New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	3186098 =	NA (NA)	3 (0.080)	3/272	NT	8.2%	intergenic (+8/‑89)	yqiG/insC1	pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein/IS2 repressor TnpA
	?	NC_000913_3_pae_tpiA	= 3546580	34 (0.870)					coding (22/1317 nt)	gntT	gluconate transporter, high‑affinity GNT I system

ATTAGTTTTAGTGGGTATCAGTCGTGGTGCCGCAATATCTCTGTTCCCGATTGGGATAATTAGAGTTTGTCGTCAGAAAATTGACGTTACCCATAACAAATGAAAGGCCAGGTAAATCATGCCATTAGTCATTGTTGCTATCGGTGTAATCTTGTTGTTGCTCCTGATGATCCGCTTCAAAATGAACGGCTTCATCGCTCTCGTCCTCGTGGCGCTTGCTGTTGGATTAATGCAAGGAATGCCGCTGGATAAAGTTATTGGCTCCATCAAAGCCGGTGTCGGCGGG  >  NC_000913_3_pae_tpiA/3546441‑3546726                                                                                                                                            |                                                                                                                                                   atTAGTTTTAGTGGGTATCAGTCGTGGTGCCGCAATATCTCTGTTCCCGATTGGGATAATTAGAGTTTGTCGTCAGAAAATTGACGTTACCCATAACAAATGAAAGGCCAGGTAAATCATGCCATTAGTCGTTGTTGCTATCGGTGTac                                                                                                                                           >  2:99166/1‑148 (MQ=255)  ttAGTTTTAGTGGGTATCAGTCGTGGTGCCGCAATATCTCTGTTCCCGATTGGGATAATTAGAGTTTGTCGTCGGAAAATTGACGTTACCCATAACAAATGAAAGGCGCGGTAAAGCATGCCCTTCGTCATCGTTGCTATCgggggcac                                                                                                                                          >  2:504202/1‑143 (MQ=255)  ttAGTTTTAGTGGGTATCAGTCGTGGTGCCGCAATATCTCTGTTCCCGATTGGGATAATTAGAGTTTGTCGTCAGAAAATTGACGTTACCCATAACAAATGAAAGGCCAGGTAAATCATGCCATTAGTCATTGTTGCTATCGGGGTAAt                                                                                                                                          >  1:662321/1‑149 (MQ=255)  ttAGTTTTAGTGGGTATCAGTCGTGGTGCAGCAATATCTCTGTTCCCGATTGGGATAATTAGAGTTTGTCGTCAGAAAATTGACGTTACCCATAACAAATGAAAGGCCAGGTAAATCATGCCATTAGTCATTGTTGCTATCGGTGTAAt                                                                                                                                          >  1:269492/1‑149 (MQ=255)      ttttAGTGGGTATCAGTCGTGGTGCCGCAATATCTCTGTTCCCGATTGGGATAATTAGAGTTTGTCGTCAGAAAATTGACGTTACCCATAACAAATGAAAGGCCAGGTAAATCATGCCATTAGTCCTTGCTGCTATCGGTGTAATCtgt                                                                                                                                      >  2:386631/1‑147 (MQ=255)       tttAGTGGGTATCAGTCGTGGTGCCGCAATATCTCTGTTCCCGATTGGGATAATTAGAGTTTGTCGTCAGAAAATTGACGTTACCCATAACAAATGAAAGGCCAGGTAAATCATGCCATTAGTCATTGTTGCTATCGGTGTAATCttgt                                                                                                                                     <  2:126583/149‑1 (MQ=255)               gTATCAGTCGTGGTGCCGCAATATCTCTGTTCCCGATTGGGATAATTAGAGTTTGTCGTCAGAAAATTGACGTTACCCATAACAAATGAAAGGCCAGGTAAATCATGCCATTAGTCATTGTTGCTATCGGTGTAATCTTGTTGTTGCTc                                                                                                                             <  1:222344/149‑1 (MQ=255)                      tCGTGGTGCCGCAATATCTCTGTTTCCGACCCCGTGGTGGGGAGTTTGTCGTCAGAAAATTGACGTTACCCATAACAAATGAAAGGCCAGGTAAATCATGCCCTTAATCCTTGTTGTCATCGGTGTAATCTTGTTTTTCCTTctgctgc                                                                                                                      >  2:156280/1‑148 (MQ=255)                       cGTGGTGCCGCAATATCTCTTTTCCCGATTGGGATAATTAGAGTTTGTCGTCAGAAAATTGACGTTACCCATAACAAATGAAAGGCCAGGTAAATCATGCCATTAGTCATTGTTGCTATCGGTGTAATCTTGTTGTTGCTCCTgatgat                                                                                                                     <  1:239892/149‑1 (MQ=255)                               cGCAATATCTCTGTTCCCGATTGGGATAATTAGAGTTTGTCGTCAGAAAATTGACGTTACCCATAACAAATGAAAGGCCAGGTAAATCATGCCATTAGTCATTGTTGCTATCGGTGTAATCTTGTTGTTGCTCCTGATGATCCGCTTCa                                                                                                             <  1:583187/149‑1 (MQ=255)                                gaaaTATCTCTGTTCCCGCTAGGGATAATTAGAGTTTATCGTCAGAAAATTGACGTTACACATAATAAATGAAAGTCCTGGTACATCATGCCATTAGGCATTCTTGCAATCGGTGTAATCTTGTTGTTACTCCTTATGATCTGCTTCac                                                                                                            >  2:939/3‑148 (MQ=255)                                gCAATATCTCTGTTCCCGATTGGGATAATTAGAGTTTGTCGTCAGACAATTGACGTTACCCATAACAAATGAAAGGCCAGGTAAATCATGCCATTAGTCATTGTTGCTATCGGTGGAATCTTGTTGTTGCTCCTGATGATCCGCTTCaa                                                                                                            >  1:103820/1‑149 (MQ=255)                                       ctctGTTCCCGATTGGGATAATTAGAGTTTGTCGTCAGAAAATTGACGTTACCAACAAAAATGGAAAGGCCAGGTAAATCATGCCATTAGTCATTGTTGCTATCGGTGTAATCTTGTTGTTGCTCCTGATGATCCGCTTCAAAATGAAc                                                                                                     <  1:722509/149‑1 (MQ=255)                                         ctGTTCCCGATTGGGATAATTAGAGTTTGTCGTCAGAAAATTGACGTTACCCATAACAAATGAAAGGCCAGGTAAATCCAGTCGGTTTGCATTGTTGCTATCGGTGTAATCTTGTTGTTGCTCCTGATGATCCGCTTCAAAATGAACgg                                                                                                   <  1:692188/149‑1 (MQ=255)                                               ccGATTGGGATAATTAGAGTTTGTCGTCAGAAAATTGACGTTACCCATAACAAATGAAAGGCCAGGTAAATCATGCCATTAGTCATTGTTGCTATCGGTGTAATCTTGTTGTTGCTCCTGATGATCCGCTTCAAAATGAACGGCTTCAt                                                                                             >  1:477961/1‑149 (MQ=255)                                               ccGATTGGGATAATTAGAGTTTGTCGTCAGAAAATTGACGTTACCCATAACAAATGAAAGGCCAGGTAAATCATGCCATTAGTCATTGTTGCTATCGGTGTAATCTTGTTGTTGCTCCTGATGATCCGCTTCAAAATGAACGGCTTCAt                                                                                             <  1:78606/149‑1 (MQ=255)                                                  aTTGGGATAATTAGAGTTTGTCGTCAGAAAATTGACGTTACCCATAACAAATGAAAGGCCAGGTAAATCATGCCATTAGTCATTGTTGCTATCGGCTTAATCTTGTTGTTGCTCCTGATGATCCGCTTCAAAATGAACGGCTTCATCGc                                                                                          <  1:509347/149‑1 (MQ=255)                                                      ggATAATGAGAGTTTTTCGTCAGAAAATTGACGTTACCCATAACAAATGAAAGGCCAGGTAAATCATGCCATTAGTCATTGTTGCTATCGGTGTAATCTTGTTGTTGCTCCTGATGATCCGCTTCAAAATGAACGGCTTCATCGCtctc                                                                                      <  1:508310/149‑1 (MQ=255)                                                         tAATTAGCGTTTGTCGTCAGAAAATTGACGTTACCCATAACAAATGAAAGGCCAGGTAAATCATGCCATTAGTCATTGTTGCTATCGGTGTAATCTTGTTGTTGCTCCTGATGATCCGCTTCAAAATGAACGGCTTCATCGCTCTCGTc                                                                                   <  2:434860/149‑1 (MQ=255)                                                                agTTTGTCGTCAGAAAATTGACGTTACCCATAACAAATGAAAGGCCAGGTAAATCATGCCATTAGTCATTGTTGCTATCGGTGTAATCTTGTTGTTGCTCCTGATGATCCGCTTCAAAATGAACGGCTTCATCGCTCTCGTCCTCGTgg                                                                            >  1:97159/1‑149 (MQ=255)                                                                         tcAGAAAATTGACGTTACCCATAACAAATGAAAGGCCAGGTAAATCATGCCATTAGTCATTGTTGCTAgactggccccctgaatctccagacaaccaatatcacttaaataagtgatagtcttaatactagtttctagactagtcattg                                                                   <  2:724438‑M2/149‑82 (MQ=255)                                                                            gcaacgggACGTTACCCATAACAAATGAAAGGCCAGGGAAATCATGCCATTAGTCATTGGTGCTATCGGTGTAATTTTGTTGTTGCTCCTGATGATCCGCTTCAAAATGAACGGCTTCATCGCTTTCGTCCTCGTGGCGCTTGCTGTTg                                                                <  1:730984/142‑1 (MQ=255)                                                                            gAAAATTGACGTTACCCATAACAAATGAAAGGCCAGGTAAATCATGCCATTAGTCATTGTTGCTATCGGTGTAATCTTGTTGTTGCTCCTGATGATCCGCTTCAAAATGAACGGCTTCATCGCTCTCGTCCTCGTGGCGCTTGCTGTTg                                                                <  1:145066/149‑1 (MQ=255)                                                                              aaaccgACGGTACCCATAACAAATGAATGGCCAGGGAAATCATGCCATTAGTCATTGTTGCTATCGGTGTAATCTTGTTGTTGCTCCTGATGATCCGCTTCAAAATGAACGGCTTCATCGCTCTCGTCCTCGTGGCGCTTGCTGTTGGa                                                              <  1:433914/144‑1 (MQ=255)                                                                              aaaTTGACGTTACCCATAACAAATGAAAGGCCAGGTAAACAATTTCATTAGTCATTGTTGCTAgactggccccctgaatctccagacaaccaatatcacttaaataagtgatagtcttaatactagtttttagactagtcattggagaa                                                              >  1:382315‑M2/1‑63 (MQ=255)                                                                                                  aaagggaaGGCCAGGTAAATCATGCGATTGGTCATTGTTGCTATCGGTGTAATCTTGTTGTTGCTCCTGATGATACGCTTCAAAATGAACGGCTTTATCGCTCTCGTCCTCGTGGCGCTTGCTGTTGGATTAATGCAAGGAATGCCGCt                                          <  2:393534/143‑1 (MQ=255)                                                                                                  aaaTGAAAGGCCAGGTAAATCATGCCATTAGTCATTGTTGCTATCGGTGTAATCTTGTTGTTGCTCCTGATGATCCGCTTCAAAATGAACGGCTTCATCGCTCTCGTCCTCGTGGCGCTTGCTGTTGGATTAATGCAAGGAATGCCGCt                                          >  1:251959/1‑149 (MQ=255)                                                                                                   aaTGAACGGCCAGGTAAATCATGCCATTAGTCATTGTTGCTATCGGTGTAATCTTGTTGTTGCTCCTGATGATCCGCTTCAAAATGAACGGCTTCATCGCTCTCGTCCTCGTGGCGCTTGCTGTTGGATTAATGCAAGGAATGCCGCTg                                         <  2:462496/149‑1 (MQ=255)                                                                                                         aGGCCAGGTAAATCATGCCATTAGTCATTGTTGCTATCGGTGTAATCTTGTTGTTGCTCCTGATGATCCGCTTCAAAATGAACGGCTTCATCGCTCTCGTCCTCGTGGCGCTTGCTGTTGGATTAATGCAAGGAATGCCGCTGGATaaa                                   <  1:438920/149‑1 (MQ=255)                                                                                                              aGGTAAATCATGCCATTAGTCATTGTTGCTAgactggccccctgaatctccagacaaccaatatcacttaaataagtgatagtcttaatactagtttttagactagtcattggagaacagatgattgatgtcttagggccggagaaacg                              <  1:556081‑M2/149‑119 (MQ=255)                                                                                                              aGGTAAATCATGCCATTAGTCATTGTTGCTATCGGTGTAATCTTGTTGTTGCTCCTGATGATCCGCTTCAAAATGAACGGCTTCATCGCTCTCGTCCTCGTGGCGCTTGCTGTTGGATTAATGCAAGGAATGCCACGGGATAAAGTTAt                              >  1:94690/1‑149 (MQ=255)                                                                                                                    aTCATGACATTAGTCATTGTTGCTATCGGTGTAATCTTGTTGTTGGTCCTGATGATCCGCTTCAAAATGAACGGCTTCATCGTTCTCGTCCTCGTGGCGCTTGCTGTTGGATTAATGCAAGGAATGCCGCTGGATAAAGTTATTGGCTc                        <  2:27375/149‑1 (MQ=255)                                                                                                                           cATTAGTCCTTGTTGCTATCGGTGTAATCTTGTTGTTGCTCCTGATGATCCGCTTCAAAATGAACGGCTTCATCGCTCTCGTCCTCGTGGCGCTTGCTGTTGGATTCATCCATATAATGCCGCTGGATAAAGTTATTGGCTCCATCaaa                 <  1:356349/149‑1 (MQ=255)                                                                                                                           cATTAGTCATTGTTGCTATCGGTGTAATCTTGTTGTTGCTCCTGATGATCCGCTTCAAAATGAACGGCTTCATCGCTCTCGTCCTCGTGGCGCTTGCTGTTGGATTAATGCAAGGAATGCCGCTGGATAAAGTTATTGGCTTCATCaaa                 >  2:672015/1‑149 (MQ=255)                                                                                                                           cATGAGTCATCGTTGCTATCGGTGTAATCTTGTTTTTGCTGCTGATGATCCGCTTCAAAATGAACGGCGTCTACTCCGTCGTCCTCTTGGCGCTTGCTGTTGGATTAATGCAAGGAATGCCGCTGGATAAAGTTATTGGCTCCATCaaa                 <  2:447422/149‑1 (MQ=255)                                                                                                                                   aTTGTTGCTATCGGTGTAATCTTGTTGTTACCAGTGAGGATCCGCTTCAAAATGAACGGCTTCATCGCTCTCGTCCTCGTGGCGCTTGCTGTTGGATTAATGCAAGGAATTCCGCTGGATAACGTTATTGGCTCCATCACATCCGgtgt         >  2:156872/1‑149 (MQ=255)                                                                                                                                    ttattgCTATCGGTGTAATCTTGTTGTTGCTCCTGATGATCCGCTTCAAAATGAACGGCTTCATCGCTCTCGTCATCGTGGCGCTTGCTGTTGGATTAATGCAAGGAATGCCGCTGGCTAAAGTTATTGGCTCCATCAAAGCCGGTGTc        >  2:160085/4‑149 (MQ=255)                                                                                                                                      gttgttAgactggccccctgaatctccagacaaccaatatcacttaaataagtgatagtcttaatactagtttttagactagtcattggagaactgatgattgatgtcttagggccggagaaacgcagacggcgtaccacacaggaaaa      >  2:734583‑M2/1‑7 (MQ=255)                                                                                                                                      gttgCTATCGGTGTAATCTTGTTGTTGCTCCTGATGATCCGCTTCAAAATGAACGGCTTCATCGCTCTCGTCCTCGTGGCGCTTGCTGTTGGATTAATGCAAGGAATGCCGCTGGATAAAGTTATTGGCTCCATCAAAGCCGGTGTcgg      <  1:366741/149‑1 (MQ=255)                                                                                                                                        tgCTATCGTTGTAATCTTGTTGTTGCTCCTGATGATCCGCTTCAAAATGAACGGCTTCATCGCTCTCGTCCTCGTGGCGCTTGCTGTTGGATTAATGCAATGAATGCCGCTGGATAAAGTTATTGGCTCCATCAAAGCCGGTTTcggcg    <  2:547980/149‑1 (MQ=255)                                                                                                                                        tatgagactggccacctgaagcgccagacaaccaatatcacttaaataagtggtagtcttaatactagtttttagactaggcattggagaacagatgattgatgtcttagggccggagaaacgcagacggcgtaccacacaggaaaaga    >  2:170984‑M2/5‑5 (MQ=255)                                                                                                                                          cTAgacttcctccctgaatctccagacaaccagtatcacttaaataagtgatagtcttaatactagtttttcgactagtcattggagaacagatgattgatgtcttagagccggagaaacgcagacggcgtaccacacaggaaaagatc  >  2:535249‑M2/1‑3 (MQ=255)                                                                                                                                          cTAgactggcccactgaaactccagacaaccaatataacttaaataagtgatagtctaaatactagtttttatactaatcattggagaacagatgactgatgtcttagagccggagaaacgcagacggcgtaccacacaggaaaagatc  >  2:535306‑M2/1‑3 (MQ=255)                                                                                                                                            |                                                                                                                                                   ATTAGTTTTAGTGGGTATCAGTCGTGGTGCCGCAATATCTCTGTTCCCGATTGGGATAATTAGAGTTTGTCGTCAGAAAATTGACGTTACCCATAACAAATGAAAGGCCAGGTAAATCATGCCATTAGTCATTGTTGCTATCGGTGTAATCTTGTTGTTGCTCCTGATGATCCGCTTCAAAATGAACGGCTTCATCGCTCTCGTCCTCGTGGCGCTTGCTGTTGGATTAATGCAAGGAATGCCGCTGGATAAAGTTATTGGCTCCATCAAAGCCGGTGTCGGCGGG  >  NC_000913_3_pae_tpiA/3546441‑3546726

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.