New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_LN832404	= 61489	0 (0.000)	10 (0.170)	10/412	NT	100%	intergenic (‑76/+87)	EK12AG100_RS23030/rapA	RNA polymerase‑associated protein RapA/RNA polymerase‑associated protein RapA
	?	NZ_LN832404	= 381811	NA (NA)					coding (847/914 nt)	EK12AG100_RS01865	IS3‑like element IS2 family transposase

AGGCGGTCACGACCCTGTTCCAGCTGTGCTTTCAGCGCTTCATGTTGCTCGCGGCAGTTTTTGATCAGATCGTCAAAGCCTTCGGTTTGATCCGGTGAAGCCAGATAGTTAATCAGATCGTTGTATACGCTATCGTAAATAGTGCGTCCGGTCGGGCAGGTGTGCTCAAATGCATCCAGACCTTCGTGATACCAGCGCACCAGCACCGACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTACCGACTGAGCGGTTTTCTCCAGATAAGGCACATGGATCTGAATATCGTGCGCCTGGCCGATACGATCCAGACGACCAATACGCTGCTCCAGTAGATCCGGGTTGAATGGCAGGTCAAACATCACCATGTGGCTGGCGAACTGGAAGTTACGTCCTTCAGAACCGATTTCTGAGCACAGCAGTACCTGTGCGCCGGT  >  NZ_LN832404/61202‑61770                                                                                                                                                                                                                                                                                                |                                                                                                                                                                                                                                                                                          agGCGGTCACGACCCTGTTCCAGCTGTGCTTTCAGCGCTTCATGTTGCTCGCGGCAGTTTTTGATCAGATCGTCAAAGCCTTCGGTTTGATCCGGTGAAGCCAGATAGTTAATCAGATCGTTGTATACGCTATCGTAAATAGTGCGTCCGGTCGGGCAGGTGTGCTCAAATGCATCCAGACCTTCGTGATACCAGCGCACCAGCACCGACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCgagcgat                                                                                                                                                                                                                                                                                    >  1:285728‑M1/1‑288 (MQ=255)         aCGACCCGGTTCCAGCTGTGCTTTCAGCGCTTCATGTTGCTCGCGGCAGTTTTTGATCAGATCGTCAAAGCCTTCGGTTTGATCCGGTGAAGCCAGATAGTTAATCAGATCGTTGTATACGCTATCGTAAATAGTGCGTCCGGTCGGGCAGGTGTGCTCAAATGCATCCAGACCTTCGTGATACCAGCGCACCAGCACCGACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCgagcgataacccagc                                                                                                                                                                                                                                                                            <  1:421935‑M1/295‑16 (MQ=255)                                      cTTCATGTTGCTCGCGGCAGTTTTTGATCAGATCGTCAAAGCCTTCGGTTTGATCCGGTGAAGCCAGATAGTTAATCAGATCGTTGTATACGCTATCGTAAATAGTGCGTCCGGTCGGGCAGGTGTGCTCAAATGCATCCAGACCTTCGTGATACCAGCGCACCAGCACCGACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCgagcgataacccagcgcactatgcggatgccattcgttataa                                                                                                                                                                                                                                                 >  1:383687‑M1/1‑251 (MQ=255)                                      cTTCATGTTGCTCGCGGCAGTTTTTGATCAGATCGTCAAAGCCTTCGGTTTGATCCGGTGAAGCCAGATAGTTAATCAGATCGTTGTATACGCTATCGTAAATAGTGCGTCCGGTCGGGCAGGTGTGCTCAAATGCATCCAGACCTTCGTGATACCAGCGCACCAGCACCGACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCgagcgataacccagcgcactatgcggatgccattcgttataa                                                                                                                                                                                                                                                 <  2:383687‑M1/293‑43 (MQ=255)                                                                              tcctTCGGTTGGGTCCCGTGAAGCCAGATAGTTAATCGGTTCGTTGTATACGATAGCGTAAATAGTGCGTCCGTGCGGGCAGGTGTGCTCAAATGCATCCAGACCTTCGCGATACCAGCGCACCAGCACCGACTGGATGTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCgagcgataacccagcgcactatgcggatgccattcgttataatgctcgaacgcctctgcaaggttctttgctgccgttaacccg                                                                                                                                                                                                       <  2:192730‑M1/294‑85 (MQ=255)                                                                                                           aggaaatcagAGCGTGGGCTAAGCTATCGTAGATAGTGCGTCCGGTCGGGCAGGGGTGCTCAAATGCAGCCAGACCTTCGTGATACCAGCGCACCAGCACCGACTGGATTCGCCCCTAGATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCgagcgataacccagcgcactatgcggatgccattcgttataatgctcgaacgcctctgcaaggttctttgctgccgttaacccgtctggtttgggcatgatactgatgtagtc                                                                                                                                                                          <  2:286687‑M1/291‑114 (MQ=255)                                                                                                           aGTTAATCAGATCGTTGTATACGCTATCGTAAATAGTGCGTCCGGTCGGGCAGGTGTGCTCAAATGCATCCAGACCTTCGTGATACCAGCGCACCAGCACCGACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTTCGGCCGATATTCCCGTGGCgcgcgataacccagcccactatgcggatgccattcgttataatgctcgaccgcctctgccaggttccttgcttccgttaacccgtccggtttgggcatgatactgctgtagtc                                                                                                                                                                          >  2:568153‑M1/1‑182 (MQ=255)                                                                                                                                    aTCGTAAATAGTGCGTCCGGTCGGGCAGGTGTGCTCAAATGCATCCAGACCTTCGTGATACCAGCGCACCAGCACCGACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCgagcgataacccagcgcactatgcggatgccattcgttataatgctcgaacgcctctgcaaggttctttgctgccgttaacccgtctggtttgggcatgatactgatgtagtcacgctttatcgttttcacgaagctc                                                                                                                                                 <  1:329852‑M1/295‑139 (MQ=255)                                                                                                                                              ttgCGTCCGGTCGGGCAGGGTTGCTCAAATGCATCCAGACCTTCGTGATACCAGCGCACCAGCACCGACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCgagcgataacccagcgcactatgcggatgccattcgttataatgctcgaacgcctctgcaaggttctttgctgccgttaacccgtctggtttgggcatgatactgatgtagtcacgctttatcgttttcacgaagctctctgctattc                                                                                                                                       <  2:389131‑M1/294‑149 (MQ=255)                                                                                                                                                                                ccAGACCTTCGTGATACCAGCGCACCAGCACCGACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCgagcgataacccagcgcactatgcggatgccattcgttataatgctcgaacgcctctgcaaggttctttgctgccgttaacccgtctggtttgggcatgatcatgaggtagtaccgctttaccggtttcacgaagctctctggtcttccgttactctcgggactccgcaccgcggtgttctt                                                                                                     >  2:146142‑M1/1‑113 (MQ=255)                                                                                                                                                                                                                         gtcccatctattgtcagacctctgttataAATTAACTCATCACAATCCCGCTGCCTCAGATATTCCCGTGGCgagcgataacccatcgcactatgcggatgccattcgttataatgctcgaacgcctcttcaaggttctttgctgccgttaacccgtctggtttgggcatgatactgatgtagtcacgctttatcgttttcacgaagctctctgctattccgttactctccggactccgcaccgccgtgttcttcggttcaagtcccaacatccgggcgaactggcgtgtttcat                                                            <  2:645008‑M1/281‑224 (MQ=255)                                                                                                                                                                                                                           cccctttgcttccagacagcTGTCTTCCCTTAACCCATTACAAGCCCGCTGCCGCGGCTATTCCCTTGGCgagcgctaacccagcgcactatgcggatgccattcgttataatgctcgaacgcctctgcaaggttctttgctgccgttaacccgtctggtttgggcatgatactgatgtagtcacgctttatcgttttcacgaagctctctgctattccgttactctccggactccgcaccgccgtgttcttcggttcaagtcccaacatccgggcgaactggcgtgtttcatta                                                          <  2:651293‑M1/286‑226 (MQ=255)                                                                                                                                                                                                                               tacatttcCAGACATCTGTTATACATTAACCCATTCCAAGCCCGGGGCCGCAGACATTCCCGTGGCgagcgataacccagcgcactatgcggatgccattcgttataatgctcgaacgcctctgcaaggttctttgctgccgttaacccgtctggtttgggcatgatactgatgtagtcacgctttatcgttttcacgaagctctctgctattccgttactctccggactccgcaccgccgtgttcttcggttcaagtcccaacatccgggcgaactggcgtgtttcattagccc                                                      <  2:774114‑M1/292‑230 (MQ=255)                                                                                                                                                                                                                                 tagttccaGACCTCTGTTATCCCTGAACCCATGACAAGCCCGCTGCCGCAGATATTCCCGCAGCgggcgataacccagcgcactatgcggaggccattcgttataatgctcgaacgcctctgcaaggttctttgctgccgttaacccgtctggtttgggcatgatactgatgtagtcacgctttatcgttttcacgaagctctctgctattccgttactctccggactccgcaccgccgtgttcttcggttcaagtcccaacatccgggcgaactggcgtgtttcattagcccgg                                                    <  2:112046‑M1/292‑232 (MQ=255)                                                                                                                                                                                                                                                       ctgaacccATTAAAAGCCCGCTGCCGCCGAGATTCCCTGGGCgagcaataacccagcgcactatgcggatgccattcgttataatgctcgaacgcctctgcaaggttctttgctgccgttaacccgtctggtttgggcatgatactgatgtagtcacgctttatcgttttcacgaagctctctgctattccgttactctccggactccgcaccgccgtgttcttcggttcaagtcccaacatccgggcgaactggcgtgtttcattagcccggtagcatgaaccattatccgtca                              <  2:253908‑M1/292‑254 (MQ=255)                                                                                                                                                                                                                                                               ataacaaGACCGCGGCCGCAGATATTCCCGTGGCgagggagaacccagcgcactatgcggatgccattcgttataatgctcgaacgcctctgcaaggtgctttgctgccgttaacccgtctggtttgggcatgatactgatgtagtcacgctttatcgttttcacgaagctctctgctattccgttactctccggactccgcaccgccgtgttcttcggttcaagtcccaacatccgggcgaactggcgtgtttcattagcccggtagcatgaaccattatccgtcagccactcc                      <  2:672794‑M1/292‑262 (MQ=255)                                                                                                                                                                                                                                                                            ggccgacgatattccCGGGTCgaacgataacccggcgcactatggggatgccagtcgttataatgctcgaacgcctctgcaaggttctttgctgccgttaacccgtctggtttgggcatgatactgatgtagtcacgctttatcgttttcacgaagctctctgctattccgttactctccggactccgcaccgccgtgttcttcggttcaagtcccaacatccgggcgaactggcgtgtttcattagcccggtagcatgaaccattatccgtcagccactccactggagacgacg         <  2:285728‑M1/288‑275 (MQ=255)                                                                                                                                                                                                                                                                                   ggtattccgtgggcgagtgataacccaccgtactatgcggatggcattcgttataatgctcgaacgcctctgcaagggtctttgctgccgttaacccgtctggtgtgggcaggatactgatgtagtcacgctttatcgttttcacgaagctttctgctattccgttactctccggactccgcaccgccgtgttcttcggttcaagtcccaacatccgggcgaactggcgtgtttcattagcccggtagcatgaaccattatccgtcagccactccactggagacgacggaagatc  <  2:669283‑M1/284‑282 (MQ=255)                                                                                                                                                                                                                                                                                                |                                                                                                                                                                                                                                                                                          AGGCGGTCACGACCCTGTTCCAGCTGTGCTTTCAGCGCTTCATGTTGCTCGCGGCAGTTTTTGATCAGATCGTCAAAGCCTTCGGTTTGATCCGGTGAAGCCAGATAGTTAATCAGATCGTTGTATACGCTATCGTAAATAGTGCGTCCGGTCGGGCAGGTGTGCTCAAATGCATCCAGACCTTCGTGATACCAGCGCACCAGCACCGACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTACCGACTGAGCGGTTTTCTCCAGATAAGGCACATGGATCTGAATATCGTGCGCCTGGCCGATACGATCCAGACGACCAATACGCTGCTCCAGTAGATCCGGGTTGAATGGCAGGTCAAACATCACCATGTGGCTGGCGAACTGGAAGTTACGTCCTTCAGAACCGATTTCTGAGCACAGCAGTACCTGTGCGCCGGT  >  NZ_LN832404/61202‑61770

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ 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.