New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 2406863	0 (0.000)	42 (0.960)	33/274	NT	100%	intergenic (‑224/‑696)	lrhA/alaA	transcriptional repressor of flagellar, motility and chemotaxis genes/glutamate‑pyruvate aminotransferase; glutamic‑pyruvic transaminase (GPT); alanine transaminase
	?	NC_000913	2996360 =	NA (NA)					intergenic (‑2/+10)	ygeO/insD1	pseudogene, orgA family, part of T3SS PAI ETT2 remnant/IS2 transposase TnpB

ATTTATTTCCAGCGGTATAGCTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCT  >  NC_000913/2996215‑2996493                                                                                                                                                  |                                                                                                                                      atttttttCCAACAGTATAGATGATAAAGAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGAt                                                                                                                                    <  1:178387/149‑1 (MQ=255)  tttatttCCAGCGGTATAGCTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGAtt                                                                                                                                   >  2:445301/1‑149 (MQ=255)                     cTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGAc                                                                                                                <  1:248685/149‑1 (MQ=255)                     cTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGAc                                                                                                                <  1:143767/149‑1 (MQ=255)                     cTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTGCTGCAAACCTTTCTCGATAAAAGTGACAACCACTCAGTAACCAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTCCCCCTAACTTTCCAgcc                                                                                                                >  2:207531/1‑147 (MQ=255)                         taaataaTCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCCATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCt                                                                                                            >  1:277571/1‑149 (MQ=255)                         taaataaTCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCt                                                                                                            >  2:88693/1‑149 (MQ=255)                         taaataaTCCCTTAGTACATCAGCAACCATATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCt                                                                                                            <  1:54351/149‑1 (MQ=255)                         gaaataaTCCCTTAGTAATTCAGTAACCTGATAAAAAACCCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCt                                                                                                            <  2:449696/148‑1 (MQ=255)                                tCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATCCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCa                                                                                                     >  1:607279/1‑149 (MQ=255)                                 cccTTAGTACATCAGGAACCGTATAAAAAAACCCGCGTTCTGCAACACTTTCATGATTAAAGCTACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCATATATTTCCAGACATCTGTTATCAc                                                                                                    <  2:282577/149‑1 (MQ=38)                                       gTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAccc                                                                                              >  2:709056/1‑149 (MQ=255)                                            tCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTTTAACTTAACCCCTTa                                                                                         >  1:314731/1‑149 (MQ=255)                                            tCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTa                                                                                         >  2:615166/1‑149 (MQ=255)                                            tCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTa                                                                                         >  2:237088/1‑149 (MQ=255)                                                   ccTTATAAAAAACCCGGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTCCAAGcac                                                                                  >  2:94198/1‑147 (MQ=255)                                                     ttATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCTCTTAACCCGTGACAAGCCCGc                                                                                >  1:264982/1‑149 (MQ=255)                                                        taAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGc                                                                             <  1:406224/149‑1 (MQ=255)                                                          aaaaaaCCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTcccc                                                                           >  2:613395/1‑148 (MQ=255)                                                           aaaaaCCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCAAATTGTTTATTGGATTTGCCACTATATTCACAGACATCTGTTATCACTTACACAATTACAAGACCGCTGCCGc                                                                          >  1:547675/1‑149 (MQ=255)                                                           aaaaaCCCGCGTACTGCAAACCTTTCTCGATAAAAGTGACACCCACAAAGTAAACAGATCAATGGAAGTAAATTCCAATTTTTTATTGGATATGCCCCTATATTTCCAGACATGTTTTACCACTTATGCCATTAAAAGACCGTTGACGc                                                                          >  2:497769/1‑149 (MQ=37)                                                             aaaCCCGCGTTCTGCAAACCTTTTTTTTTTTTTTTTACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACCTCTGTTATCACTTAACCCATTACAATCCCGCTGCCGccg                                                                        >  2:294566/1‑147 (MQ=21)                                                              caCCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGa                                                                       <  1:327236/148‑1 (MQ=255)                                                              aaCCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTTTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGa                                                                       <  2:718066/149‑1 (MQ=255)                                                              aaCCCGCGCTCTGCAAACCTTACTCGATAAAGGTGACAACCACTGAGTAAACAGCTCAAGGTAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACAGATTACAAGCCCACGGCCGCGGa                                                                       >  2:654493/1‑149 (MQ=25)                                                                        cTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTg                                                             <  2:679230/149‑1 (MQ=255)                                                                          gCAAACCTTCCACGATAAAAGTCACCACCACTGAGTAAACAGCTCTATGGATGTAAATTCCTATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGgc                                                           <  2:666739/149‑1 (MQ=18)                                                                          gCAAACCTGTCGCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGgc                                                           <  2:332916/149‑1 (MQ=255)                                                                            aaaCCTGTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGgcga                                                         <  2:33292/149‑1 (MQ=255)                                                                                cTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCCGATATTCCCGTGgcgagcgt                                                     >  1:388250/1‑148 (MQ=255)                                                                                 tttCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGGCATCTGTTATCCCTCAACCCATTACACGCCCGCTGCCGCGGATATTCACGTGcggagcgct                                                    >  2:117632/1‑147 (MQ=25)                                                                                      cGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAAccc                                               >  1:447667/1‑149 (MQ=255)                                                                                              gTGACAACCACGGGGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCATGGCGAGCGATAACCCAGCGCACt                                       >  2:482861/1‑149 (MQ=255)                                                                                                  cAACCACTGAGTAAACAGATCAAGGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGc                                   <  2:312647/149‑1 (MQ=255)                                                                                                      cACTGAGTAAACAGGTCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGAt                               <  1:490928/149‑1 (MQ=255)                                                                                                                aCAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGtt                     >  1:301053/1‑149 (MQ=255)                                                                                                                aCAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGtt                     >  2:483171/1‑149 (MQ=255)                                                                                                                aCAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGtt                     >  1:552124/1‑149 (MQ=255)                                                                                                                    aTCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTCTCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCACCGCCCTATGCGGATGCCATTCGTTATaa                 >  2:47074/1‑149 (MQ=255)                                                                                                                    aTCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCACCGCCCTATGCGGATGCCACTCGTtatag                 >  2:312787/1‑148 (MQ=255)                                                                                                                       aaTGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTGATTATAATGc              >  2:108804/1‑149 (MQ=255)                                                                                                                       aaTGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCACCGCACTATGCGGATGCCATTCGTCATAATGc              >  2:604562/1‑149 (MQ=255)                                                                                                                            aaGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGaa         <  2:95332/149‑1 (MQ=255)                                                                                                                            aaGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGaa         <  1:88693/149‑1 (MQ=255)                                                                                                                            aaGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGaa         <  1:46577/149‑1 (MQ=255)                                                                                                                            aaGTAAATTCCAATTGTTTATTGGATGTGCCCCTTTATTGCCAGACGTCTGGTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGaa         <  2:277571/149‑1 (MQ=14)                                                                                                                                   ttCCGATTGTTTATTGGATTTGCCCCTATATTGCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCCTTCGTTATAATGCTCGAACGCctct  <  2:189654/149‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                      ATTTATTTCCAGCGGTATAGCTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCT  >  NC_000913/2996215‑2996493

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.