New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_007779	3876427 =	NA (NA)	4 (0.030)	4/412	NT	16.7%	coding (1806/4134 nt)	Y75_RS19225	RHS element protein RhsA
	?	NC_007779	3876545 =	21 (0.130)					coding (1688/4134 nt)	Y75_RS19225	RHS element protein RhsA

CGTCCGGCAGCATCGTATTCCATACTGCGCGTTAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTCAGCCCTTCCTCGCGGTGCACCGCCGTCATCTGCCCGAAGCGGTCATGGTCATAACGGGTTACATAACCGGAACAGTCGGTGAAGCTCAGCAACTGACCGTAACGGCTCCACGTCATGGTTTTCCGGCTGCCGGTGGCATCTTCCGTTGCGCAGGGTAAGTCACTGTGTGGATTATCATAACGGTAGCGGGTGATATCGCCG  >  NC_007779/3876308‑3876727                                                                                                                                                                                                                                              |                                                                                                                                                                                       gccaccggcagccggaaaaccatgacgtggagccgttacggtcagttgctgagcttcaccgactgttccggttatgtaacccgttatgaccatgaccgcttcgggcagatgacggcggtgcaccgcgaggaagggctgagtcagtaccgcgcatacgacagccgtggacagttaattgccgtgaaagacacgcagggccatgaaacgcggtatgaatacaacatcgccggtgacctga                                                                                                                                                                                        >  1:782768‑M2/238‑238 (MQ=255) gccaccggcagccggaaaaccatgacgtggagccgttacggtcagttgctgagcttcaccgactgttccggttatgtaacccgttatgaccatgaccgcttcgggcagatgacggcggtgcaccgcgaggaagggctgagtcagtaccgcgcatacgacagccgtggacagttaattgccgtgaaagacacgcagggccatgaaacgcggtatgaatacaacatcgccggggaactga                                                                                                                                                                                        >  1:1951638‑M2/238‑238 (MQ=255) cGTCCGGCAGCATCGTATTCCATACTGCGCGTTAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTCAGCCCTTCCTCGCGGTGCa                                                                                                                                                                                        >  1:1878370/1‑238 (MQ=31)  gTCCGGCAGCATCGTATTCCATACTGCGCGTTAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTCAGCCCTTCCTCGCGGTGCAc                                                                                                                                                                                       >  1:1936348/1‑238 (MQ=31)    ccgggcagccggaaaaccatgacgtggagccgttacggtcagttgctgggcttcaccgactgttccggttatgtaacccgttaggaccatgaccgcttcgggcagatgacggcggtgcgccgcgaggaagggctgagtcagtaccgcgcattcgacagccgtggacagttaattgccgtgaaagacacgcagggccatgaaacgcggtatgaatacaacatcgccggtgacctgAccgc                                                                                                                                                                                    <  2:1322893‑M2/5‑1 (MQ=255)    ccggacggccggaaaccaaggccgtggggccgttacggtaagttgcggggctcaaccgactgttccggttatgtaccccgttaggcccatgaccgctccgggcagatgacggcggggccccgcgaggaagggctgagtcagtaccgggcatacgacagccgtggacagttaattgccgtgaaagacacgcagggccatgaaacgcggtatgaatacaacatcgccggtgacctgAccgc                                                                                                                                                                                    <  2:1504992‑M2/5‑1 (MQ=255)    accggcagccggaaaaccatgacgtggagccgttacggtcagttgctgagcttcaccgactgttccggttatgtaacccgttatgaccatgaccgcttcgggcagatgacggcggtgcaccgcgaggaagggctgagtcagtaccgcgcatacgacagccgtggacagttaattgccgtgaaagacacgcagggccatgaaacgcggtatgaatacaacatcgccggtgacctgAccgc                                                                                                                                                                                    <  1:153657‑M2/5‑1 (MQ=255)    accggcagccggaaaaccatgacgtggagccgttacggtcagttgctgagcttcaccgactgttccggttatgtaacccgttatgaccatgaccgcttcgggcagatgacggcggtgcaccgcgaggaagggctgagtcagtaccgcgcatacgacagccgtggacagttaattgccgtgaaagacacgcagggccatgaaacgcggtatgaatacaacatcgccggtgacctgAccg                                                                                                                                                                                     >  1:1499467‑M2/235‑238 (MQ=255)       ggcagccggaaaaccatggcgtggagcctttacggtcagttgctgagcttccccgactgttccggttatgtaacccgttatgaccatgaccgcttcgggcagatgacggcggtgccccgcgaggaagggctgagtcagtaccgcgcatacgacagccgtggacagttaattgccgtgaaagacacgcagggccatgaaacgcggtatgaatacaacatcgccggtgacctgACCGCCGt                                                                                                                                                                                 <  1:397022‑M2/8‑1 (MQ=255)       ggcagccggaaaaccatgacgtggagccgttacggtcagttgctgagcttcaccgactgttccggttatgtaacccgttatgaccatgaccgcttcgggcagatgacggcggtgcaccgcgaggaagggctgagtcagtaccgcgcatacgacagccgtggacagttaattgccgtgaaagacacgcagggccatgaaacgcggtatgaatacaacatcgccggtgacctgACCGCCGt                                                                                                                                                                                 <  1:1050321‑M2/8‑1 (MQ=255)          agccggaaacccagggcggggagccgttccggtcagtggctgggcttcaccgacggttccggttatgtaacccgtgatgaccaggaccgcttcgggcagatgacggcggtgccccgcgaggaagggctgagtcagtcccgcgcatacgacagccgtggacagttaattgccgtgaaagacacgcagggccatgaaacgcggtatgaatacaacatcgccggtgacctgACCGCCGTCa                                                                                                                                                                               <  2:1835118‑M2/10‑1 (MQ=255)            aTCGTATTCCATACTGCGCGTTAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTCAGCCCTTCCTCGCGGTGCACCGCCGTCa                                                                                                                                                                               <  1:801853/236‑1 (MQ=31)             tCGTATTCCATACTGCGCGTTAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTCCGCCCTTCCTCCCGGGGCAccgccgcactcc                                                                                                                                                                            >  2:1499467/1‑232 (MQ=9)                  ttCCATACTGCGCGTTAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTCAGCCCTTCCTCGCGGTGCACCGCCGTCATCTGCCCGa                                                                                                                                                                      <  1:1495942/239‑1 (MQ=31)                    ccATACTGCGCGTTAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTCAGCCCTTCCTCGCGGTGCACCGCCGTCATCTGCCCGAAg                                                                                                                                                                    <  2:1936348/239‑1 (MQ=31)                    ccATACTGCGCGTTAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTCAGCCCTTCCTCGCGGTGCACCGCCGTCATCTGCCCGAAg                                                                                                                                                                    <  1:1137439/239‑1 (MQ=31)                    ccATACTGCGCGTTAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGGCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTGCACGGCAATTAGCTGTCCACGGCTGTCGTATGCGCGGTACTGACTCAGCCCTTCCTCGCGGTGCACCGCCGTCATCTGCCCGAAg                                                                                                                                                                    <  1:304773/239‑1 (MQ=14)                        aCTGCGCGTTAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTCAGCCCTTCCTCGCGGTGCAccgcc                                                                                                                                                                                   <  2:14711/220‑1 (MQ=31)                        aCTGCGCGTTAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTCAGCCCTTCCTCGCGGTGCAccgcc                                                                                                                                                                                   >  1:14711/1‑220 (MQ=31)                         cTGCGCGTTAGCCCGCCCTGCGTGGTACGGCCGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGGCCACGGCTGTCGTATGCGCGGTACTGACTCAGCCCTTCCTCGCGGTGCACCGCCGTCATCTGCCCGAAGCggtc                                                                                                                                                               <  1:201423/239‑1 (MQ=14)                         cTGCGCGTTAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTCAGCCCTTCCTCGCGGTGCACCGCCGTCATCTGCCCGAAGCggtc                                                                                                                                                               <  1:1371724/239‑1 (MQ=31)                          tGCGCGTTAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTCAGCCCTTCCTCGCGGTGCACCGCCGTCATCTGCCCGAAGCggtca                                                                                                                                                              <  1:414171/239‑1 (MQ=31)                          tGCGCGTTAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTCAGCCCTTCCTCGCGGTGCACCGCCGTCATCTGCCCGAAGCggtca                                                                                                                                                              <  1:1180140/239‑1 (MQ=31)                          tGCGCGTTAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTCAGCCCTTCCTCGCGGTGCACCGCCGTCATCTGCCCGAAGCggtca                                                                                                                                                              <  2:138053/239‑1 (MQ=31)                            cgcgTTAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTCAGCCCTTCCTCGCGGTGCACCGCCGTCATCTGCCCGAAGCggtcctg                                                                                                                                                            >  1:282107/1‑239 (MQ=14)                            cgcgTTAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTCAGCCCTTCCTCGCGGTGCACCGCCGTCATCTGCCCGAAGCggtcatg                                                                                                                                                            >  1:378832/1‑239 (MQ=31)                            cgcgTTAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTCAGCCCTTCCTCGCGGTGCACCGCCGTCATCTGCCCGAAGCggtcatg                                                                                                                                                            >  1:1388734/1‑239 (MQ=31)                            cgcgTTAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCCGCGATGTTGTATTCATACCCCGTTTCATGGCCCTGCGTGTCTTTCACGGCCATTAACTGTCCACGGCTTTCGTATGCCCGGTACTGCACCAGCCCTTCCTCGCGGGGCCCCCCCGTCATCTGCCCCCAGCggtgctg                                                                                                                                                            >  2:1044130/1‑235 (MQ=11)                              cgTTAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGGCATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTCAGCCCTTCCTCGCGGTGCACCCCCGTCATCTGCCCGAAGCggtcatgg                                                                                                                                                           >  1:193261/1‑238 (MQ=14)                              cgTTAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTCAGCCCTTCCTCGCGGTGCACCGCCGTCATCTGCCCGAAGCgggcatgg                                                                                                                                                           >  1:389025/1‑238 (MQ=14)                               gTTAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGGATTCATACCGCGTTTCATGGCCCCGCGTGTCTTTCACGGCAATTTACTGTCCACGGCTGGCCTATGCGCGGTACTTACTCAGCCCCTCCCCCCCGTGCACCGCCGTCCTCTGCCCCAAGCgggcagggc                                                                                                                                                          >  2:728836/1‑237 (MQ=11)                                 tAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTCAGCCCTTCCTCGCGGTGCACCGCCGTCATCTGCCCGAAGCggtcatggtcat                                                                                                                                                       >  1:390443/1‑239 (MQ=11)                                                                                                                               gaggaagggctgagtcagtaccgcgcatacgacagccgtggacagttaattgccgtgaaagacacgcagggccatgaaacgcggtatgaatacaacatcgccggtgacctgACCGCCGTCATCTGCCCGAAGCGGTCATGGTCATAACGGGTTACATAACCGGTACAGTCGGTGAAGCTCAGCAACTGACCGTAACGGCTCCACGTCATGGTTTTCCGGCTGCCGGTGGCATCTTCCGt                                                         >  2:143587‑M2/112‑239 (MQ=255)                                                                                                                                                 taccgcgcatacgacagccgtggacagttaattgccgtgaaagacacgcagggccatgaaacgcggtatgaatacaacatcgccggtgacctgAccgc                                                                                                                                                                                    <  1:415112‑M2/5‑1 (MQ=255)                                                                                                                                                 taccgcgcatacgacagccgtggacagttaattgccgtgaaagacacgcagggccatgaaacgcggtatgaatacaacatcgccggtgacctgAccgc                                                                                                                                                                                    >  2:415112‑M2/94‑98 (MQ=255)                                                                                                                                                         gcgcatacgacagccgtggacagttaattgccgtgaaagacacgcagggccatgaaacgcggtatgaatacaacatcgccggtgcACCGCCGTCATCTGCCCGAAGCGGTCATGGTCATAACGGGTTACATAACCGGAACAGTCGGTGAAGCTCAGCAACTGACCGTAACGGCTCCACGTCATGGTTTTCCGGCTGCCGGTGGCATCTTCCGTTGCGCAGGGTAAGTCACTGTGTGGAt                               >  1:746172‑M2/86‑239 (MQ=255)                                                                                                                                                                                    cgtgaaagacacgtagggccatgaaacgcggtatgaatacaacatcgccggtgacctgACCGCCGTCATCTGCCCGAAGCGGTCATGGTCATAACGGGTTACATAACCGGAACAGTCGGTGAAACTCAGCAACTGACCGTAACGGCTCCACGTCATGGTTTTCCGGCTGCCGGTGGCATCTTCCGTTGCGCAGGGTAAGTCACTGTGTGGATTATCATAACGGTAGCGGGTGATATCg     <  1:1384138‑M2/180‑1 (MQ=255)                                                                                                                                                                                      tgaaagacacgcagggccatgaaacgcggtatgaatacaacatcgccggtgacctgACCGCCGTCATCTGCCCGAAGCGGTCATGGTCATAACGGGTTACATAACCGGAACAGTCGGTGAAGCTCAGCAACTGACCGTAACGGCTCCACGTCATGGTTTTCCGGCTGCCGGTGGCATCTTCCGTTGCGCAGGGTAAGTCACTGTGTGGATTATCATAACGGTAGCGGGTGATATCGCCg  >  1:508702‑M2/57‑239 (MQ=255)                                                                                                                                                                                                                                              |                                                                                                                                                                                       CGTCCGGCAGCATCGTATTCCATACTGCGCGTTAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTCAGCCCTTCCTCGCGGTGCACCGCCGTCATCTGCCCGAAGCGGTCATGGTCATAACGGGTTACATAACCGGAACAGTCGGTGAAGCTCAGCAACTGACCGTAACGGCTCCACGTCATGGTTTTCCGGCTGCCGGTGGCATCTTCCGTTGCGCAGGGTAAGTCACTGTGTGGATTATCATAACGGTAGCGGGTGATATCGCCG  >  NC_007779/3876308‑3876727

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ 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.