New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_KO_pgi	= 2662483	39 (0.770)	7 (0.210) +CTACAGTGAACAGAACCGTAGGTCGGATAAGGCGTTCACGCCGCATCCG	4/188	5.2	21.5%	noncoding (175/266 nt)	REP184 (repetitive extragenic palindromic) element; contains 6 REP sequences	REP184 (repetitive extragenic palindromic) element; contains 6 REP sequences
	?	NC_000913_3_KO_pgi	= 2662583	NA (NA)					coding (741/741 nt)	trmJ	tRNA mC32,mU32 2'‑O‑methyltransferase, SAM‑dependent
Rejected: Coverage evenness skew score above cutoff.

TTCACTGTAGGCCTGATAAGACGCATTACGCGTCGCATCAGGCAACGGCTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACGGTTCTGTTCACTGTAGGCCTGATAAGACGCA‑TTACGCGTCGCATCAGGCAACGGCTGTTATTCGGCCTTGTTACCTTTATTCTGCTGCTCAATAGAAGCCAGAATCCCGCGCAGGATATTCAACTCCTGGCTTTCCGGGCGCGCACGGGTAAACAGACGGCGCAATTTATTCATCACCTGCCCCGGATGGTTTTCACGGATAAA  >  NC_000913_3_KO_pgi/2662441‑2662729                                                                                                                                                |                                                                                                                                                   ttCACTGTAGGCCTGATAAGACGCATTACGCGTCGCATCAGGCAACGGCTGTCAGATGCGGCGGGAACCCCTTATCCGACCTACGATTCTGGTCACTGTAGGCCGGAGGAGACGCA‑TCACCCGCCTCATCCGCCGACGGCTGTTaacca                                                                                                                                              >  2:645523/1‑145 (MQ=11)  tCACTGTAGGCCTGATAAGACGCATTACGCGTCGCATCAGGCAACGGCTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACGGTTCTGTTCACTGTAGGCCTGATAAGACGCA‑TTACGCGTCGCATCAGGCAACGGCTGTTATTCgg                                                                                                                                             <  1:745156/149‑1 (MQ=35)      tGTAGGCCTGATAAGACGCATTACGCGTCACAACAAGGAGCTGCTGTCTGATGCGCCGTGAACGACTTATCCGACCTACGGGTCTGTTCACTGTATGCCCCATGAGA‑GCACTTACGCGCCGCATCATGCGCCGGCGGTTATTCTGGCtt                                                                                                                                         >  2:874509/1‑149 (MQ=2)        tAGGCCTGATAAGACGCATTACGCGTCGCATCAGGCAACGGCTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACGGTTCTGTTCACTGTAGGCCTGATAAGACGCA‑TTACGCGTCGCATCAGGCAACGGCTGTTATTCGGCCTTGt                                                                                                                                       <  2:880189/149‑1 (MQ=40)           gCCTGATAAGGCGCATTCCCCGTCGCATCCGGCAACGGCTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACGGTTCTGTTCACTGTAGGCCTGATAAGACGCA‑TTACGCGTCGCATCAGGCAACGGCTGTTATTCGGCCTTGTTAc                                                                                                                                    <  1:49105/149‑1 (MQ=255)                  aaGACGCGTTACGCGTCGCATCAGGCAACGGCTGTCGGATGCGGCGTGAACGCCTTATCCGTCCTACGGTTCTGTTCACTGTAGGCCTGATAAGACGCA‑TTACGCGTCGCATCAGGCAACGGCTGTTATTCGGCCTTGTTACCTTTAtt                                                                                                                             <  1:353013/149‑1 (MQ=255)                     ccgttttACGCGGCGCGGCAGGCAACGGCTGTCGGATGCGGCGTGAACGCCTTATCCGCCCTACGGTTCTGTTCACTGTAGGCCTGATAAGACGCA‑TTACGCGTCGCATCAGGCAACGGCTGTTATTCGGCCTTGTTACCTTTATTctg                                                                                                                          <  2:380912/144‑1 (MQ=17)                        cATTACGCGTCGCATCAGGCAACGGCTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACGGTTCTGTTCACTGTAGGCCTGATAAGACGCA‑TTACGCGTCGCATCAGGCAACGGCTGTTATTCGGCCTTGTTACCTTTATTctactg                                                                                                                       <  1:863938/149‑1 (MQ=255)                          ttACGCGTCGCATCAGGCAACGGCTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACGGTTCTGTTCACTGTAGGCCTGATAAGACGCA‑TTACGCGTCGCATCAGGCAACGGCTGTTATTCGGCCTTGTTACCTTTATTCTgctgct                                                                                                                     >  1:570280/1‑149 (MQ=255)                               ggTCGCATAAGGCAACGGCTGTCGGATGCGGCGTTAACGCCTTATCCGACCTACGGTTCTGTTCACTGTAGGCCTGATAAGACGCA‑TTATGCGTCGCATCAGGCAACGGCTGTTATTCGGCCTTGTTACCTTTATTCTGCTGCTCAATa                                                                                                                <  2:720078/148‑1 (MQ=255)                                gTCGCATCAGGAAACGGCTGTCGGATGCGGCGTGAACGCCTTCTTCGACCTACGGTTCTGTTAACTGTGGGCCTGATAAGCAGCA‑TTACGCGTCGGATATGGCGACGGCTGTTCTTCGGCCTTGTTAGCTTTAATGTGATGCCCAATac                                                                                                               >  2:732502/1‑148 (MQ=14)                                  cGCATCAGGCAACGGCTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACGGTTCTGTTCACTGTAGGCCTGATAAGACGCA‑TTACGCGTCGCATCAGGCAACGGCTGTTATTCGGCCTTGTTACCTTTATTCTGCTGCTCAATAGaa                                                                                                             <  1:89517/149‑1 (MQ=255)                                     aTCAGGCAACGGCTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACGGTTCTGTTCACTGTAGGCCTGATAAGACGCA‑TTACGCGTCGCATCAGGCAACGGCTGTTATTCGGCCTTGTTACCTTTATTCTGCTGATCAATAGCAGcc                                                                                                          >  2:91807/1‑149 (MQ=255)                                      tCAGGCAACGGCTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACGGTTCTGTTCACTGTAGGCCTGATAAGACGCA‑TTACGCGTCGCATCAGGCAACGGCTGTTATTCGGCCTTGTTACCTTTATTCTGCTGCTCAATAGAAGCCa                                                                                                         <  1:16494/149‑1 (MQ=255)                                        aGGCAACGGCTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACGGTTCTGTTCACTGTAGGCCTGATAAGACGCA‑TTACGCGTCGCATCAGGCAACGGCTGTTATTCGGCCTTGTTACCTTTATTCTGCTGCTCAATAGAAGCCAGa                                                                                                       >  1:857109/1‑149 (MQ=255)                                          gCAACGGCTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACGGTTCTGTTCACTGTAGGCCTGATAAGACGCA‑TTACGCGTCGCATCAGTCAACGGCTGTTATTCGCGCTTGGTACCCTTATTCCGCTGCACAATAGGAGTCACAAt                                                                                                     >  2:289968/1‑149 (MQ=14)                                            aaCGGCTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACGGTTCTGTTCACTGTAGGCCTGATAAGAGGCA‑TTACGCGTCGCATCAGGCAACGGCTGTTATTCGGCCTTGTTACCTTTATTCTGCTGCTCCATAGAAGCCAGAAtgc                                                                                                   >  2:744086/1‑147 (MQ=255)                                                       gATGCGGCGGTAACGCCTGATCGGACCTCTGGTACTGTTCACTGTAGGCCTGATAAGACGCA‑TTACGCGTCGCATCAGGCAACGGCTGTTATTCGGCCTTGTTACCTTTATTCTGCTGCTCAATAGAAGCCAGAATCCCGCGCAGGata                                                                                        <  2:125883/149‑1 (MQ=25)                                                         tGCGGCGTGAACGCCTTATCCGACCTACGGTTCTGTTCACTGTAGGCCTGATAAGACGCA‑TTACGCGTCGCATCAGGCAACGGCTGTTATTCGGCCTTGTTACCTTTATTCTGCTGCTCAATAGAAGCCAGAATCCCGCGCAGGATAtt                                                                                      <  2:13699/149‑1 (MQ=255)                                                          gcggctTGAACCCCTCATCCGGCCTACGGTTTCGTTCACTGTAGGCCTGATAAGACGCA‑TTACGCGCCTCATCACGCAACTGCTGTTATTCGGCCTTGTTACCTTTTTTCTGCTGCTCAATAGAAGCCAGAATCCCGCGCAGGATATTc                                                                                     <  2:145835/149‑1 (MQ=25)                                                            ggcgTGAAGGGCTTATCCGGCCTAGGGTTCTGTTCGCTGTAGGCCTGATAAGACGCA‑TTACGCGTCGCATCAGGCAACGGCTGTTATTCGGCCTTGTTACCTTTATTCTGCTGCTCAATAGAAGCCAGAATCCCGCGCAGGATATTCaa                                                                                   <  2:86726/149‑1 (MQ=25)                                                             ccgTGAATGCCTTGGCCGACCTACGGTTCTATTCACTGTAGGCCTGATAAGACGCA‑TTACGCGTCGCATCAGGCAACGGCTGTTATTCGGCCTTGTTACCTTTATTCTGCTGCCCAATAGAAGCCAGAATCCCGCCCCGGATCTTCAAc                                                                                  >  2:689214/2‑149 (MQ=21)                                                                    cGCCTTATCCGACCTACGGTTCTGTTCACTGTAGGCCTGATAAGACGCA‑TTACGCGTCGCATCAGGCAACGGCTGTTATTCGGCCTTGTTACCTTTa                                                                                                                               <  2:900366/97‑1 (MQ=255)                                                                    cGCCTTATCCGACCTACGGTTCTGTTCACTGTAGGCCTGATAAGACGCA‑TTACGCGTCGCATCAGGCAACGGCTGTTATTCGGCCTTGTTACCTTTa                                                                                                                               >  1:900366/1‑97 (MQ=255)                                                                       cTTATCCGACCTACGGTTCTGTTCACTGTAGGCCTGATAAGACGCA‑TTACGCGTCGCATCAGGCAACGGCTGTTATTCGGCCTTGTTACCTTTATTCTGCTGCTCAATAGAAGCCAGAATCCCGCGCAGGATATTCAACTCCTGGCttt                                                                        <  1:289968/149‑1 (MQ=255)                                                                           tCCGACCTACGGTTCTGTTCACTGTAGGCCTGATAAGACGCA‑TTACGCGTCGCATCAGGCAACGGCTGTTATTCGGCCTTGTTACCTTTATTCTGCTGCTCAATAGAAGCCAGAATCCCGCGCAGGATATTCAACTCCTGGCTTTCCgg                                                                    >  1:431755/1‑149 (MQ=255)                                                                              gACCTACGGTTCTGTTCACTGTAGGCCTGATAAGACGCA‑TTACGCGTCGCATCAGGCAACGGCTGTTATTCGGCCTTGTTACCTTTATTCTGCTGCTCAATAGAAGCCAGAATCCCGCGCAGGATATTCAACTCCTGGCTTTCCGGgcg                                                                 >  1:41827/1‑149 (MQ=255)                                                                                  tACGGTTCTGTTCACTGTAGGCCTGATAAGACGCA‑TTACGCGTCGCATCAGGCAACGGCTGTTATTCGGCCTTGTTACCTTTATTCTGCTGCTCAATAGAAGCCAGAATCCCGCGCAGGATATTCaa                                                                                   >  2:718203/1‑127 (MQ=255)                                                                                  tACGGTTCTGTTCACTGTAGGCCTGATAAGACGCA‑TTACGCGTCGCATCAGGCAACGGCTGTTATTCGGCCTTGTTACCTTTATTCTGCTGCTCAATAGAAGCCAGAATCCCGCGCAGGATATTCaa                                                                                   <  1:718203/127‑1 (MQ=255)                                                                                       ttatGTCCACTGTAGGCTTGATAAGACGCA‑TTACGCGTCGCATCAGGCAACGGCTGTTATTCGGCCTTGTTACCTTTATTCTGCTGCTCAATAGAAGCCAGAACCCCGCGCAGGATATTCAACTCCTGGCTTTCCGGGCGCGCACGGGt                                                        <  1:502217/146‑1 (MQ=255)                                                                                           gTTCACTGTAGGCCTGATAAGACGCA‑TTACGCGTCGCATCAGGCAACGGCTGTTATTCGGCCTTGTTACCTTTATTCTGCTGCTCAATAGAAGCCAGAATCCCGCGCAGGATATTCAACTCCTGGCTTTCCGGGCGCGCACGGGTAAAc                                                    >  1:627910/1‑149 (MQ=255)                                                                                            gtCAATGTAGGCCTGATAAGACGCA‑TTACGCGACGCATCAGACAAAAACGAAAATTCGGCCTTGTTACCTTTATTCTGCGGCTCAATAGAAGCCTGAATACCGCGCAGGATATTCAACTCCTGGCTTTCCAGACGCGCAAGGGTAAACa                                                   >  2:685143/2‑149 (MQ=25)                                                                                                  gTAGGCCTGATAAGACGCA‑TTACGCGTCGCATCAGGCAACGGCTGTTATTCGGCCTTGTTACCTTTATTCTGCTGCTCAATAGAAGCCAGAATCCCGCGCAGGATATTCAACTCCTGGCTTTCCGGGCGCGCACGGGTAAACAGACGgc                                             <  2:145535/149‑1 (MQ=255)                                                                                                  agagtccTGATAAGACGCA‑TTACGCGTCGCATCAGGCAACGGCTGTTATTCGGCCTTGTTACCTTTATTCTGCTGCTCAATAGAAGCCAGAATCCCGCGCAGGATATTCAACTCCTGGCTTTCCGGGCGCGCACGGGTAAACAGACGgc                                             <  2:447153/144‑1 (MQ=255)                                                                                                   tAGGCCTGATAAGACGCA‑TTACGCGTCGCATTAGGCAACGGCTTTTATTCGGCCTTGTTACCTTTATTCTGCTGCCCAATAGAAGCCACAATCCCGCCCAGAATCTTAAACTCCTTGCGTTCCTGGCCCGCACAGGGAACCAGCCGgcg                                            >  2:120710/1‑149 (MQ=25)                                                                                                     ggCCTGATAAGACGCA‑TTACGCGTCGCATCAGGCAACGGCTGTTATTCGGCCTTGTTACCTTTATTCTGCTGCTCAATAGAAGCCAGAATCCCGCGCAGGATATTCAACTCCTGGCTTTCCGGGCGCGCACGGGTAGACAGACGGCGCa                                          >  1:652521/1‑149 (MQ=255)                                                                                                        cTGATAAGACGCA‑TTACGCGTCGCATCAGGCAACGGCTGTTATTCGGCCTTGTTACCTTTATTCTGCTGCTCAATAGAAGCCAGAATCCCGCGCAGGATATTCAACTCCTGGCTTTCCGGGCGCGCACGGGTAAACAGACGGCGCAAtt                                       >  1:103056/1‑149 (MQ=255)                                                                                                          gATAAGACGCA‑TTACGCGTCGCATCAGGCAACGGCTGTTATTCGGCCTTGTTACCTTTATTCTGCTGCTCAATAGAAGCCAGAATCCCGCGCAGGATATTCAACTCCTGGCTTTCCGGGCGCGCACGGGTAAACAGACGGCGCAATTTa                                     <  1:50272/149‑1 (MQ=255)                                                                                                            tAAGACGCA‑TTACGCGTAGTATCAGGCAACGGCTGTTATTCGGCCTTGTTACCTTTATTCTGCTGCTCAATAGAAGCCAGAATCCCGCGCAGGATATTCAACTCCTGGCTTTCCGGGCGCGCACGGGTAAACAGACGGCGCAATTTAtt                                   <  2:166839/149‑1 (MQ=255)                                                                                                               gACGCA‑TTACGCGTCGCATCAGGCAAAGGCTGTTATTCGGCCTTGTTACCTTTATTCTGCTGCTCAATAGAAGCCAGAATCCCGCGCAGGATATTCAACTCCTGGCTTTCCGGGCGCGCACGGGTAAACAGACTGGGCAATATATtcat                                >  2:240155/1‑149 (MQ=255)                                                                                                                aCGCA‑TTACGCGTCGCATCAGGCAACGGCTGTTATTCGGCCTTGTTACCTTTATTCTGCTGCTCAATAGAAACCAGAATCCCGCGCAGGATATTCAACTCCTGGCTTTCCGGGCGCGCACGGGTCAACAGAAGGCGCAATTTATtcatc                               >  1:905658/1‑149 (MQ=255)                                                                                                                             tCGCATCAGGCAACGGCTGTTATTCGGCCTTGTTACCTTTATTCTGCTGCTCAATAGAAGCCAGAATCCCGCGCAGGATATTCAACTCCTGGCTTTCCGGGCGCGCACGGGTAAACAGACGGCGCAATTTATTCATCACCTGCCCCGGa                   <  2:368717/149‑1 (MQ=255)                                                                                                                             tCGCATCAGGCAACGGCTGTTATTCGGCCTTGTTACCTTTATTCTGCTGCTCAATAGAAGCCAGAATCCCGCGCAGGATATTCAACTCCTGGCTTTCCGGGCGCGCACGGGTAAACAGACGGCGCAATTTATTCATCACCTGCCCCGGa                   <  1:789378/149‑1 (MQ=255)                                                                                                                               gCATCAGGCAACGGCTGTTATTCGGCCTTGTTACCTTTATTCTGCTGCTCAATAGAAGCCAGAATCCCGCGCAGGATATTCAACTCCTGGCTTTCCGGGCGCGCACGGGTAAACAGACGGCGCAATTTATTCATCACCTGCCCCGGATg                 <  2:648962/149‑1 (MQ=255)                                                                                                                                    aGGCAACGGCTGTTATTCGGCCTTGTTACCTTTATTCTGCTGCTCAATAGAAGCCAGAATCCCGCGCAGGATATTCAACTCCTGGCTTTCCGGGCGCGCACGGGTAAACAGACGGCGCAATTTATTCATCACCTGCCCCGGATGGtttt            <  1:54171/149‑1 (MQ=255)                                                                                                                                       cAACGGCTGTTATTCGGCCTTGTTACCTTTATTCTGCTGCTCAATAGAAGCCAGAATCCCGCGCAGGCTATTCAACTCCGGGCTTTCCGGGCGCGCACGGGTAAACAGACGGCGCAATTTATTAATCGCCTGCCCCGGGGGGTTTTCAc         >  1:730291/1‑149 (MQ=255)                                                                                                                                        aaCGGCTGTTATTCGGCCTTGTTACCTTTATTCTGCTGCTCAATAGAAGCCAGAATCCCGCGCAGGATATTCAACTCCTGGCTTTCCGGGCGCGCACGGGTAAACAGACGGCGCAATTTATTCATCACCTGCCCCGGATGGTTTTCACg        <  1:647077/149‑1 (MQ=255)                                                                                                                                         aCGGCTGTTATTCGGCCTTGTTACCTTTATTCTGCTGCTCAATAGAAGCCAGAATCCCGCGCAGGATATTCAACTCCTGGCTTTCCGGGCGCGCACGGGTAAACAGACGGCGCAATTTATTCATCACCTGCCCCGGATGGTTTTCACgg       <  1:580953/149‑1 (MQ=255)                                                                                                                                           ggCTGTTGTTCGGCCTTGTTACCTTTATTCTGCTGCTCAATAGAAGCCCGAATCCCGCGCAGGATATTCAACTCCTGGCTTTCCGTGCGCGCACGGGTAAACAGACGGCGCACTTTAGTCTACACGTGCCCGGATTAGTTTGCACgcgc     >  2:236920/1‑146 (MQ=255)                                                                                                                                              tGTTATTCGGCCTTGTTACCTTTATTCTGCTGCTCAATAGAAGCCAGAATCCCGCGCAGGATATTCAACTCCTGGCTTTCCGGGCGCGCACGGGTAAACAGACGGCGCAATTTATTCATCACCTGCCCCGGATGGTTTACACGGATaaa  >  1:798047/1‑149 (MQ=255)                                                                                                                                                |                                                                                                                                                   TTCACTGTAGGCCTGATAAGACGCATTACGCGTCGCATCAGGCAACGGCTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACGGTTCTGTTCACTGTAGGCCTGATAAGACGCA‑TTACGCGTCGCATCAGGCAACGGCTGTTATTCGGCCTTGTTACCTTTATTCTGCTGCTCAATAGAAGCCAGAATCCCGCGCAGGATATTCAACTCCTGGCTTTCCGGGCGCGCACGGGTAAACAGACGGCGCAATTTATTCATCACCTGCCCCGGATGGTTTTCACGGATAAA  >  NC_000913_3_KO_pgi/2662441‑2662729

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ 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.