New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 4049918	2 (0.040)	53 (1.200)	46/280	0.0	96.4%	noncoding (21/109 nt)	spf	Spot 42 sRNA antisense regulator of galK translation, Hfq‑dependent
	?	NC_000913	= 4499510	NA (NA)					intergenic (+9/+84)	insD1/yjgX	IS2 transposase TnpB/pseudogene fragment

CTTGCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGATTACCTGTGATCAGGAAGAATAAGTGGCTGAGGTTTCAAACTGTCTGCCGGTATATT  >  NC_000913/4499373‑4499650                                                                                                                                          |                                                                                                                                             cTTGCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCACATCCACCt                                                                                                                                         >  1:332707/1‑143 (MQ=14)         ggCGTTCGCGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGa                                                                                                                                 <  1:222455/143‑1 (MQ=38)          gggttggggCATTGTAAGGAAGGGCATCCGGTTAGTGCGGTGGGTTGTCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTCTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGat                                                                                                                                <  2:359109/135‑1 (MQ=14)             ttCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCCCGGGAATATCTGCGGCAGCGGGCTGGGAATGGGTTAAGTGATAAGAGAAGGCTGGAAATCTAGGGGCACATCCACCTTGTGCTGatagg                                                                                                                             >  1:122514/1‑141 (MQ=14)                gAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATCACAGATGTCTGGACATGTAGGGGCCACTCCACCTTGCGCTAataaaaat                                                                                                                          >  1:520845/1‑138 (MQ=11)                    aTTATCACGAATCGCATCCGCATAGTGCGGTGGCTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTTCAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACgg                                                                                                                      <  1:201517/143‑1 (MQ=14)                    aTTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACgg                                                                                                                      <  2:484806/143‑1 (MQ=255)                     ttATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGa                                                                                                                     <  2:613237/143‑1 (MQ=255)                        taACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGatag                                                                                                                  >  1:101288/1‑142 (MQ=255)                        taACGAATGGCATCCGCATAGTGCGCGGCGTTATCGCTCGCCACACGAATATCTGCGCCACCGGGCTAACAGTGGGATAAGTGATAACAGATGTCGGGAAGTAGAGGTGCAAATCCACCTTGTGCTGATATGAATACGGatat                                                                                                                  >  2:680299/1‑143 (MQ=17)                             gatggtgtCCGCATAGGGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGGTAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGCTATGAATACGGATATTTtat                                                                                                             <  2:42214/136‑1 (MQ=17)                                  cATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGa                                                                                                        >  1:308856/1‑143 (MQ=255)                                   ggcgggggagggcggTGGGTTAGCGCTCGGCACGGGAATATAGGCGGCAGCGGGCTTGTGATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGaa                                                                                                       <  2:28078/132‑1 (MQ=18)                                   aTCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAATGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGaa                                                                                                       <  1:291170/143‑1 (MQ=255)                                            gTGCGCTGGGTTATCGGTCGCCACGGGAATACCTGCGGACGCACCGGAGGAAGGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCa                                                                                              <  1:174439/143‑1 (MQ=21)                                            gTGCGCTGGGTTATCGCTCGGCACGGGAATATTAGATGCACCTTGCGTTTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCa                                                                                              <  2:757115/143‑1 (MQ=21)                                             tGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAg                                                                                             >  2:774399/1‑143 (MQ=255)                                                 cTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATCCAGAATGCTTTTCAGTACa                                                                                         >  1:7166/1‑143 (MQ=255)                                                  cgggTTGTCGGTCGCCACGGGAATGTCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATGTGCGTACGGATATTTTATACAGAATACTTTTCAGTACaa                                                                                        <  2:557520/142‑1 (MQ=18)                                                   gggTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAg                                                                                       <  1:131795/143‑1 (MQ=255)                                                     gTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCATGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAACTACACCTTGTGCTGATATGAATACGGATAATTTATACAGAATACTTTTCATTACAAACg                                                                                     >  2:384910/1‑143 (MQ=21)                                                      ttATCGCTCGGCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGa                                                                                    <  2:526911/143‑1 (MQ=255)                                                       tATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCggc                                                                                   >  2:709473/1‑141 (MQ=255)                                                       tATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGAc                                                                                   <  2:711107/143‑1 (MQ=255)                                                       tATCACGCGCCACGGGAATATCTGCGGCCGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGAc                                                                                   <  1:23461/143‑1 (MQ=255)                                                         tgcctcgcCACGGGAATATCTTCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTg                                                                                 <  2:292558/140‑1 (MQ=255)                                                          cggtcgcCACGGGAATATCTGCGGCAGCCGGCTGGGGCTTAGATAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGt                                                                                <  2:341887/140‑1 (MQ=25)                                                             tcgcCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTAtt                                                                             >  2:675531/1‑143 (MQ=255)                                                                  acgtggatatCTGACGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGt                                                                        <  2:122514/137‑1 (MQ=255)                                                                  aCGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATATAGAATACTTTTCAGTACAAGCGACTGTATTACAGt                                                                        <  2:400116/143‑1 (MQ=255)                                                                  aCGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGt                                                                        >  1:655559/1‑143 (MQ=255)                                                                     ggAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTg                                                                     <  2:383924/143‑1 (MQ=255)                                                                      gAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGCCTGTATTACAGTCTGc                                                                    >  1:702448/1‑143 (MQ=255)                                                                         tatCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGAAAAACCACCTTGTGCTGATGTGGATACGGATATTTTATACAGAATACGTTTCAGTACGGGCGACGGTAATACAGTCGGccct                                                                 >  2:468227/1‑141 (MQ=21)                                                                             tGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGCATACTTTTCCGTACAAGCGACTGTATTACAATCTGCCatatat                                                             >  2:509253/1‑143 (MQ=255)                                                                              gCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATg                                                            >  1:551187/1‑143 (MQ=255)                                                                              gCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATg                                                            >  1:534066/1‑143 (MQ=255)                                                                               cgcaatcGGGCTTGTAATGTGTTAAGTGATAACAGATGTCTGGAAAGATAGGGGCAAATCCGCCTTGTGCTGATATGACTACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGa                                                           <  2:12376/137‑1 (MQ=37)                                                                               cGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGa                                                           <  1:435987/143‑1 (MQ=255)                                                                                 gCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGACTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGCATTACAGTCTGCCATATATGAtt                                                         >  1:505132/1‑143 (MQ=255)                                                                                   aGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGATTAc                                                       >  2:434677/1‑143 (MQ=255)                                                                                      gggCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGATTACCtg                                                    >  2:177480/1‑143 (MQ=255)                                                                                         cTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATACACCTTGTGGTGATATGAATACGGATATTATATACAGAATACTTTTCAGTACAAGGGACTGTATTACAATCTGCAATATAGGATTACCtgtaa                                                 >  2:8690/1‑141 (MQ=37)                                                                                          ttGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGATTACCTGTGAt                                                >  1:63171/1‑143 (MQ=255)                                                                                          ttGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATAATTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGAGTAcagatgat                                                >  2:644962/1‑136 (MQ=255)                                                                                          ttGTAATGGGTTAAATGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGAAATGGCTACTGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGATTACCTGTGAt                                                <  1:657468/143‑1 (MQ=38)                                                                                             tAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGATTACCTGTGATCAg                                             <  2:647003/143‑1 (MQ=255)                                                                                               aTGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGATTACCTGTGATCAGga                                           <  1:53776/143‑1 (MQ=255)                                                                                               aTGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGATTACCTGTGATCAGga                                           <  1:56580/143‑1 (MQ=255)                                                                                                tGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGATTACCTGTGATCAGgaa                                          <  2:126656/143‑1 (MQ=255)                                                                                                ggggTTGCGTGATAAGAGATGTCTGGAAATATATGGGCAAATTCTCCTTGTGCTGTTATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGATTACCTGTGATCAGgaa                                          <  2:716927/142‑1 (MQ=255)                                                                                                    ttAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGATTACCTGTGATCAGGAAGAAt                                      <  1:304305/143‑1 (MQ=255)                                                                                                     tAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGATTACCTGTGATCAGGAAGAATa                                     >  2:734989/1‑143 (MQ=255)                                                                                                          gATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGATTACCTGTGATCAGGAAGAATAAGTgg                                <  1:774399/143‑1 (MQ=255)                                                                                                            tAAGAGATGTTGGGAAATATAGGGGTAAAGCCATCTTGTGCTGATATGAAGACGGATATTTTATACATATTACTTTTCAGTACAAGCTACTGTATTACAGTCTGCCATATATGATTACCTGTGATCAGGAAGAATAAGTGGCt                              <  2:215456/143‑1 (MQ=255)                                                                                                            tAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGATTACCTGTGATCAGGAAGAATAAGTGGCt                              >  2:77047/1‑143 (MQ=255)                                                                                                               cAGATGTCTGGAAATATAGGGTTAAATCCATTTTGTTCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGATTACCTGTGATTAGGAAGAATAAGTGGCTGAg                           <  2:629669/143‑1 (MQ=255)                                                                                                               cAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGGATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGATTACCTGTGATCAGGGAGAATAAGTGGGTgcg                           >  2:399171/1‑141 (MQ=255)                                                                                                                      cTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGATTACCTGTGATCAGGAAGAATAAGTGGCTGAGGTTTCaa                    >  1:431291/1‑143 (MQ=255)                                                                                                                         gAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGATTACCTGTGATCAGGAAGAATAAGTGGCTGAGGTTTCAAACt                 >  1:82610/1‑143 (MQ=255)                                                                                                                                      aaaTCCACCTTGTGCTGATATGAACACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGATTACCTGTGATCAGGAAGAATAAGTGGCTGAGGTTTCAAACTGTCTGCCGGtata    >  2:585380/1‑143 (MQ=255)                                                                                                                                        aTCCGCCTTGTGCTGATATGAATACGGATATTTTACACAGAAGACTTTTCAGTACAAGCGACCGTATTACAGTCTGCCATATATGATTACCTGTGATCAGGAAGAATAAGTGGCTGAGGTTTCAAACTGTCTGCCGGTATAtt  <  1:395399/143‑1 (MQ=255)                                                                                                                                          |                                                                                                                                             CTTGCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGATTACCTGTGATCAGGAAGAATAAGTGGCTGAGGTTTCAAACTGTCTGCCGGTATATT  >  NC_000913/4499373‑4499650

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.