New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	258676 =	0 (0.000)	24 (0.900) +CGAATATACGGGCCTAGTGCGGTAAATTTTTTGATCAATCTGCTCTTCGGGTGTCCACTCGGTAACGTCATTGCTATCTCC	24/320	0.2	100%	pseudogene (1/331 nt)	crl	RNA polymerase holoenzyme assembly factor Crl
	?	NC_000913	= 1469241	NA (NA)					intergenic (‑92/‑5)	insC2/ydbA	IS2 insertion element repressor InsA/putative outer membrane protein, N‑terminal fragment

CATTCATGGCCATATCAATGATTTTCTGGTGCGTACCGGGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCAGGAATCCCGTTTTACCTACAGTTACCAGTTTGGTCTGTTCGATAAAGCAGGCGACTGGAAGAGTGTTCCGGTAAAAGACACTGAAGTGGTTGAACGACTGGAGCACACCCTGCGTGAGTTTCACGAGAAGCTG  >  NC_000913/258434‑258925                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                                          ctgaacaattgcgatcttttcctgtgtggtacgccgtctgcgtttctccggccctaagacatcaatcatctgttctccaatgactagtctaaaaactagtattaagactatcacttatttaagtgatattggttgtctggagattcagggggccagtctaaggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgTGAAGGTa                                                                                                                                                                                                                                                    <  1:392911‑M1/8‑1 (MQ=255)   gaacaattgcgatcttttcctgtgtggtacgccgtctgcgtttctccggccctaagacatcaatcatctgttctccaatgactagtctaaaaactagtattaagactatcacttatttaagtgatattggttgtctggagattcagggggccagtctaaggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgTGAAGGTAAg                                                                                                                                                                                                                                                  >  1:352969‑M1/241‑250 (MQ=255)                  tttcctgtgtggtacgccgtctgcgtttctccggccctaagacatcaatcatctgttctccaatgactagtctaaaaactagtattaagactatcacttatttaagtgatattggttgtctggagattcagggggccagtctaaggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgTGAAGGTAAGTGCAAAGATa                                                                                                                                                                                                                                        >  2:169451‑M1/226‑245 (MQ=255)                     cctgtgtggtacgccgtctgcgtttctccggccctaagacatcaatcatctgttctccaatgactagtctaaaaactagtattaagactatcacttatttaagtgatattggttgtctggagattcagggggccagtctaaggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgTGAAGGTAAGTGCAAAGATAATCGATTCt                                                                                                                                                                                                                               >  2:383241‑M1/223‑251 (MQ=255)                       tgtgtggtacgccgtctgcgtttctccggccctaagacatcaatcatctgttctccaatgactagtctaaaaactagtattaagactatcacttatttaagtgatattggttgtctggagattcagggggccagtctaaggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgTGAAGGTAAGTGCAAAGATAATCGATTCttt                                                                                                                                                                                                                             <  2:330904‑M1/31‑1 (MQ=255)                        gtgtggtacgccgtctgcgtttctccggccctaagacatcaatcatctgttctccaatgactagtctaaaaactagtattaagactatcacttatttaagtgatattggttgtctggagattcagggggccagtctaaggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgTGAAGGTAAGTGCAAAGATAATCGATTCtt                                                                                                                                                                                                                              >  1:257163‑M1/220‑249 (MQ=255)                            ggtacgccgtctgcgtttctccggccctaagacatcaatcatctgttctccaatgactagtctaaaaactagtattaagactatcacttatttaagtgatattggttgtctggagattcagggggccagtctaaggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCg                                                                                                                                                                                                                         >  1:126876‑M1/216‑250 (MQ=255)                                 gccgtctgcgtttctccggccctaagacatcaatcatctgttctccaatgactagtctaaaaactagtattaagactatcacttatttaagtgatattggttgtctggagattcagggggccagtctaaggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTc                                                                                                                                                                                                                   >  2:207294‑M1/211‑251 (MQ=255)                                       tgcgtttctccggccctaagacatcaatcatctgttctccaatgactagtctaaaaactagtattaagactatcacttatttaagtgatattggttgtctggagattcagggggccagtctaaggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTg                                                                                                                                                                                                             <  2:347161‑M1/47‑1 (MQ=255)                                                             atcaatcatctgttctccaatgactagtctaaaaactagtattaagactatcacttatttaagtgatattggttggctggagattcagggggccagtctaaggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGc                                                                                                                                                                                       >  2:141016‑M1/183‑251 (MQ=255)                                                                               aatgactagtctaaaaactagtattaagactatcacttatttaagtgatattggttttctggagattcagggggccagtctaaggagatagcaatgacgttaccgagtggacaccctaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGTCTGTATTCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAAtt                                                                                                                                                                     >  1:381930‑M1/165‑251 (MQ=255)                                                                                            aaaactagtattaagactatcacttatttaagtgatattggttgtctggagattcagggggccagtctaaggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgTGAAGGTAAGTGCACAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCtggtgg                                                                                                                                                        <  2:68642‑M1/100‑1 (MQ=255)                                                                                                     attaagactatcacttatttaagtgatattggttgtctggagattcagggggcaagtctaaggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTg                                                                                                                                               <  1:127725‑M1/109‑1 (MQ=255)                                                                                                              atcacttatttaagtgatattggttgtctggagattcagggggccagtctaaggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCa                                                                                                                                       >  2:158888‑M1/134‑250 (MQ=255)                                                                                                              atcacttatttaagtgatattggttgtctggagattcagggggccagtctaaggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCAg                                                                                                                                      >  1:206574‑M1/134‑251 (MQ=255)                                                                                                                         aagtgatattgggtgtctggagattcagggggccagtctcaggagatagcaatgacgttaccgagtggacacccgacgagcagattgatcaaaaaatttaccgcactaggcccgtatattcgTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGTCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGAGGATGGAACTGGAAGCGCATGAATCCCGttt                                                                                                                           <  2:212943‑M1/129‑1 (MQ=255)                                                                                                                              atattggttgtctggagattcagggggccagtctaaggagatagcaatgacgttaccgagtggacacccgaagagcatattgatcaaaaaatttaccgcactaggcccgtatattcgTGATGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGGCTGGCTGTATGCTTCAACGTGAAACCTGCACCTGAAGTGCGTGAATTCTGGGGCTTGTGGATGGAGCTGGAAGCGCAGGAATCCCGTTTTACCt                                                                                                                      >  1:60985‑M1/118‑251 (MQ=255)                                                                                                                                  tggttgtctggagattcagggggccagtctaaggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCAGGAATCCCGTTTTACCTAc                                                                                                                    <  1:264631‑M1/136‑1 (MQ=255)                                                                                                                                    gttgtctggagattcagggggccagtctaaggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCAGGAATCCCGTTTTACCTACAGtt                                                                                                                <  2:151209‑M1/140‑1 (MQ=255)                                                                                                                                                  cagggggccagtctaaggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCAGGAATCCCGTTTTACCTACAGTTACCAGTTTGGTCTg                                                                                                  >  2:139997‑M1/98‑251 (MQ=255)                                                                                                                                                  cagggggccagtctaaggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCAGGAATCCCGTTTTACCTACAGTTACCAGTTTGGTCTg                                                                                                  <  1:10160‑M1/154‑1 (MQ=255)                                                                                                                                                     ggggccagtctaaggagctagcaatgaagttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatcttcgTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCAGGAATCCCGTTTTACCTACAGTTACCAGTTTGGTCTGTTc                                                                                               <  1:294206‑M1/157‑1 (MQ=255)                                                                                                                                                            gtctaaggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCAGGAATCCCGTTTTACCTACAGTTACCAGTTTGGTCTGTTc                                                                                               >  1:50864‑M1/88‑244 (MQ=255)                                                                                                                                                            gtctaaggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCAGGAATCCCGTTTTACCTACAGTTACCAGTTTGGTCTGTTc                                                                                               <  2:50864‑M1/157‑1 (MQ=255)                                                                                                                                                                              gacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCAGGAATCCCGTTTTACCTACAGTTACCAGTTTGGTCTGTTCGATAAAGCAGGCGACTGGAAGAgt                                                                       >  1:82172‑M1/70‑250 (MQ=255)                                                                                                                                                                                 gttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCAGGAATCCCGTTTTACCTACAGTTACCAGTTTGGTCTGTTCGATAAAGCAGGCGACTGGAAGAGTGTTc                                                                   >  1:274383‑M1/67‑251 (MQ=255)                                                                                                                                                                                 gttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCAGGAATCCCGTTTTACCTACAGTTACCAGTTTGGTCTGTTCGATAAAGCAGGCGACTGGAAGAGTGTTc                                                                   <  2:51988‑M1/185‑1 (MQ=255)                                                                                                                                                                                                                  caaaaaatttaccgcactaggcccgtatattcgTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCAGGAATCCCGTTTTACCTACAGTTACCAGTTTGGTCTGTTCGATAAAGCAGGCGACTGGAAGAGTGTTCCGGTAAAAGACACTGAAGTGGTTGAACGACTgg                                  >  2:127725‑M1/34‑251 (MQ=255)                                                                                                                                                                                                                                               ttcgTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCAGGATTCCCGTTTTACCTACAGTTACCAGTTTGGTCTGTTCGATAAAGCAGGCGACTGGAAGAGTGTTCCGGTAAAAGACACTGAAGTGGTTGAACGACTGGAGCACACCCTGCGTGAGTTTCACgaga       <  2:290702‑M1/245‑1 (MQ=255)                                                                                                                                                                                                                                                  gTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCAGGAATCCCGTTTTACCTACAGTTACCAGTTTGGTCTGTTCGATAAAGCAGGCGACTGGAAGAGTGTTCCGGTAAAAGACACTGAAGTGGTTGAACGACTGGAGCACACCCTGCGTGAGTTTCACGAGAAGCTg  <  1:157581‑M1/250‑1 (MQ=255)                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                                          CATTCATGGCCATATCAATGATTTTCTGGTGCGTACCGGGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCAGGAATCCCGTTTTACCTACAGTTACCAGTTTGGTCTGTTCGATAAAGCAGGCGACTGGAAGAGTGTTCCGGTAAAAGACACTGAAGTGGTTGAACGACTGGAGCACACCCTGCGTGAGTTTCACGAGAAGCTG  >  NC_000913/258434‑258925

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ 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.