New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	= 394471	34 (1.030)	5 (0.170)	5/260	3.6	14.7%	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	27 (0.900)					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.

TTCAGCGCCTATACCGATGCTAACTACCTCGGTGGTGGTGACGTAGATCAAGACTGGTCCGCGAACGTGGGTGTTAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAATAATGCCCGTCAAGGATTTGACGGGCATTACTGCAAAGGACGCGCAAATGTTATCTGTAGTTAAACCTCTTCAGGAATTTGGTAAGCTCGATAAATGTTTGTCCAGATACGGTACGCGCTTCGAGTTTAATAATGAAAAGCAAGTTATATTTTCCAGTGA  >  NC_000913_3_pae_tpiA/394329‑394618                                                                                                                                                   |                                                                                                                                                ttCAGCGCCTATACCGATGCTAACTACCTCGGTGGTGGTGACGTAGATCAAGACTGGTCCGCGAACGTGGGTGTTAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAATAATGCCCGTCAAGGAttt                                                                                                                                               >  1:427831/1‑149 (MQ=255)     gcgcCTATTCCGATGCTAACTACCCCGGTGGTGGCGACGTAGATCAAGACTGGTCCGCCAACGTGGGTGTTAAATATACCTGGTAATATTCTTCTCTCCGAATAAATACTGGTAATTTAATCTAAATAATGCCCGTCAAGGATTTGACg                                                                                                                                           <  1:2516/149‑1 (MQ=255)        ccTATACCGATGCTAACTACCTCGGTGGTGGTGACGTAGATCAAGACTGGTCCGCGAACGTGGGTGTTAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAATAATGCCCGTCAAGGATTTGACGGGc                                                                                                                                        <  2:334074/149‑1 (MQ=255)         cTATACCGATGCTAACTACCTCGGTGGTGGTGACGTAGATCAAGACTGGTCCGCGAACGTGGGTGTTAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAATAATACCCGTCAAGGATTTGACGGCCa                                                                                                                                       >  1:565523/1‑149 (MQ=255)            taCCGATGCTAACTACCTCGGTGGTGGTGACGTAGATCAAGACTGGTCCGCGAACGTGGGTGTTAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAATAATGCCCGTCAAGGATTTGACGGGCATTa                                                                                                                                    >  2:486691/1‑149 (MQ=255)              ccGATGCGAACTACCTCCGTGGTGGTTACGTAGATCAAGACTGTACCGCCAACGTGGGTGTTAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAATAATGCCCGTCAAGGATTTGACGGGCATTACt                                                                                                                                  <  1:84864/149‑1 (MQ=255)               cGATGCTAACTACCTCGGTGGTGGTGACGTAGATCAAGACTGGTCCGCGAACGTGGGTGTTAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAATAATACCAGGCAAGGGTTTGACGGGCATTACTg                                                                                                                                 >  1:511224/1‑149 (MQ=255)                  tGCTAACTACCTCGGTGGTGGTGACGTAGATCAAGACTGGTCCGCGAACGTGGGTGTTAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAATAATGCCCGTCAAATCCTTGACGGGCATTatttaga                                                                                                                              <  1:28186/149‑7 (MQ=39)                   gCTAACTACCTCGGTGGTGGTGACGTAGATTAAGACTGGTCCGCGAACGTGGGTGTTAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAATAATGCCCGTCAAGGATTTGACGGGCATTACTGCaaa                                                                                                                             <  2:196271/149‑1 (MQ=255)                             tCGGTGGTGGTGACGTAGATCAAGACTGGTCCGCGAACGTGGGTGTTAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAATAATGCCCGTCAAGGATTTGACGGGCAt                                                                                                                                      >  2:341847/1‑130 (MQ=255)                             tCGGTGGTGGTGACGTAGATCAAGACTGGTCCGCGAACGTGGGTGTTAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAATAATGCCCGTCAAGGATTTGACGGGCAt                                                                                                                                      <  1:341847/130‑1 (MQ=255)                             tCGGTGGTGGTGACGTAGATCAAGACTGGTCCGCGAACGTGGGTGTTAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAATAATGCCCGTCAAGGATTTGACGGGCAGTACTGCAAAGGACGCGCaa                                                                                                                   >  1:338388/1‑149 (MQ=255)                                 tggtggtgACGTAGATCAAGACTGGTCCGCGAACGTGGGTGTTAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAATAATGCCCGTCAAGGATTTGACGGGCATTACTGCAAAGGACGCGCAAATGt                                                                                                               >  1:76465/1‑149 (MQ=255)                                    tggtgACGTAGATCAAGACTGGTCCGCGAACGTGGGTGTTAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAATAATGCCCGTCAAGGATTTGACGGGCATTACTGCAAAGGACGCGCAAATGTTAt                                                                                                            <  2:76465/149‑1 (MQ=255)                                       tgACGTAGATCAAGACTGGTCCGCGAACGTGGGTGTTAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAAGCTAAATAATGCCTGTCAACGATTTGACGGGCATTACTGCAAAGGACGCGCAAATGTTATCTg                                                                                                         <  1:424044/149‑1 (MQ=255)                                        gACGTAGATCAAGACTGGTCCGCGAACGTGGGTGTTAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAATAATGCCCGTCAAGGAATTGACGAGCTATACTGCTAAGGACGTGCAAATCTTATCTGt                                                                                                        >  1:157421/1‑149 (MQ=255)                                                           ccGCGAACGTGGGTGTTAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAATAATGCCCGTCAAGGATTTGACGGGCATTACTGCAAAGGACGCGCAAATGTTATCTGTAGTTAAACCTCTTCAGGaa                                                                                     <  2:419503/149‑1 (MQ=255)                                                           ccGCGAACGTGGGTGTTAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAATAATGCCCGTCAAGGATTTGACGGGCATTACTGCAAAGGACACGCAAATGTTATCTGTAGTTAAACCTCTTCAGGaa                                                                                     <  2:419502/149‑1 (MQ=255)                                                             gcgAACGTGGGTGTTAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAATAATGCCCGTCAAGGATTTGACGGGCATTACTGCAAAGGACGCGCAAATGTTATCTTTAGTTAAACCTCTTCAGGAAtt                                                                                   >  1:45444/1‑149 (MQ=255)                                                                 aCGTGGGTGTTAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAATAATGCCCGTCAAGTATTTGACGGGCATTACTGCAAAGGACGCGCAAATGTTATCTGTAGTTAAACCTCTTCAGGAATTTGGt                                                                               <  1:224278/149‑1 (MQ=255)                                                                          ttgaaTATACATGCTAATAGTCTGCAGACCGTTGAAATACTGGGAATTTAAGCTAAAGAATGCCGGTAAAGGATTTGACGGGTATTACTGCAAAGGACGCGCAAATGTTATCTGTAGTTAAACCTCTTCAGGAATTTGGTAAGCTCGAt                                                                      <  2:164284/146‑1 (MQ=255)                                                                          ttAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAATAATGCCCGTCAAGGATTTGACGGGCATTACTGCAAAGGACGCGCAAATGTTATCTGTAGTTAAACATCTTCAGGTATTTGGTGAGCTCGAt                                                                      >  1:83806/1‑149 (MQ=255)                                                                                    cTGGTAATATTCTTCACTCCGAAGAAATACTTGTAATTTAATCTAAATAATGCCCGTCAAGGATTTGACGGGCATTACTGCAAAGGACGCGCAAATGTTATCTGTAGTTAAACCTCTTCAGGAATTTGGTAAGCTCGATAAATGTTTGt                                                            <  2:227211/149‑1 (MQ=255)                                                                                      ggTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAATAATGCCCGTCAAGTATTTGACGGGCATTACTGCAAAGGACGCGCAAATGTTATCTGTAGTTAAACCTCTTCAGGAATTTGGTAAGCTCGATAAATGTTTGTcc                                                          <  2:569173/149‑1 (MQ=255)                                                                                      ggTAATATTCTTCACTACAAAGAAATACTGGTAATTTAATTTAAATAATGCCCGTCAAGGATTTGACGGGCACTACTGCAACGGACGCGCAAATGTTATCTGTAGTTAAACCTCTTCAGGAATTTGGTAAGCTCGATAAATGTTTGTcc                                                          <  2:315907/149‑1 (MQ=255)                                                                                                     tCCGAAGAAATACTGGTAATTTAATCTAAATAATGCCCTTCAAGGATTTGACGGGCATTACTGCAAAGGACGCGCAAATGTTATCTGTAGTTAAACCTCTTCAGGAATTTGGTAAGCTCGATAAATGTTTGTCCAGATACGGTACgcgc                                           >  2:505060/1‑149 (MQ=255)                                                                                                     tCCGAAGAAATACTGGTAATTTAATCTAAATAATGCCCGTCAAGGATTTGACGGGCATTACTGCAAAGGACGCGCAAATGTTATCTGTAGTTAAACCTCTTCAGGAATTTGGTAAGCTCGATAAATGTTTGTCCAGATACGGTACgcgc                                           >  1:183801/1‑149 (MQ=255)                                                                                                        gaagaaATACTGGTAATTTAATCTAAATAATGCCCGTCAAGGATTTGACGGGCATTACTGCAAAGGACGCGCAAATGTTATCTGTAGTTAAACCTCTTCCGGAATTTGGTAAGCTCGATAAATGTTTGTCCAGATACGGTACGCGCTTc                                        >  1:60164/1‑149 (MQ=255)                                                                                                        gaagaaATACTGGTAATTTAATCTAAATAATGCCCGTCAAGGATTTGACGGGCATTACTGCAAAGGACGCGCAAATGTTATCTGTAGTTAAACCTCTTCAGGAATTTGGTAAGCTCGATAAATGTTTGTCCAGATACGGTACGCGCTTc                                        <  1:486691/149‑1 (MQ=255)                                                                                                        gaagaaATACTGGTAAATTAATCTAAATAATGCCCGTCAAGGATTTGACCGGCATTACTGCACAGGACGCGCAAATGTTATCAGTTGTTAAACCTCTTCACGAATTTGGTAAGCTCGATAAATGTTTGTCCAGCTACGGTACGCGCTTc                                        >  2:519794/1‑149 (MQ=255)                                                                                                             aaTATTTGTAATTTAATCTAAATACTGCCCGGCAAGGATTTGACGGGCATTACTGCAAAGGACGCGCAAATGTTATCTGTAGTTAAACCTCTTCAGGAATTTGGTAAGCTCGATAAATGTTTGTCCAGATACGGTACGCGCTTCGAGtt                                   <  2:310982/149‑1 (MQ=255)                                                                                                                   ggTAATTTAATCTAAATAATGCCCGTCAAGGATTTGACGGGCATTACTGCAAAGGACGCGCAAATGTTATCTGTAGTTAAACCTCTTCAGGAATTTGGTAAGCTCGATAAATGTTTGTCCAGATACGGTACGCGCTTCGAGTTtaataa                             >  1:298254/1‑149 (MQ=255)                                                                                                                        tttAATCTAAATAATGCCCGTCAAGGATTTGACGGGCATTACTGCAAAGGACGCGCAAATGTTATCTGTAGTTAAACCTCTTCAGGAATTTGGTAAGCTCGATAAATGTTTGTCCAGATACGGTACGCGCTTCGAGTTTAATAATGaaa                        <  2:21219/149‑1 (MQ=255)                                                                                                                           aaTCTAAATAATGCCCGTCAAGGATTTGACGGGCATTACTGCAAAGGACGCGCAAATGTTATCTGTAGTTAAACCTCTTCAGGAATTTGGTAAGCTCGATAAATGTTTGTCCAGATACGGTACGCGCTTCGAGTTTAATAATGAAAAGc                     <  1:20965/149‑1 (MQ=255)                                                                                                                                              aaGGATTTGACGGGCATTACTGCAAAGGACGCGCAAATGTTATCTGTAGTTAAACCTCTTCAGGAATTTGGTAAGCTCGATAAATGTTTGTCCAGATACGGTACGCGCTTCGAGTTTAATAATGAAAAGCAAGTTATATTTTCCAGTGa  >  1:311687/1‑149 (MQ=255)                                                                                                                                                   |                                                                                                                                                TTCAGCGCCTATACCGATGCTAACTACCTCGGTGGTGGTGACGTAGATCAAGACTGGTCCGCGAACGTGGGTGTTAAATATACCTGGTAATATTCTTCACTCCGAAGAAATACTGGTAATTTAATCTAAATAATGCCCGTCAAGGATTTGACGGGCATTACTGCAAAGGACGCGCAAATGTTATCTGTAGTTAAACCTCTTCAGGAATTTGGTAAGCTCGATAAATGTTTGTCCAGATACGGTACGCGCTTCGAGTTTAATAATGAAAAGCAAGTTATATTTTCCAGTGA  >  NC_000913_3_pae_tpiA/394329‑394618

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ 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.