New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	= 253532	32 (0.950)	3 (0.120) +AAGGGACGAATATATTTGCCCATGTACCATTCCATT	3/210	3.7	12.0%	pseudogene (54/207 nt)	ykfJ	pseudogene
	?	NC_000913_3_pae_tpiA	596980 =	27 (0.800)					intergenic (+7/‑151)	cusC/cusF	copper/silver efflux system, outer membrane component/periplasmic copper‑ and silver‑binding protein
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

TCGCCAGGAGCTTACATAAGTAAGTGACTGGGGTGAACGAACGCAGTCGCAGTACATGCAACTTGAAGTATGACGAGTATAAATGGAATGGTACATGGGCAAATATATTCGTCCCTTATCCGATGCGGTATTTACCATCGCATCTGATGACCTGTGGATCGAGAGTTTAGCGATCCAACAATTACACACCACGGCAAATTTACCCAACATGCAGCGCGTAGTGGGGATGCCAGATTTACACCCCGGACGCGGCTACCCGATTGGCGCAGCGTTCTTCTCTGTTGGTCGTTT  >  NC_000913_3_pae_tpiA/253385‑253675                                                                                                                                                    |                                                                                                                                                tCGCCAGGAGCTTACATAAGTAAGTGACTGGGGTGAACGAACGCAGTCGCAGTACATGCAACTTGAAGTATGACGAGTATAAATGGAATGGTACATGGGCAAATATATTCGTCCCTTATCCGATGCGGTATTTACCATCGCATCtgatga                                                                                                                                               >  2:292355/1‑150 (MQ=255)    ccAGGAGCTTACATAAGTAAGTGACTGGGGTGAACGAACGCAGTCGCAGTACATGCAACTTGAAGTATGACGAGTATAAATGGAATAGTACATGGGCAAATATATCCGTCCCTTATCCGATGCGGCATTTACCATCCCATCTGATGACCt                                                                                                                                            >  2:203906/1‑150 (MQ=255)    ccAGGAGCTTAAATAAGTAAGTGACTGGGGTGAACGAACGCAGTCGCAGTACATGCAACTTGAAGTATGACGAGTATAAATGGAATGGTACATGGGCAAATATATTCGTCCCTTATCCGATGCGGTATTTACCATCGCATCTGATGACCt                                                                                                                                            <  1:267669/150‑1 (MQ=255)      aGGCGCTTACATAAGTAAGTGACTGGGGTGAACGAACGCAGTCGCAGTACATGCAACTTGAAGTATGACGAGTATAAATGGAATGGTACATGGGCAAATATATTCGTCCCTTATCCGATGCGGTATTTACCATCGCATCTGATGACCtgt                                                                                                                                          <  1:203906/150‑1 (MQ=255)      aGGAGCTTACATAAGTAAGTGACTGGGGTGAACGAACGAAGTCGCAGTACATGCAACTTGAAGTATGACGAGTATAAATGGAATGGTACATGGGCAAATATATTCGTCCCTTATCCGATGCGGTATTTACCATCGCATCTGATGACCtgt                                                                                                                                          <  2:397757/150‑1 (MQ=255)        gAGCTTACATAAGTAAGTGACTGGGGTGAACGAACGCAGTCGCAGTACATGCAACTTGAAGTATGACGAGTATAAATGGAATGGTACATGGGCAAATATATTCGTCCCTTATCCGATGCGGTAATTACCATCGCATCTGATGACCTGTgg                                                                                                                                        >  1:159425/1‑150 (MQ=255)              aCATAAGTAAGTGACTGGGGTGAACGAACGACGTAGCAGTACATGCAACTTGAAGTATGACGAGTATAAATGGAATGGTACATGGGCAAATATATTCGTCCCTTATCCGATGCGGTATTTACCATCGCATCTGATGACCTGTGGATCgag                                                                                                                                  >  1:442999/1‑150 (MQ=255)                aTAAGAAAGTGACTAAGACGAACGTACGCCCGCGCTGTGCAGTCATGTTGAAGTATGACTTGTATTAATGGAATGGTACATGGGCAAATATATTCGTCCCTTATCCGATGCGGTATTTACCATCGCATCTGATGACCTTTGGATCGacag                                                                                                                                >  2:354946/1‑150 (MQ=255)                  aagtaagtGACTGGGGTGAACGAACGCAGTCGCAGTACATGCAACTTGAAGTATGACGAGTATAAATGGAATGGTACATGGGCAAATATATTCGTCCCTTATCCGATGCGGTATTTACCATCGCATCTGATGACCTGTGGATCGAGAGtt                                                                                                                              >  1:550410/1‑150 (MQ=255)                     taagtGACTGGGGTGAACGAACGCAGTCGCAGTACATGCAACTTGAAGTATGACGAGTATAAATGGAATGGTACATGGGCAAATATATTCGTCCCTTATCCGATGCGGTATTTACCATCGCATCTGATGACCTGTGGATCGAGAGTTTAg                                                                                                                           >  2:241231/1‑150 (MQ=255)                           acgggggTGAACGAACGCAGTCGCAGTACATGCAACTTGAAGTATGACGAGTATAAATCGAATGGTACATGGGCAAATATATTCGTCCCTTATCCGATGCGGTATTTACCATCGCATCTGATGACCTGTGGATCGAGAGTTTAGCGATcc                                                                                                                     <  2:504753/147‑1 (MQ=255)                                 gTGAACGAACGCAGTCGCAGTACATGCAACTTGAAGTATGACGAGTATAAATGGAATGGTACATGGGCAAATATATTCGTCCCTTATCCGATGCGGTATTTACCATCGCATCTGATGACCTGTGGATCGAGAGTTTAGCGATCCAACAAt                                                                                                               >  1:467972/1‑150 (MQ=255)                                    aacgaacgCAGTCGCAGTACATGCAACTTGAAGTATGACGAGTATAAATGGAATGGTACATGGGCAAATATATTCGTCCCTTATCCGATGCGGTATTTACCATCGCATCTGATGACCTGTGGATCGAGCGTTTAGCGATCCAACAATTac                                                                                                            <  2:442999/150‑1 (MQ=255)                                     acgaacgCAGTCGCAGTACATGCAACTTGAAGTATGACGAGTATAAATGGAATGGTACATGGGCAAATATATTCGTCCCTTATCCGATGCGGTATTTACCATCGCATCTGATGACCTGTGGATCGAGAGTTTAGCGATCCAACAATTaca                                                                                                           <  1:133732/150‑1 (MQ=255)                                                      aCATGCAAATTGAAGTATGACGAGTATAAATGGAATGGTACATGGGCAAATATATTCGTCCCTTATCCGATGCGGTATTTACCATCGCATCTGATGACCTGTGGATCGAGAGTTTAGCGATCCAACAATTACACACCACGGCAAATTTAc                                                                                          <  2:40764/150‑1 (MQ=255)                                                               ttGAAGTATGACGAGTATAAATGGAATGGTACATGGGCAAATATATTCGTCCCTTATCCGATGCGGTATTTACCATCGCATCTGATGACCTGTGGATCGAGAGTTTAGCGATCCAACAATTACACACCACGGCAAATTTACCCAACATGc                                                                                 >  2:44607/1‑150 (MQ=255)                                                                  aaGTATTACGAGTATAAATGGAATGGTACATGGGCAAATATATTCGTCCCGTATCCGATGCGGTATTTACCATCGCATCTGATGACCTGTGGATCGAGAGTTTAGCGATCCAACAATTACACACCACGGCAAATTTACCCAACATGCAgc                                                                              <  2:293113/150‑1 (MQ=255)                                                                       tGACGAGTATAAATGGAATGGTACATGGGCAAATATATTCGTCCCTTATCCGATGCGGTATTTACCATCGCATCTGATGACCTGTGGATCGAGAGTTTAGCGATCCAACAATTACACACCACGGCAAATTTACCCAACATGCAg                                                                               >  2:550786/1‑144 (MQ=255)                                                                       tGACGAGTATAAATGGAATGGTACATGGGCAAATATATTCGTCCCTTATCCGATGCGGTATTTACCATCGCATCTGATGACCTGTGGATCGAGAGTTTAGCGATCCAACAATTACACACCACGGCAAATTTACCCAACATGCAg                                                                               <  1:550786/144‑1 (MQ=255)                                                                              tataAATGGAATGGGACATGGGTAAATATATTCGTCCCTTATCCGATGCGGTATTTACCATCGCATCTGATGACCTGTGGATCGAGAGTTTAGCGATCCAACAATTACTCCTCTCGGCAAATTCACCCAACATGCAGCGCGTAGTGGGGa                                                                  <  2:547081/150‑1 (MQ=255)                                                                                 aaaTGGAATGGTACATGGGCAAATATATTCGTCCCTTATCCGATGCGGTATTTACCATCGCATCTGATGACCTGTGGATCGAGAGTTTAGCGATCCAACAATTACACCCCACGGCAAATTTACCCAACCTGCAGCGCGTAGTGGGGATGc                                                               >  2:361681/1‑150 (MQ=255)                                                                                  aatggaatggTACATGGGCAAATATATTCGTCCCTTATCCGATGCGGTATTTACCATCGCATCTGATGACCTGTGGATCGAGAGTTTAGCGATCCAACAATTACACACCACGGCAAATTTACCCAACATGCAGCGCGTAGTGGGGATGcc                                                              <  1:241231/150‑1 (MQ=255)                                                                                      gaatggTACATGGGCAAATATATTCGTCCCTTATCCGATGCGGTATTTACCATCGCATCTGATGACCTGTGGATCGAGAGTTTAGCGATCCAACAATTACACACCACGGCAAATTTACCCAACATGCAGCGCGTAGTGGGGATGCCAGAt                                                          >  1:107403/1‑150 (MQ=255)                                                                                                tGGGCAAATATATTCGTCCCTTATCCGATGCGGTATTTACCATCGCATCTGATGACCTGTGGATCGAGAGTTTAGCGATCCAACAATTACACACCACGGCAAATTTACCCAACATGCAGCGCGTAGTGGGGATGCCAGATTTACAccccc                                                >  2:337258/1‑149 (MQ=255)                                                                                                     aaaTATATTCGTCCCTTATCCGATGCGGTATTTACCATCGCATCTGATGACCTGTGGATCGAGAGTTTAGCGATCCAACAATTACACACCACGGCACATTTCCCCAACATGCAGGGCGGAGTGGGGGTGCCAGATTTACACCCCGGAcgc                                           >  1:166285/1‑150 (MQ=255)                                                                                                          tatTCGTCCCTTATCCGATGCGGTATTTACCATCGCATCTGATGACCTGTGGATCGAGAGTTTAGCGATCCAACAATTACACACCACGGCAAATTTACCCAACATGCAGCGCGTAGTGGGGATGCCAGATTTACACCCCGGACGCCGCTa                                      <  2:159425/150‑1 (MQ=255)                                                                                                                tCCCTTATCCGATGCGGTATTTACCATCGCATCTGATGACCTGTGGATCGAGAGTTTAGCGATCCAACAATTACACACCACGGCAAATTTACCCAACATGCAGCGCGTAGTGGGGATGCCAGATTTACACCCCGGACGCGGCTACCCGAt                                <  1:44607/150‑1 (MQ=255)                                                                                                                  ccTTATCCGATGCGGTATTTACCATCGCATCTGATGACCTGTGGATCGAGAGTTTAGCGATCCGACAATTACACACCACGGCAAATTTACCCAACATGCAGCGCGTAGTGGGGATGCCAGATTGACACCCAGGACGCGGCTACCCGATTg                              >  1:378635/1‑150 (MQ=255)                                                                                                                  ccTTATCCGATGCGGTATTTACCATCGCATCTGATGACCTGTGGATCGAGAGTTTAGCGATCCAACAATTACACACCACGGCAAATTTACCCAACATGCAGCGCGTAGTGGGGATGCCAGATTTACACCCCGGACGCGGCTACCCGATTg                              >  1:257451/1‑150 (MQ=255)                                                                                                                                      aCCATCGCATCTGATGACCTGTGGATCGAGAGTTTAGCGATCCAACAATTACACACCACGGCAAATTTACCCAACATGCAGCGCGTAGTGGGGATGCCAGATTTACACCCCGGACGCGGCTACCCGATTGGCGCAGCGTTCTTCTCTGtt          <  2:107403/150‑1 (MQ=255)                                                                                                                                            ccaccTGATGACCTGTGGATCGCGAGTTTAGCGATCCAACAATGACACGCCACGGCAAATTTACCCAACACGCAGCGCGTAGTGGGGATGCCAGATTTACACCCCTGACGCGGCTACCCGATTGGCGCAGCGTTCTTCTCTGTTGGTCGt    <  2:319909/146‑1 (MQ=255)                                                                                                                                              aTCTGATGACCTGTGGATCGAGAGTTTAGCGATCCAACAATTACACACCACGGCAAATTTACCCAACATGCAGCGCGTAGTGGGGATGCCAGCTTTACACCCCGGACGCGGCTACCCGCTTGGCGCAGCGTTCTTCTCTGTTTGTCGttt  >  2:406346/1‑150 (MQ=255)                                                                                                                                                    |                                                                                                                                                TCGCCAGGAGCTTACATAAGTAAGTGACTGGGGTGAACGAACGCAGTCGCAGTACATGCAACTTGAAGTATGACGAGTATAAATGGAATGGTACATGGGCAAATATATTCGTCCCTTATCCGATGCGGTATTTACCATCGCATCTGATGACCTGTGGATCGAGAGTTTAGCGATCCAACAATTACACACCACGGCAAATTTACCCAACATGCAGCGCGTAGTGGGGATGCCAGATTTACACCCCGGACGCGGCTACCCGATTGGCGCAGCGTTCTTCTCTGTTGGTCGTTT  >  NC_000913_3_pae_tpiA/253385‑253675

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.