New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 1589993	3 (0.060)	67 (1.270)	57/284	0.0	95.7%	pseudogene (87/1227 nt)	ydeT	pseudogene, putative outer membrane protein
	?	NC_000913	4498181 =	NA (NA)					intergenic (+240/‑92)	intB/insC1	pseudogene, integrase homology,IS, phage, Tn, Phage‑related functions and prophages, KpLE2 phage‑like element, P4‑like integrase/IS2 repressor TnpA

GCAGGGGGGATTATCAGAATCCGCGGTTATTCATTATTTATATACATTCAATAAAAAAGTAACCTCATAAAAAATCCTGTACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGA  >  NC_000913/4498040‑4498322                                                                                                                                              |                                                                                                                                              gCAGGGGGGATTATCAGAATCCGCGGTTATTCATTATTTATATACATTCAATAAAAAAGTAACCTCATAAAACATCCTGTACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGt                                                                                                                                              <  1:544052/143‑1 (MQ=255) gCAGGGGGGATTATCAGAATCCGCGGTTATTCATTATTTATATACATTCAATAAAAAAGTAACCTCATAAAAAATCCTGTACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGt                                                                                                                                              >  1:210825/1‑143 (MQ=255)  cAGGGGTGACTATCAGAAACCGCGGTTATTCATTATTTATATACATTCAATAAAAAAGTAACCTCATAAATAGTCCTTTAGTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTa                                                                                                                                             <  1:110036/143‑1 (MQ=255)     gggggATTATCAGAATCCGCGGTTATTCATTATTTATATACATTCAATAAAAAAGTAACCTCATAAAAAATCCTGTACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGAATTGATGGGGCCTTGTAGAc                                                                                                                                          >  2:809978/1‑143 (MQ=255)       gggATTATCAGAATCCGCGGTTATTCATTATTTATATACATTCAATAAAAAAGTAACCTCATAAAAAATCCTGTACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTg                                                                                                                                        >  2:647931/1‑143 (MQ=255)       gggATTATCAGAATCCGCGGATATTCATTATTTATATACATTCAATAAAAAAGTAACCGCATAAAAAATCCTGTACTCACAGGGAGATGCGGGATAACTGAAGTAAGGAGTGCAGCAGGGAATAGATGGTCGCTTGGAGGCTg                                                                                                                                        >  1:231864/1‑143 (MQ=255)          aTTATCAGAATCCGCGGTTATTCATTATTTATATACATTCAATAAAAAAGTAACCTCATAAAAAATCCTGTGCTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGcc                                                                                                                                     >  2:443676/1‑143 (MQ=255)              tCAGAATCCGCGGTTATTCATTATTTATATACATTCAGTAAAAAAGTGACCTCATAAAAAATCCTGTACTCACAGGGTGATGCGGGCTAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCt                                                                                                                                 <  1:103780/143‑1 (MQ=255)              tCAGAATCCGCGGTTATTCATTATTTATATACATTCAATAAAAAAGTAACCTCATAAAAAATCCTGTACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCt                                                                                                                                 <  2:381877/143‑1 (MQ=255)                      cgcgGTTATTCATTATTTATATACATTCAATAAAAAAGTAACCTCATAAAAAATCCTGTACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTcc                                                                                                                         <  2:349138/143‑1 (MQ=255)                       gcgGTTATTCATTATTTATATACATTCAATAAAAAAGTAACCTCATAAAAAATCCTGTACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCa                                                                                                                        >  2:425328/1‑143 (MQ=255)                        ctgtgactCATTCTTTATATACTTTCAATAAAAGCGTCCCCTCATACAAAATCCTGTCCTCCCCGCCTCCTGCCCCATCCCTGTCGTAATGAGGGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAg                                                                                                                       <  2:211754/136‑1 (MQ=255)                            tATTCATTATTTATATACATTCAATAAAAAAGTAACCTCATAAAAAATCCTGTACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACaa                                                                                                                   >  2:732288/1‑143 (MQ=255)                                     tttatATACATTCAATAAAAAAGTAACCTCATAAAAAATCCTGTACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCa                                                                                                          <  2:297912/143‑1 (MQ=255)                                            aCATTCAATAAAAAAGTAACCTCATAAAAAATCCTGTACTCACAGGGTGATGCGGGATAACTGACGAAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAAt                                                                                                   >  2:818726/1‑143 (MQ=255)                                               ttCAATAAAAAAGTAACCTCATAAAAAATCCTGTACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAg                                                                                                <  2:194112/143‑1 (MQ=255)                                                taatgatgcaaGAAAACTCATAAAATATGGTGTACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGt                                                                                               <  2:416048/134‑1 (MQ=37)                                                tCAATAAAAAAGTAACCTCATAAAAAATCCTGTACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGt                                                                                               <  1:912202/143‑1 (MQ=255)                                                 caagaagataGTACCCTCAGAAACAGTCCTGTACTCGCGGGGTGATGCGGGATCACTGACGTAAGGAGTCCTGCACCGATTTGATGTTCCCTTCTAGACTGGCCCCCTGAATCTCCAGACAACCCATATCACTTAAATAAGTg                                                                                              <  1:614528/134‑1 (MQ=21)                                                  aaTAAAAAAGTAACCTCATAAAAAATCCTGTACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCAATTAACTAAGTGa                                                                                             >  1:907179/1‑143 (MQ=255)                                                    tAACAAAGTAACCTCACAAAAAATCCTGTCCTCACCGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCCGGGATTTGCTGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGGCAACCAATATCACTTAAATAAGTGATa                                                                                           <  2:299768/143‑1 (MQ=37)                                                           gTAACCTCATAAAAAATCCTGTACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTaa                                                                                    <  1:115273/143‑1 (MQ=255)                                                            tAACCGCATAAAAAATCCTGTACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAAt                                                                                   <  1:652780/143‑1 (MQ=255)                                                                 tCATAAAAAATCCTGTACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACCTAAATAAGTGAGAGTCTTAATACTAg                                                                              >  1:817169/1‑143 (MQ=255)                                                                    tAAAAAATCCTGTACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACGTAGATAAGTGATAGTCCTAATACCAgatg                                                                           >  1:134325/1‑140 (MQ=37)                                                                      aaaaaTCCTGTACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGttttt                                                                         <  1:466661/143‑1 (MQ=255)                                                                      aaaaaTCCTGTACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGttttt                                                                         >  2:488545/1‑143 (MQ=255)                                                                      aaaaaTCCTGTACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGttttt                                                                         <  2:602529/143‑1 (MQ=255)                                                                       tataTCCTGTACTCACAGGGTGATGCGGGATAACTGACGTAGGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCACCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTa                                                                        <  1:127272/140‑1 (MQ=255)                                                                       aaaaTGCTGTACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTa                                                                        <  1:409980/143‑1 (MQ=255)                                                                            gcTGGACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCTGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTATTTCGACtt                                                                   <  1:609407/142‑2 (MQ=255)                                                                            ccTGTACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTa                                                                   <  1:425328/143‑1 (MQ=255)                                                                            ccTGTACTCACAGGGTGATGCGGGAGAACTGAAGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTa                                                                   <  1:527423/143‑1 (MQ=255)                                                                               gTACTCACAGGGTGATGCGGGATAACTGACGTAAGGATTGCGGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTCAATAAGTGATAGTCTTAATACTAGCTTTTAGACTAGTc                                                                >  1:798270/1‑143 (MQ=255)                                                                                   tCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGACCCCTGAATCTCAAGACAAACAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTg                                                            <  2:255087/143‑1 (MQ=255)                                                                                         ggTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCACTATCACCTAAATCAGTGATAGTCTTAATACTAGTTTTTAGGCTACTCATCGGCGAAc                                                      >  1:64180/1‑143 (MQ=21)                                                                                           tGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGCGACCAg                                                    >  2:657601/1‑143 (MQ=255)                                                                                             aTGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAgat                                                  <  2:587347/143‑1 (MQ=255)                                                                                                cGGGATAACTGACTTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTATACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAgatgat                                               <  1:18899/143‑1 (MQ=255)                                                                                                 gcgATCACTGACGTAAGGAGCGCTGCAGGGATTTGAGGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGAtgatt                                              <  1:719709/141‑1 (MQ=255)                                                                                                    aTAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGAtgattgat                                           <  1:644402/143‑1 (MQ=255)                                                                                                      aaCTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAGGTGATAGTCTNAATACTAGTTTTTAGACTAGGCATTGGAGAACAGATGATTGATgg                                         >  1:467641/1‑142 (MQ=255)                                                                                                      aaCTGACGTAAGGAGCGGTGCAGGGAGTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGt                                         <  1:356940/143‑1 (MQ=255)                                                                                                            cGTAAGGAGGGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAgg                                   <  2:752019/143‑1 (MQ=255)                                                                                                               aaGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGcc                                <  1:795251/143‑1 (MQ=255)                                                                                                               aaGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGcc                                >  1:251483/1‑143 (MQ=255)                                                                                                                aggaggGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCGCTGCAGCTCCAGAGCACCACTATCACTTAACTAAGTGATAGTCTTAATCGTCGTTTTTCGACTAGTGATTGGAGAACAGATGATTGATGACTTAGGGGCg                               >  1:332032/1‑143 (MQ=17)                                                                                                                 ggAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTCTTTAGACTAGACATAGGAGAACAGATGATTGATGTCTTAGGACCgg                              >  1:635893/1‑143 (MQ=255)                                                                                                                  aaGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGGCATTGGAGAAAAGATGATTGGTGTCTTAGGGCCGga                             >  2:149916/2‑143 (MQ=255)                                                                                                                       ctgcAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCCGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAAc                        >  2:642823/1‑143 (MQ=255)                                                                                                                            gggATTTGATGGTCCCTTGTAGACTGGCCCCGTGAAGCTCCAGACAGCCAATATCACGTAAATAAGTGATAGTCTGAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGa                   <  1:460308/143‑1 (MQ=14)                                                                                                                                tttGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGc               >  1:896495/1‑143 (MQ=255)                                                                                                                                 ttGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCg              >  2:892044/1‑143 (MQ=40)                                                                                                                                      ggTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTGTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACca         <  2:210825/143‑1 (MQ=37)                                                                                                                                      ggTCCCTTGTACACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTACTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACca         <  2:134693/143‑1 (MQ=255)                                                                                                                                          ccTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTCGTCATTGGAGAACAGATGATTGATGTCTTGGGGCCGGAGGAACGCAGGCGGCGTACcgcaca     >  1:706716/1‑143 (MQ=11)                                                                                                                                          ccTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGAAGACGGCGTACcacaca     >  1:139356/1‑143 (MQ=18)                                                                                                                                            ttGTAGACTGGCCCCCTGAATCTCTAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTCGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAgg   <  1:873730/143‑1 (MQ=17)                                                                                                                                             tGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTCTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGa  <  1:443676/143‑1 (MQ=14)                                                                                                                                              |                                                                                                                                              GCAGGGGGGATTATCAGAATCCGCGGTTATTCATTATTTATATACATTCAATAAAAAAGTAACCTCATAAAAAATCCTGTACTCACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGA  >  NC_000913/4498040‑4498322

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.