New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	= 394471	92 (0.970)	10 (0.120)	9/248	11.0	10.8%	intergenic (+53/‑35)	yaiT/yaiV	pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein/putative transcriptional regulator
	?	NC_000913_3_pae_tpiA	= 394475	82 (0.960)					intergenic (+57/‑31)	yaiT/yaiV	pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein/putative transcriptional regulator
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

CACCAAGAACTTCAGCGCCTATACCGATGCTAACTACCTCGGTGGTGGTGACGTAGATCAAGACTGGTCCGCGAACGTGGGTGTTAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAATAATGCCCGTCAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913_3_pae_tpiA/394319‑394471 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑taatgcccgtcaaATCCTTGACGGGCATTATTTAGATTAAATTACCAGTATTTCTTCGGAGTGAAGAATATTACCAGGTATATTTAACACCCACGTTCGCGGACCAGTCTTGATCTACGTCACCACCACCGAGGTAGTTAGCATCGGTATAGGCGCTGAAG  <  NC_000913_3_pae_tpiA/394475‑394328                                                                                                                                                                                                                                                                                                               CACCAAGAACTTCAGCGCCTATACCGATGCTAACTACCTCGGTGGTGGTGACGTAGATCAAGACTGGTCCGCGAACGTGGGTGTTAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAATAATGCCCGT                                                                                                                                                         <  3:547643/150‑1    CAAGAACTTCAGCGCCTATACCGATGCTAACTACCTCGGTGGTGGTGACGTAGATCAAGACTGGTCCGCGAACGTGGGTGTTAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAATAATGCCCGTCAA                                                                                                                                                      >  1:346922/1‑150    CAAGAACTTCAGCGCCTATACCGATGCTAACTACCTCGGTGGTGGTGACGTAGATCAAGACTGGTCCGCGAACGTGGGTGTTAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAATAATGCCCGTCAA                                                                                                                                                      >  1:405854/1‑150    CAAGAACTTCAGCGCCTATACCGATGCTAACTACCTCGGTGGTGGTGACGTAGATCAAGACTGGTCCGCGAACGTGGGTGTTAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAATAATGCCCGTCAA                                                                                                                                                      >  3:216043/1‑150     AAGAACTTCAGCGCCTATACCGATGCTAACTACCTCGGTGGTGGTGACGTAGATCAAGACTGGTCCGCGAACGTGGGTGTTAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAAT                                                                                                                                                                  <  1:200973/137‑1     AAGAACTTCAGCGCCTATACCGATGCTAACTACCTCGGTGGTGGTGACGTAGATCAAGACTGGTCCGCGAACGTGGGTGTTAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAAT                                                                                                                                                                  >  2:200973/1‑137         ACTTCAGCGCCTATACCGATGCTAACTACCTCGGTGGTGGTGACGTAGATCAAGACTGGTCCGCGAACGTGGGTGTTAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAGTAATGCCCGTCAAATCCT                                                                                                                                                 <  4:225219/150‑1               GCGCCTATACCGATGCTAACTACCTCGGTGGTGGTGACGTAGATCAAGACTGGTCCGCGAACGTGGGTGTTAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAATAATGCCCGTCAAATCCTTGACGG                                                                                                                                           <  1:573624/150‑1               GCGCCTATACCGATGCTAACTACCTCGGTGGTGGTGACGTAGATCAAGACTGGTCCGCGAACGTGGGTGTTAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAATAATGCCCGTCAAATCCTTGACGG                                                                                                                                           <  2:960421/150‑1                  CCTATACCGATGCTAACTACCTCGGTGGTGGTGACGTAGATCAAGACTGGTCCGCGAACGTGGGTGTTAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAATAATGCCCGTCAAATCCTTGACGGGCA                                                                                                                                        <  4:186708/150‑1                         CGATGCTAACTACCTCGGTGGTGGTGACGTAGATCAAGACTGGTCCGCGAACGTGGGTGTTAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAATAATGCCCGTCAAATCCTTGACGGGCATTATTTA                                                                                                                                 <  1:698136/150‑1                                   TACCTCGGTGGTGGTGACGTAGATCAAGACTGGTCCGCGAACGTGGGTGTTAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAATAATGCCCGT                                                                                                                                                         <  1:230577/116‑1                                   TACCTCGGTGGTGGTGACGTAGATCAAGACTGGTCCGCGAACGTGGGTGTTAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAATAATGCCCGT                                                                                                                                                         >  2:230577/1‑116                                        CGGTGGTGGTGACGTAGATCAAGACTGGTCCGCGAACGTGGGTGTTAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAATAATGCCCGTCAAATCCTTGACGGGCATTATTTAGATTAAATTACCAGT                                                                                                                  <  3:602522/150‑1                                                         ATCAAGACTGGTCCGCGAACGTGGGTGTTAATTATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAATAATGCCC                                                                                                                                                           <  1:602071/92‑1                                                         ATCAAGACTGGTCCGCGAACGTGGGTGTTAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAATAATGCCC                                                                                                                                                           >  2:602071/1‑92                                                            AAGACTGGTCCGCGAACGTGGGTGTTAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAATAATGCCCGTCAAATCCTTCACGGGCATTATTTAGATTAAATTACCAGTATTTCTTCGGAGTGAAGAAT                                                                                              <  4:216043/150‑1                                                                   GTCCGCGAACGTGGGTGTTAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAATAATGCCCGTCAAATCCTTGACGGGCATTATTTAGATTAAATTACCAGTATTTCTTCGGAGTGAAGAATATTACCA                                                                                       >  3:161590/1‑150                                                                       GCGAACGTGGGTGTTAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAATAATGCCCGTCAAATCCTTGACGGGCATTATTTAGATTAAATTACCAGTATTTCTTCGGAGTGAAGAATATTACCAGGTA                                                                                   <  4:161590/150‑1                                                                                GGTGTTAAATATACCTTGTAATATTCTACACACCGAAGAAATACTGGTAATTTAAACGAAATAATGCCCGTCAAATCCTTGACGGGCATTATTTAGATTAAATTACCAGTATTTCTTCGGAGTGAAGAATATTACCAGGTATATTTAACA                                                                          <  2:906568/150‑1                                                                                                                                             TAATGCCCGTCAAATCCTTGACGGGCATTATTTAGATTAAATTACCAGTATTTCTTCGGAGTGAAGAATATTACCAGGTATATTTAACACCCACGTTCGCGGACCAGTCTTGATCTACGTCACCTCCACCGAGGTATTTAGCATCGGTAT             <  1:808906/150‑1                                                                                                                                              AATGCCCGTCAAATCCTTGACGGGCATTATTTAGATTAAATTACCAGTATTTCTTCGGAGTGAAGAATATTACCAGGTATATTTAACACCCACGTTCGCGGACCAGTCTTGATCTACGTCACCACCACCGAGGTAGTTAGCATCGGTATA            <  2:657980/150‑1                                                                                                                                               ATGCCCGTCAAATCCTTGACGGGCATTATTTAGATTAAATTACCAGTATTTCTTCGGAGTGAAGAATATTACCAGGTATATTTAACACCCACGTTCGCGGACCAGTCTTGATCTACGTCACCACCACCGAGGTAGTTAGCATCGGTATAG           <  2:905697/150‑1                                                                                                                                                   CCGTCAAATCCTTGACGGGCATTATTTAGATTAAATTACCAGTATTTCTTCGGAGTGAAGAATATTACCAGGTATATTTAACACCCACGTTCGCGGACCAGTCTTGATCTACGTCACCACCACCGAGGTAGTTAGCATCGGTATAGGCGC       >  1:878841/1‑150                                                                                                                                                      TCAAATCCTTGACGGGCATTATTTAGATTAAATTACCAGTATTTCTTCGGAGTGAAGAATATTACCAGGTATATTTAACACCCACGTTCGCGGACCAGTCTTGATCTACGTCACCACCACCGAGGTAGTTAGCATCGGTATAGGCGCTGA    <  2:952289/150‑1                                                                                                                                                      TCAAATCCTTGACGGGAATTATTTAGATTAGATTACCAGTATTTCTTCGGAGTGAAGAATATTACCAGGTATATTTAACACCCACGTTCGCGGACCAGTCTTGATCTACGTCACCACCACCCAGGTAGTTAGCATCGGTATAGGCGCTGc    >  2:537699/1‑149                                                                                                                                                       CAAATCCTTGACGGGCATTATTTAGATTAAATTACCAGTATTTCTTCGGAGTGAAGAATATTACCAGGTATATTTAACACCCACGTTCGCGGACCAGTCTTGATCTACGTCACCACCACCGAGGTAGTTAGCATCGGTATAGGCGCTGAA   <  1:945420/150‑1                                                                                                                                                        AAATCCTTGACGGGCATTATTTAGATTAAATTACCAGTATTTCTTCGGAGTGAAGAATATTACCAGGTATATTTAACACCCACGTTCGCGGACCAGTCTTGATCTACGTCACCACCACCGAGGTAGTTAGCATCGGTATAGGCGCTGAAG  >  3:553788/1‑150                                                                                                                                                                                                                                                                                                               CACCAAGAACTTCAGCGCCTATACCGATGCTAACTACCTCGGTGGTGGTGACGTAGATCAAGACTGGTCCGCGAACGTGGGTGTTAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAATAATGCCCGTCAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913_3_pae_tpiA/394319‑394471 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑taatgcccgtcaaATCCTTGACGGGCATTATTTAGATTAAATTACCAGTATTTCTTCGGAGTGAAGAATATTACCAGGTATATTTAACACCCACGTTCGCGGACCAGTCTTGATCTACGTCACCACCACCGAGGTAGTTAGCATCGGTATAGGCGCTGAAG  <  NC_000913_3_pae_tpiA/394475‑394328

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ 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.