New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	= 2014974	32 (0.890)	5 (0.140)	5/272	4.3	11.9%	coding (95/996 nt)	fliG	flagellar motor switching and energizing component
	?	NC_000913_3_pae_tpiA	= 2014992	43 (1.230)					coding (113/996 nt)	fliG	flagellar motor switching and energizing component
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

ATAACGATCCGCGCGTGGTGGCGCTGGTCATTCGCCAGTGGATAAATAACGATCATGAGTAACCTGACAGGCACCGATAAAAGCGTCATCCTGCTGATGACCATTGGCGAAGACCGGGCGGCAGAGGTGTTCAAGCACCTCTCCCAGCGTGAAGTACAAACCCTGAGCGCTGCAATGGCGAACGTCACGCAGATCTCCAACAAGCAGCTAACCGATGTGCTGGCGGAGTTTGAGCAAGAAGCTGAACAGTTTGCCGCACTGAATATCAACGCCAACGATTATCTGCGCTCGGTATTG  >  NC_000913_3_pae_tpiA/2014826‑2015122                                                                                                                                                     |                                                                                                                                                     aTAACGATCCGCGCGTGGTGGCGCTGGTCATTCGCCAGTGGATAAATAACGATCATGAGTAACCTGACAGGCACCGGTGAAAGCGTCATCCTGCAGATGACCAGTGGCGAAGACCGGGCGGTAGCGCTGTTGAAGCACCTCTCCCAGCg                                                                                                                                                      >  2:537802/1‑149 (MQ=255)     cGATCCGCGCGTGGTGGCGCTGGTCATTCGCCAGTGGATAAATAACGATCATGAGTAACCTGACAGGCACCGATACAATCGTCAGCCTGCTGATGACCATTGGCGAAGACCGGGCGGCAGAGGTGTTCAAGCACCTCTCCCAGCGTGaa                                                                                                                                                  <  1:88950/149‑1 (MQ=255)                           gTCATTCGCCAGTGGATAAATAACGATCATGAGTAACCTGACAGGCACCGATAAAAGCGTCATCCTGCTGATGACCATTGGCGAAGACCGGGCGGCAGAGGTGTTCAAGCACCTCTCCCAGCGTGAAGTACAAACCCTGAGCGCTGCaa                                                                                                                            >  1:239379/1‑149 (MQ=255)                              aTTCGCCAGAGGATAAATAACGATCATGAGTAACCTGACAGGCACCGATAAAAGCGTCATCCTGCTGATGACCATTGGCGAAGACCGGGCGGCAGAGGTGTTCAAGCACCTCTCCCATCGTGAAGTACAAACCCTGAGCGCTGCAATgg                                                                                                                         <  2:40095/149‑1 (MQ=255)                                  gCCAGTGGATAAATAACCATCATGAGTACCCTGACCGGCACCGATAAAAGCGTCATCCTGCTGATGCAGATTGGCGAAGAACCCCAGACGGGTGGGTTCAAGCACCTCTCCCAGCGTGAAGTACAAACCCTGAGCGCTGCAATGGCGaa                                                                                                                     <  1:310668/149‑1 (MQ=255)                                       tGGATAAATAACGATCATGAGTAACCTGACAGGCACCGATAAAAGCGTCATCCTGCTGATGACCATTGGCGAAGACCGGGCGGCAGAGGTGTTCAAGCACCTCTCCCAGCGTGAAGTACAAACCCTGAGCGCTGCAATGGCGACCGTCa                                                                                                                <  2:430652/149‑1 (MQ=255)                                         gATAAATAACGATCATGAGTAACCTGACAGGCACCGATAAAAGCGTCATCCTGCTGATGACCATTGGCGAAGACCGGGCGGCAGAGGGGTTCGAGCACCTCTCCCAGCGTGAAGTACAAACCCTGAGCGCTCCAATGGCGAGCGTCCCg                                                                                                              >  2:321446/1‑149 (MQ=255)                                                                        cACCGATAAAAGCGTCATCCTGCTGATGACCATTGGCGAAGACCGGGCGGCAGAGGTGTTCAAGCACCTCTCCCAGCGTGAAGTACAAACCCTGAGCGCTGCAATGGCGAACGTCACGCAGATCTCCAACAAGCAGCTAACCGATGTGc                                                                               <  1:250500/149‑1 (MQ=255)                                                                        cACCGATAAAAGCGTCATCCTGCTGATGACCATTGGCGAAGACCGGGCGGCAGAGGTGTTCAAGCACCTCTCCCAGCGTGAAGTACAAACCCTGAGCGCTGCAATGGCGAACGTCAAGCAGATCTCCAACAAGCAGCTAAcccagcagc                                                                               >  2:306167/1‑142 (MQ=255)                                                                            gATAAAAGCGTCATCCTGCTGATGACCATTGGCGAAGACCGGGCGGCAGAGGTGTTCAAGCACCTCTCCCAGCGTGAAGTACAAACCCTGAGCGCTGCAATGGCGAACGTCACGCAGATCTCCAACAAGCAGCTACCCGATGTGCTGGc                                                                           >  1:8397/1‑149 (MQ=255)                                                                                 aaGCGTCGTTCTGCTGATGACCGTTGGCGAAGACCGGGCGGCAGAGGTGTTCAAGCACCTCTCCCAGCGTGAAGTACAAACCCTGAGCGCTGCAATGGCGAACGTCACGCAGATCTCCAACAAGCAGCTAACCGATGTGCTGGCGGAGt                                                                      >  2:396719/1‑149 (MQ=255)                                                                                    cGTCATCCTGCTGATGACCATTGGCGAAGACCGGGCGGCAGAGGTGTTCAAGCACCTCTCCCAGCGTGAAGTACAAACCCTGAGCGCTGCAATGGCGAACGTCACGCAGATCTCCAACAAGCAGCTAACCGATGTGCTGGCGGAGtt                                                                     >  1:31381/1‑147 (MQ=255)                                                                                    cGTCATCCTGCTGATGACCATTGGCGAAGACCGGGCGGCAGAGGTGTTCAAGCACCTCTCCCAGCGTGAAGTACAAACCCTGAGCGCTGCAATGGCGAACGTCACGCAGATCTCCAACAAGCAGCTAACCGATGTGCTGGCGGAGtt                                                                     <  2:31381/147‑1 (MQ=255)                                                                                    cGTCATCCTGCTGATGACCATTGGCGAAGACCGGGCGGCAGAGGTGTTCAAGCACCTCTCCCAGCGTGAAGTACAAACCCTGAGCGCTGCAATGGCGAACGTCACGCAGATCTCCAACAAGCAGCTAACCGATGTGCTGGCGGAGTTTg                                                                   <  1:81841/149‑1 (MQ=255)                                                                                     gTCATCCTGCTGATGACCATTGGCGAAGACCGGGCGGCAGAGGTGTTCAAGCACCTCTCCCAGCGTGAAGTACAAACCCTGAGCGCTGCAATGGCGAACGTCACGCAGATCTCCAACAAGCAGCTAACCGATGTGCTGGCGGAGTTTGa                                                                  <  1:173428/149‑1 (MQ=255)                                                                                     gTCATCCTGCAGATGACCATTGGCGAAGACCGGGCGGCAGAGGTGTTCAAGCACCTCTCCCAGCGTGAAGTACAAACCCTGAGCGCTGCAATGGCGAACGTCACGCAGATCTCCAACAAGCAGCTAACCGATGTGCTGGCGGAGTTTGa                                                                  <  2:476968/149‑1 (MQ=255)                                                                                      tCATCCTGCTGATGACCATTGGCGAAGACCGGGCGGCAGAGGTGTTCAAGCACCTCTCCCAGCGTGAAGTACAAACCCTGAGCGCTGCAATGGCGAACGTCACGCAGATCTCCAACAAGCAGCTAACCGATGTGCTGGCGGAGTTTGAg                                                                 <  2:323198/149‑1 (MQ=255)                                                                                      tCATCCTGCTGATGACCATTGGCGAAGACCGGGCGGCAGAGGTGTTCAAGCACCTCTCCCAGCGTGAAGTACAAACCCTGAGCGCTGCAATGGCGAACGTCACGCAGATCTCCAACAAGCAGCTAACCGATGTGCTGGCGGAGTTTGAg                                                                 >  1:96120/1‑149 (MQ=255)                                                                                           ctgctgATGACCATTGGCGAAGACCGGGCGGCAGAGGTGTTCAAGCACCTCTCCCAGCGTGAAGTACAAACCCTGAGCGCTGCAATGGCGAACGTCACGCAGATCTCCAACAAGCGGCTAACCGATGTGCTGGCGGAGGTTGAGCaaga                                                            >  2:384982/1‑149 (MQ=255)                                                                                                        ttGGCGAAGACCGGGCGGCAGAGGTGTTCAAGCACCTCTCCCAGCGTGAAGTACAAACCCTGAGCGCTGCAATGGCGAACGTCACGCAGATCTCCAACAAGCAGCTAACCGATGTGCTGGCGGAGTTTGAGCAAGAAGCTGAACAGttt                                               <  2:96120/149‑1 (MQ=255)                                                                                                                    gggCGGCAGAGGTGTTCAAGCACCTCTCCCAGCGTGAAGTACAAACCCTGAGCGCTGCAATGGCGAACGTCACGCAGATCTCCAACAAGCAGCTAACCGATGTGCTGGCGGAGTTTGAGCAAGAAGCTGAACAGTTTGCCGCACTGAat                                   >  1:29615/1‑149 (MQ=255)                                                                                                                           agagGTGTTCAAGCACCTCTCCCAGCGTGAAGTACAAACCCTGAGCGCTGCAATGGCGAACGTCACGCAGATCTCCAACAAGCAGCTAACCGATGTGCTGGCGGAGTTTGAGCAAGAAGCTGAACAGTTTGCCGCACTGAATATCAACg                            >  1:488200/1‑149 (MQ=255)                                                                                                                               gtgtTCAAGCACCTCTCCCAGCGTGAAGTACAAACCCTGAGCGCTGCAATGGCGAACGTCACGCAGATCTCCAACAAGCAGCTAACCGATGTGCCGGCGTACCTTTAGCAAGAAGCTGAACAGTTTGCCGCACTGAATATCAACGCCaa                        >  2:295365/1‑149 (MQ=255)                                                                                                                                 gtTCAAGCACCTCTCCCAGCGTGAAGTACAAACCCTGAGCGCTGCAATGGCGAACGTCACGCAGATCTCCAACAAGCAGCTAACCGAt                                                                                   <  1:578661/88‑1 (MQ=255)                                                                                                                                 gtTCAAGCACCTCTCCCAGCGTGAAGTACAAACCCTGAGCGCTGCAATGGCGAACGTCACGCAGATCTCCAACAAGCAGCTAACCGAt                                                                                   >  2:578661/1‑88 (MQ=255)                                                                                                                                     aaGCACCTCTCCCAGCGTGAAGTACAAACCCTGAGCGCTGCAATGGCGAACGTCACGCAGATCTCCAACAAGCAGCTAACCGATGTGCTGGCGGAGTTTGAGCAAGAAGCTGAACAGTTTGCCGCACTGAATATCAACGCCAACGATTa                  >  1:84786/1‑149 (MQ=255)                                                                                                                                      aGCACCTGCCCCAGCGTGAAGTACAAACCCTGAGCGCTGCAATGGCGAACGTCACGCAGATCTCCAACAAGCAGCTAACCGATGTGCTGGCGGAGTTTGAGCAAGAAGCTGAACAGTTTGCCGCACTGAATATCAACGCCAACGATTAt                 <  1:519059/149‑1 (MQ=255)                                                                                                                                        cACCTCTCCCGGCGTGAAGTACAAACCCTGAGCGCTGCAATGGCGAACGTCACGCAGATCTCCAACAAGCAGCTAACCGATGTGCTGGCGGAGTTTGAGCAAGAAGCTGAACAGTTTGCCGCACTGAATATCAACGCCAACGATTATCt               >  1:235929/1‑149 (MQ=255)                                                                                                                                            tctcCCAGCGTGAAGTACAAACCCTGAGCGCTGCAATGGCGAACGTCACGCAGATCTCCAACAAGCAGCTAACCGATGTGCTGGCGGAGTTTGAGCAAGAAGCTGAACAGTTTGCCGCACTGAATATCAACGCCAACGATTATCTgcgc           >  2:321145/1‑149 (MQ=255)                                                                                                                                             ctcCCAGCGTGAAGTACAAACCCTGAGCGCTGCAATGGCGAACGTCACGCAGATCTCCAACAAGCAGCTAACCGATGTGCTGGCGGAGTTTGAGCAAGAAGCTGAACAGTTTGCCGCACTGAATATCAACTCCAACGATTATCTGCGCt          >  2:436173/1‑149 (MQ=255)                                                                                                                                                     gTGAAGTACAAGACCGGAGCGCTGCAATGGCGAACGTCACGCAGATCGCCAACTAGCAGCTAACCGATGTGCTGGCGGAGTTTGAGCAAGAAGCTGAACAGTTTGCCGCACTGAATATCAACGCCAACGATTATCTGCGCTCGGTATTg  <  1:60044/149‑1 (MQ=255)                                                                                                                                                     gTGAAGTACAAACCCTGCGCGCTGCAATGGCTTACGTTACGCATATCTCCAACACGCAGCTAACCGATGTGCTGGCGGAGTTTGAGCAAGAATCTGAACAGTTTGCCGCACTGAATATCAACGCCAACGATTATCTGTGCTAGGTATTg  <  2:303021/149‑1 (MQ=255)                                                                                                                                                     gTGAAGTACAAACCCTGAGCGCTGCAATGGCGAACGTCACGCAGATCTCCAACAAGCAGCTAACCGATGTGCTGGCGGAGTTTGAGCAAGAAGCTGAACAGTTTGCCGCACTGAATATCAACGCCAACGATTATCTGCGCTCGGTATTg  <  2:79257/149‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                     ATAACGATCCGCGCGTGGTGGCGCTGGTCATTCGCCAGTGGATAAATAACGATCATGAGTAACCTGACAGGCACCGATAAAAGCGTCATCCTGCTGATGACCATTGGCGAAGACCGGGCGGCAGAGGTGTTCAAGCACCTCTCCCAGCGTGAAGTACAAACCCTGAGCGCTGCAATGGCGAACGTCACGCAGATCTCCAACAAGCAGCTAACCGATGTGCTGGCGGAGTTTGAGCAAGAAGCTGAACAGTTTGCCGCACTGAATATCAACGCCAACGATTATCTGCGCTCGGTATTG  >  NC_000913_3_pae_tpiA/2014826‑2015122

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.