New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	1399590 =	38 (0.970)	3 (0.080)	3/276	NT	7.3%	intergenic (‑64/+131)	fnr/ogt	oxygen‑sensing anaerobic growth regulon transcriptional regulator FNR; autorepressor/O‑6‑alkylguanine‑DNA:cysteine‑protein methyltransferase
	?	NC_000913_3_pae_tpiA	2101749 =	NA (NA)					intergenic (‑5/+146)	wbbL/insH1	pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator

AAAGCTGGCTGATGCTGCAATCCTGGCAATGGATAGCACAACCGCCAGACTGAATGCGCCGTATAATTCGCTTTTCCGGGATCATAGGTCTGCTCAAGCCGTAATTGATATTTGTCAATTTTAACATCTTTTTAGGGAGCAAGTAAGTCTAAGCAAACCTTAACAGCAGAGAATTCCGATATTAGATGTAAATATATGTCTATCTATTTGAAAACCCTTAAGTTGTTAAGGGTAACTTTACATAAAAGTGTGAACAAGCTGGCACAAATTGTTTAATGTTTACAGCAAAAGATAACC  >  NC_000913_3_pae_tpiA/1399442‑1399738                                                                                                                                                     |                                                                                                                                                     aaaTCTGGCTGATGCGGCAAGCGTGGCAATTGATAGCACAACCGCCAGACTGAATGCGCCGTATAATTCGCTTTTCCGTGATCATAGGTCTGCTCAAGCCGTAATTGATATTTGTCAATTTTAACATCTTTTTAGGGAGCAAGTAAGTc                                                                                                                                                      <  2:71076/149‑1 (MQ=255)               ttgcAATCCTGGGAATGGATAGCACGACCGCCAGGCTGGATGCGCCGTAGAATTGGTTTTTCCGGGATCATAGGTCTGCTCAAGCCGTAATTGATATTTGTCAATTTTAACATCTTTTTAGGGAGCAAGTAAGTCTAAGCAAACCTTaa                                                                                                                                        <  2:403309/148‑1 (MQ=255)                tgcAATCCTGGCAATGGATAGCACAACCGCCAGACTGAATGCGCCGTATAATTCGCTTTTCCGGGATCATAGGTCTGCTCAAGCCGTAATTGATATTTGTCAATTTTAACATCTTTTTAGAGAGCAAGTAAGTCTAAGCAAACCTTAAc                                                                                                                                       >  2:102328/1‑149 (MQ=255)                  cAATCCTGGCAATGGATAGCACAACCGCCAGACTGAATGCGCCGTATAATTCGCTTTTCCGGGATCATAGGTCTGCTCAAGCCGTAATTGATATTTGTCAATTTTAACATCTTTTTAGGGAGCAAGTAAGTCTAAGCAAACCTTAAcag                                                                                                                                     >  2:516561/1‑149 (MQ=255)                   aaTCCTGGCAATGGATAGCACAACCACCAGACTGAATGCGCCGTATAATTCGCTTTTCCGGGATCATAGGTCTGCTCAAGCCGTAATTGATATTTGTCAATTTTAACATCTTTTTAGGGAGCAAGTAAGTCTAAGCACACCTTAAcaca                                                                                                                                    >  1:130193/1‑147 (MQ=255)                     tCCTGGCAATGGATAGCACAACCGCCAGACTGAATGCGCCGTATAATTCGCTTTTCCGGGATCATAGGTCTGCTCAAGCCGTAATTGATATTTGTCAATTTTAACATCTTTTTAGGGAGCAAGTAAGTCTAAGCAAACCTTAAcagcag                                                                                                                                  <  1:588708/149‑1 (MQ=255)                      ccTGGAAATGGATATCACAACCGCCAGACTGAATGCGCCGTATAATTCGCTTTTCCGGGATTATAGGTCTGCTCAAGCCGTAATTGATATTTGTCAATTTTAACATCTTTTTAGGGAGCAAGTAAGTCTAAGCAAACCTTAACAGCaga                                                                                                                                 <  1:116107/149‑1 (MQ=255)                        tGGCAATGGATAGCACAACCGCCAGACTGAATGCGCCGTATAATTCGCTTTTCCGGGATCATAGGTCTGCTCAAGCCGTAATTGATATTTGTCAATTTTAACATCTTTTTAGGGAGCAAGTAAGTCTAAGCAAACCTTAACAGCAgaga                                                                                                                               >  1:52017/1‑149 (MQ=255)                            caggtctAGAACATCCGCCAGACTGAATTCTCCGTATAATTCGCTGTTCCGGGATCATAGGTCTGCTCAAGCCGTAACTGATATTTGTCAATTTTAACATCTTTTTAGGGAGCAAGTAAGTCTAAGCAAACCTTAACAGCAGAGAATTc                                                                                                                           <  2:47173/143‑1 (MQ=255)                                             ccAGACTGAATGCGCCGTATAATTCGCTTTTCCGGGATCATAGGTCTGCTCAAGCCGTAATTGATATTTGTCAATTTTAACATCTTGTTACGGCGCAACCGAGTCTAAGCAAACCTTAACAGCAGAGAATTCCGATATTAGATGTAAat                                                                                                          >  1:691893/1‑149 (MQ=255)                                                     aaTGCGCCGTATAATTCGCTTTTCAGGGATCATAGGTCTGCTCAAGCCGTAATTGATATTTGTCAATTTTAACATCTTTTTAGGGAGCAAGTAAGTCTAAGCAAACCTTACCAGCAGATCATTCCGATATTAGCTGTAAataacagtct                                                                                                  >  2:735088/1‑142 (MQ=255)                                                        gcgcCGTATAATTCGCTTTTCCGGGATCATAGGTCTGCTCAAGCCGTAATTGATATTTGTCAATTTTAACATCTTTTTAGGGAGCAAGTAAGTCTAAGCAAACCTTAACAGCAGAGAATTCCGATATTAGATGTAAATATATTtctatc                                                                                               >  1:107042/1‑149 (MQ=255)                                                            gatttacgggagaaaaaagtggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttatgcgcaccttccCTAAGAAAACCTTAACAGCAGAGAATTCCGATATTAGATGTAAATATATGTCTATCTAtt                                                                                           >  2:226427‑M1/90‑149 (MQ=255)                                                                taATTGGCTTTTCCGGGATCATAGGTCTGCTCAAGCCGTAATTGATATTTGTCAATTTTAACATCTTTTTAGGGAGCAAGTAAGTCTAAGCAAACCTTAACAGCAGAGAATTCCGATATTAGATGTAAATATATGTCTATCTATTTGaa                                                                                       >  2:638891/1‑149 (MQ=255)                                                                   ttCGCTTTTCCGGGATCATAGGTCTGCGCAAGCCGTAATTGATATTTGTCAATTTTAACATCTTTTTAGGGAGCCAGTAAGTCTAAGCAAACCTTAACAGCCGAGAATTCCGATATTAGATGTAAATAGCTGTCTATCTATTTGAAAAc                                                                                    >  2:122914/1‑149 (MQ=255)                                                                    ggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccCTAAGCAAACCTTAACAGCAGAGAATTCCGATATTAGATGTAAATATATGTCTATCTATTTGAAAAcc                                                                                   >  1:519066‑M1/82‑149 (MQ=255)                                                                     cGCTTTTCCGGGATCATAGGTCTGCTCAAGCCGTAATTGATATTTGTCCATTTTAACGTCCGATTGTGGAGCAAGTAAGTCTAAGCAAACCTTAACAGCAGAGAATTCCGATATTAGATGTAAATATATGTCTATCTATTTGAAAAccc                                                                                  <  1:722765/149‑1 (MQ=255)                                                                          ttCCGGGATCATAGGTCTGCTCAAGCCGTAATTCATCCCTTTTTATTTTAACATCTTTTTAGGGAGCAAGTAAGTCTAAGCAAACCTTAACAGCAGAGAATTCCGATATTAGATGTAAATATATGTCTATCTATTTGAAAACCCTTAAg                                                                             >  1:543989/1‑149 (MQ=255)                                                                            ccGGGATCATAGGTCTGCTCAAGCCGTAATTGATATTTGTCAATTTTAACATCTTTTTAGGGAGCAAGTAAGTCTAAGCAAACCTTAACAGCAGAGAATTCCGATATTAGATGTAAATATATGTCTATCTATTTGAAAACCCTTAAgtt                                                                           <  1:516561/149‑1 (MQ=255)                                                                                    aTAGGTCTGCTCAAGCCGTAATTGATATTTGTCAATTTTAACATCTTTTTAGGGAGCAAGTAAGTCTAAGCAAACCTTAACAGCAGAGAATTCCGATATTAGATGTAAATATATGTCTATCTATTTGAAAACCCTTAAGTTGTTAAggg                                                                   >  1:668184/1‑149 (MQ=255)                                                                                       tgTCTCCTCAAGCCGTAAATGACATTGGTCAAATTTAACAACTTTTTAGGGAGCAAGTAAGTCGAAGCAAACCATAACACCAGAGAATTCCGATATTAGATGTAAATATATGTCTATCTATTTGAAAACCCTTAAGTCATTAAGGGTaa                                                                <  2:234746/148‑1 (MQ=255)                                                                                         tCTGCTCAAGCCGTAATTGATATTTGTCAATTTTAACATCTTTTTAGGGAGCAAGTAAGTCTAAGCAAACCTTAACAGCAGAGAATTCCGATATTAGATGTAAATATATGTCTATCTATTTGAAAACCCTTAAGTTGTTAAGGGTAACt                                                              >  1:731824/1‑149 (MQ=255)                                                                                             ctgaaGCCGGAATTGATATTTGTCAATTTTACATTACTTTTAAAGAGAAAGTCAATGTAAGCAAATTTTGACAGAATATAAGTCTGATATTATATGTAAATATATGTTTATGTATTTTAAAACCCTTAAGTTGTTAAGGGTAACTTTAc                                                          <  2:541619/146‑1 (MQ=255)                                                                                             agaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccCTAAGCAAACCTTAACAGCAGAGAATTCCGATATTAGATGTAAATATATGTTTACCTATTTGAAAACCCTTAAGTTGTTTAGGGTAACTTTAc                                                          <  2:628791‑M1/93‑1 (MQ=255)                                                                                                   cagTAATTTATATTTGTCAATTTTAACATCTTTTTAGGGAGCAAGTAAGTCTAAGCAAACCTTAACAGCAGAGAATTCCGATATTAGATGTAAATATATGTCTATCTATTTGAAAACCCTTAAGTTGTTAAGGGTAACTTTACATaaaa                                                    <  2:73340/147‑1 (MQ=255)                                                                                                      aaagtGATATTTGTCAATTTTAACATCTTTTTAGGGAGCAAGTAAGTGTAAGCAAACCTTAACAGCAGAGAATTCCGAGATTAGATGTAAATATATGGCTATCTATTTGAAAACCCTTAAGTTGTTAAGGGTAACTTTACATAAAAgtg                                                 <  2:83669/145‑1 (MQ=255)                                                                                                        aTTGATATTTGTCAATTTTAACATCTTTTTAGGGAGCAAGTAAGTCTAAGCAAACCTTAACAGCAGAGAATTCCGATATTAGATGTAAATATATGTCTATCTATTTGAAAACCCTTAAGTTGTTAAGGGTAACTTTACATAAAAGtgtg                                               >  1:269572/1‑149 (MQ=255)                                                                                                        aTTGATATTTGTCAATTTTAACATCTTTTTAGGGAGCAAGTAAGTCTAAGCAAACCTTAACAGCAGAGAATTCCGATATTAGATGTAAATATATGTCTATCTATTTGAAAACCCTTAAGTTGTTAAGGGTAACTTTACATAAAAGtgtg                                               >  1:409908/1‑149 (MQ=255)                                                                                                         ttGATATTTGTCAATTTTAACATCTTTTTAGGTTGTAAGTAAGTGTAAGCAAACCTTAACAGCAGAGAATTCCGCTATTAGATGTAAATATATGTCTATCTTTTTGAAAACCCTTAAGTTGTTAAGAGTAACTTTAAATaaaatgatga                                              >  2:651543/1‑143 (MQ=255)                                                                                                           gATATTTGTCAATTTTAACACCCTTTTAGGGAGCAAGTAAGTCTAAGCAAACCTTAACAGCAGAGAATTACGATATCAGATTTAAATATATGTCTATCTATTTGAAAACCCTTAAGTTCTTAAGGGTAACTTTACATAAAAGTGTGAAc                                            <  1:429489/149‑1 (MQ=255)                                                                                                                 tGTCAATTTTAACATCTTTTTAGGGAGCAAGTAAGTCTAAGCAAACCTTAACAGCAGAGAATTCCGATATTAGATGTAAATATATGTCTATCTATTTGAAAACCCTTAAGTTGTTAAGGGTAACTTTACATAAAAGTGTGAACAAGCTg                                      <  1:369399/149‑1 (MQ=255)                                                                                                                   tCAATTTTAACATCTTTTTAGGGAGCAAGTAAGTCTAAGCAAACCTTAACAGCAGAGAATTCCGATATTAGATGTAAATATATGTCTATCTATTTGAAAACCCTTAAGTTGTTAAGGGTAACTTTACATAAAAGTGTGAACAAGCTgga                                    >  1:91095/1‑148 (MQ=255)                                                                                                                     aaTTTTAACATCTTTTTAGGGAGCAAGTAAGTCTAAGCAAACCTTAACAGCAGAGAATTCCGATATTAGATGTAAATATATGTCTATCTATTTGAAAACCCTTAAGTTGTTAAGGGTAACTTTACATAAAAGGTTGAACAAGATGGcac                                  >  1:260907/1‑149 (MQ=255)                                                                                                                             cagttttttAGTGAGCGAGTAGGTCTAAGCACACCTTAAGAGCAGAGAATTCCGATATTAGATGTAAATATATGGGTATCTATTTGAAAACCCTTGAGTTGTTAAGGGTAACTTTACATAAAAGTGTGAACAAGCTGGCACAAATTGtt                          <  2:39291/145‑1 (MQ=255)                                                                                                                             caccTTTTGAGGGGACAAGTAAGTCTAAGCAAACCTTAACAGCAGAGAATTCCGATATTAGATGTAAATATATGTCTATCTATTTGAAAACCCTTAAGTTGTTAAGGGTAACTTTACATAAAAGTGTGAACAAGCTGGCACAAATTGtt                          <  1:128263/146‑1 (MQ=255)                                                                                                                             cATCTTTTTAGGGAGCAAGTAAGCCTAAGCAAACCTTAAGAGCAGAGAATTCCGATATTAGATGTAAATATATGTCTATCTATTTGAAAACCCTTAAGTTGTTAAGGGTAACTTTACATAAAAGTGTGAACAAACTGGCACAAATTGtt                          <  2:604289/149‑1 (MQ=255)                                                                                                                              aTCTTTTTAGGGAGCAAGTAAGTCTAAGCAAACCTTAACAGCAGAGAATTCCGATATTAGATGTGAATATATGGCTATCTATTTGGAAACCCTTAAGTTGTTAAGGGTAACTTTACTTAAAAATGTGAACAAGCAGGGACAAAATGatt                         >  1:196778/1‑149 (MQ=255)                                                                                                                              aTCTTTTTAGGGAGCAAGTAAGTCTAAGCAAACCTTAACAGCAGAGAATTCCGATATTAGATGTAAATATATGTCTATCTATTTGAAAACCCTTAAGTTGTTAAGGGTAACTTTACATAAAAGTGTGAACAAGCTGGCACAAATTGttt                         >  1:321822/1‑149 (MQ=255)                                                                                                                                 tttttAGGGAGCAAGTAAGTCTAAGCAAACCTTAACAGCAGAGAATTCCGATATTAGATGTAAATATATGTCTATCTATTTGAAAACCCTTAAGTTGTTAAGGGTAACTTTACATAAAAGTGTGAACAAGCTGGCACAAATTGTTTAAt                      >  2:126697/1‑149 (MQ=255)                                                                                                                                 tttttAGGGAGCAAGTAAGTCTAAGCAAACCTTAACAGCAGAGAATTCCGATATTAGATGTAAATATATGTCTATCTATTTGAAAACCCTTAAGTCGTTAAGGGTAACTTTCCATAAAAGTGTGCACAAGCTGGCACAAATTGTTTCAt                      >  2:595729/1‑149 (MQ=255)                                                                                                                                      aGGGAGCAAGTAAGTCTAAGCAAACCTTAACAGCAGAGAATTCCGATATTAGATGTAAATATATGTCTATCTATTTGAAAACCATTAAGTTGTTATGGGTAACTTTTTATAAAAGTGTGAACAAGCTGGCACAAATTGTTTAATGTTTa                 <  2:265835/149‑1 (MQ=255)                                                                                                                                        ggAGCAAGTAAGTCTAAGCAAACCTTAACAGCAGAGAATTCCGATATTAGATGTAAATATATGTCTATCTATTTGAAAACCCTTAAGTTGTTAAGGGTAACTTTACATAAAAGTGTGAACAAGCTGGCACAAATTGTTTAATGTTTACa               <  1:529602/149‑1 (MQ=255)                                                                                                                                                   gtCTAAGCAAACCTTAACAGCAGAGAATGCCAATATTAGATGTAAATATATGTCTATCTATTTGAAAACCCTTAAGTTGTTAAGGGTAACTTTACATAAAAGTGTGAACAAGCTGGCACAAATTGTTTAATGTTTACAGCAAAAGATaa    <  2:200245/149‑1 (MQ=255)                                                                                                                                                     cTAAGCAAACCTTAACAGCAGAGAATTCCGATATTAGATGTAAATATATGTCTATCTATTTGAAAACCCTTAAGTTGTTAAGGGTAACTTTACATAAAAGTGTGAACAAGCTGGCACAAATTGTTTAATGTTTACAGCAAAAGATAAcc  <  2:637984/149‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                     AAAGCTGGCTGATGCTGCAATCCTGGCAATGGATAGCACAACCGCCAGACTGAATGCGCCGTATAATTCGCTTTTCCGGGATCATAGGTCTGCTCAAGCCGTAATTGATATTTGTCAATTTTAACATCTTTTTAGGGAGCAAGTAAGTCTAAGCAAACCTTAACAGCAGAGAATTCCGATATTAGATGTAAATATATGTCTATCTATTTGAAAACCCTTAAGTTGTTAAGGGTAACTTTACATAAAAGTGTGAACAAGCTGGCACAAATTGTTTAATGTTTACAGCAAAAGATAACC  >  NC_000913_3_pae_tpiA/1399442‑1399738

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ 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.