGATGACGGAGCGAAAAAGACATTATTATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCG                                                                                                                   <  1:919609/151‑1                               AGTTGAACACGCCTGATTTGTATCATAGCTTAAGAATTAACTCAAAATATTTTCACTTCTTTACCTGAGCGGTTTGATTTTCGTTATGATGACGGAGCGAAAAAGACATTATTATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTC                                                                                                                    <  1:529697/150‑1                                GTTGAACACGCCTGATTTGTATCATAGCTTAAGAATTAACTCAAAATATTTTCACTTCTTTACCTGAGCGGTTTGATTTTCGTTATGATGACGGAGCGAAAAAGACATTATTATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCG                                                                                                                   <  1:68408/150‑1                                    AACACGCCTGATTTGTATCATAGCTTAAGAATTAACTCAAAATATTTTCACTTCTTTACCTGAGCGGTTTGATTTTCGTTATGATGACGGAGCGAAAAAGACATTATTATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGA                                                                                                              <  2:339257/151‑1                                    AACACGCCTGATTTGTATCATAGCTTAAGAATTAACTCAAAATATTTTCACTTCTTTACCTGAGCGGTTTGATTTTCGTTATGATGACGGAGCGAAAAAGACATTATTATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTG                                                                                                               >  2:519961/1‑150                                       ACGCCTGATTTGTATCATAGCTTAAGAATTAACTCAAAATATTTTCACTTCTTTACCTGAGCGGTTTGATTTTCGTCATGATGACGGAGCGAAAAAGACATTATTATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTC                                                                                                           >  2:238090/1‑151                                        CGCCTGATTTGTATCATAGCTTAAGAATTAACTCAAAATATTTTCACTTCTTTACCTGAGCGGTTTGATTTTCGTTATGATGACGGAGCGAAAAAGACATTATTATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCA                                                                                                          <  2:319999/151‑1                                                TTGTATCATAGCTTAAGAATTAACTCAAAATATTTTCACTTCTTTACCTGAGCGGTTTGATTTTCGTTATGATGACGGAGCGAAAAAGACATTATTATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTT                                                                                                   <  1:246316/150‑1                                                 TGTATCATAGCTTAAGAATTAACTCAAAATATTTTCACTTCTTTACCTGAGCGGTTTGATTTTCGTTATGATGACGGAGCGAAAAAGACATTATTATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTC                                                                                                  >  2:268455/1‑150                                                   TATCATAGCTTAAGAATTAACTCAAAATATTTTCACTTCTTTACCTGAGCGGTTTGATTTTCGTTATGATGACGGAGCGAAAAAGACATTATTATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATT                                                                                               >  1:900179/1‑151                                                             TAAGAATTAACTCAAAATATTTTCACTTCTTTACCTGAGCGGTTTGATTTTCGTTATGATGACGGAGCGAAAAAGACATTATTATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGT                                                                                      <  2:872386/150‑1                                                               AGAATTAACTCAAAATATTTTCACTTCTTTACCTGAGCGGTTTGATTTTCGTTATGATGACGGAGCGAAAAAGACATTATTATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTG                                                                                   >  2:193249/1‑151                                                                GAATTAACTCAAAATATTTTCACTTCTTTACCTGAGCGGTTTGATTTTCGTTATGATGACGGAGCGAAAAAGACATTATTATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTCCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTT                                                                                    >  1:469717/1‑149                                                                  ATTAACTCAAAATATTTTCACTTCTTTACCTGAGCGGTTTGATTTTCGTTATGATGACGGAGCGAAAAAGACATTATTATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGC                                                                                <  1:359893/151‑1                                                                        TCAAAATATTTTCACTTCTTTACCTGAGCGGTTTGATTTTCGTTATGATGACGGAGCGAAAAAGACATTATCATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTT                                                                          >  1:632318/1‑151                                                                                 TTTCACTTCTTTACCTGAGCGGTTTGATTTTCGTTATGATGACGGAGCGAAAAAGACATTATTATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCG                                                                 >  2:125493/1‑151                                                                                    CACTTCTTTACCTGAGCGGTTTGATTTTCGTTATGATGACGGAGCGAAAAAGACATTATTATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTA                                                               >  2:114942/1‑150                                                                                      CTTCTTTACCTGAGCGGTTTGATTTTCGTTATGATGACGGAGCGAAAAAGACATTATTATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAAT                                                            >  1:552141/1‑151                                                                                        TCTTTACCTGAGCGGTTTGATTTTCGTTATGATGACGGAGCGAAAAAGACATTATTATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATG                                                           <  2:59111/150‑1                                                                                        TCTTTACCTGAGCGGTTTGATTTTCGTTATGATGACGGAGCGAAAAAGACATTATTATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAAT                                                            <  2:138337/149‑1                                                                                           TTACCTGAGCGGTTTGATTTTCGTTATGATGACGGAGCGAAAAAGACATTATTATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTT                                                       >  2:783313/1‑151                                                                                                 GAGCGGTTTGATTTTCGTTATGATGACGGAGCGAAAAAGACATTATTATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATC                                                  >  2:769435/1‑150                                                                                                 GAGCGGTTTGATTTTCGTTATGATGACGGAGCGAAAAAGACATTATTATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATC                                                  >  2:318765/1‑150                                                                                                   GCGGTTTGATTTTCGTTATGATGACGGAGCGAAAAAGACATTATTATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGC                                               <  2:52366/151‑1                                                                                                     GGTTTGATTTTCGTTATGATGACGGAGCGAAAAAGACATTATTATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCT                                             <  2:221963/151‑1                                                                                                      GTTTGATTTTCGTTATGATGACGGAGCGAAAAAGACATTATTATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTA                                            <  2:438681/151‑1                                                                                                         TGATTTTCGTTATGATGACGGAGCGAAAAAGACATTATTATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTT                                         >  2:444614/1‑151                                                                                                              TTCGTTATGATGACGGAGCGAAAAAGACATTATTATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACC                                    >  2:135785/1‑151                                                                                                              TTCGTTATGATGACGGAGCGAAAAAGACATTATTATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGAC                                     <  2:625307/150‑1                                                                                                               TCGTTATGATGACGGAGCGAAAAAGACATTATTATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACC                                    <  2:45973/150‑1                                                                                                                CGTTATGATGACGGAGCGAAAAAGACATTATTATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGT                                  >  1:320513/1‑151                                                                                                                    ATGATGACGGAGCGAAAAAGACATTATTATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCT                              >  2:700924/1‑151                                                                                                                       ATGACGGAGCGAAAAAGACATTATTATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCG                           <  2:138254/151‑1                                                                                                                                 GAAAAAGACATTATTATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGG                 >  2:844983/1‑151                                                                                                                                     AAGACATTATTATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTT             <  2:493799/151‑1                                                                                                                                         CATTATTATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCC         <  1:879786/151‑1                                                                                                                                         CATTATTATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCC         <  1:208124/151‑1                                                                                                                                            TATTATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCC       >  2:801030/1‑150                                                                                                                                             ATTATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCC       >  2:545966/1‑149                                                                                                                                                ATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCAGTTT  <  2:652869/151‑1                                                                                                                                                ATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCAGTTT  <  2:435461/151‑1                                                                                                                                                ATTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCAGTTT  >  2:14339/1‑151                                                                                                                                                                                                                                                                                                        TCGTCATCGCGGATGATAATTGTCCTCGGTAGTTGAACACGCCTGATTTGTATCATAGCTTAAGAATTAACTCAAAATATTTTCACTTCTTTACCTGAGCGGTTTGATTTTCGTTATGATGACGGAGCGAAAAAGACATTATTATTAG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/1673739‑1673886 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCAGTTT  >  NC_000913/2101749‑2101894

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ 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.