New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 2406863	2 (0.040)	46 (1.030)	37/274	NT	95.9%	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

ATTTATTTCCAGCGGTATAGCTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTC  >  NC_000913/2996215‑2996502                                                                                                                                                  |                                                                                                                                               atttatttCCAGCGGTATACCTGACAAATAATCCCTTATGAAATAGCGGCGAGGAGAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGAt                                                                                                                                             <  1:579651/149‑1 (MQ=255)  tttatttCCAGCGGTATAGCTGATAACTAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGCTCTGCAAACCTTTCTCGATACAGATGACAAACACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTAATTGGAtt                                                                                                                                            >  2:62788/1‑149 (MQ=255)  tttatttCAAGAGGTATAGCTGATAAATACTCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAACCAGATCACTGGAAGTACATTCCAATTGTTTATTGAAtt                                                                                                                                            >  2:158206/1‑149 (MQ=255)   ttatttCCAGCGGTATAGCTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGAttt                                                                                                                                           <  1:627891/149‑1 (MQ=255)     atttCCAGCGGTATAGCTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGGGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGc                                                                                                                                         <  1:138288/149‑1 (MQ=255)       ttCCAGCGGTATAGCTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGccc                                                                                                                                       <  2:95844/149‑1 (MQ=255)       ttCCAGCGGTATAGCTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGccc                                                                                                                                       <  1:299374/149‑1 (MQ=255)         ccAGCGGTATAGCTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCt                                                                                                                                     >  1:245738/1‑149 (MQ=255)         ccAGCGGTATAGCTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTGGCCCCt                                                                                                                                     >  1:321896/1‑149 (MQ=255)          cAGCGGTATAGCTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTGTATTGGATTTGCCCCta                                                                                                                                    >  1:367531/1‑149 (MQ=255)               gTATAGCTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTCTTTAATGGATTTGCCCCTATAttt                                                                                                                               >  2:586079/1‑149 (MQ=255)               gTATAGCTACCAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTATTCATTGGCTTTGCCCCCATCttt                                                                                                                               >  2:8398/1‑149 (MQ=255)                        ataaataaTCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATGGTTTATTGGATTTGCCCCTATATTTCCAGACagc                                                                                                                      >  1:159139/1‑147 (MQ=255)                           aataatTCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGt                                                                                                                   <  2:660895/149‑1 (MQ=255)                           aataatCCCTTAGTACATCAGGAACCTTATAAAAACACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGAAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGt                                                                                                                   >  2:369601/1‑149 (MQ=255)                              aatCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTACCAATGTGATTTGCCCCTATATTTCCAGACATCTGTTAt                                                                                                                <  1:792851/149‑1 (MQ=255)                              aatCCCTGAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTAt                                                                                                                <  1:236349/149‑1 (MQ=255)                                tCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCa                                                                                                              <  1:660214/149‑1 (MQ=255)                                tCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCa                                                                                                              <  2:116120/149‑1 (MQ=255)                                tCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCa                                                                                                              <  2:230891/149‑1 (MQ=255)                                         aCATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCa                                                                                                     <  1:702959/149‑1 (MQ=255)                                           aTCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCCCTTAACCCAtt                                                                                                   >  1:14071/1‑149 (MQ=255)                                                       ataAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTg                                                                                       <  1:647846/149‑1 (MQ=255)                                                          aaaaaaCCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACACCTTTTATCACTTAACCCATTACAAGCCCGCTGCCg                                                                                    <  2:369967/149‑1 (MQ=255)                                                           aaaaaCCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGc                                                                                   >  2:385057/1‑149 (MQ=255)                                                                     gTTCTGCAAACCTTTCTCGATGAGAGTGACAACCGCTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGTATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTccc                                                                         <  1:708720/149‑1 (MQ=255)                                                                        cTGCAAACCTTCCCCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTATTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTg                                                                      <  1:635479/149‑1 (MQ=255)                                                                         tGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAACCCCGCTGCCGCAGATATTCCCGTgg                                                                     >  2:5164/1‑149 (MQ=255)                                                                             aaCCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGgcgag                                                                 <  2:739806/149‑1 (MQ=255)                                                                             aaCCTTTCGCGATAAAAGTGACAACCACTGAGTAAACAGATCTATGGAAGTAAATTCCAATTGTTTATTGGATTTGCGCCTATATTGCCAGACCTCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGgcgag                                                                 <  2:88819/149‑1 (MQ=25)                                                                                     tcGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCATATATTTCCAGACATCTGTTATCACTTAACACATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATaaac                                                         >  2:420210/1‑147 (MQ=255)                                                                                         tAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAgc                                                     <  1:404970/149‑1 (MQ=255)                                                                                                   aaCCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCg                                           >  1:11409/1‑149 (MQ=255)                                                                                                        cTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGc                                      <  2:320438/149‑1 (MQ=255)                                                                                                               aaCAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGt                               <  2:403552/149‑1 (MQ=255)                                                                                                               aaCAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTAGATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGTGGATGCCATTCGt                               <  2:486393/149‑1 (MQ=255)                                                                                                                 cAGATTAAGTGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCCGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTta                             <  1:158206/149‑1 (MQ=255)                                                                                                                        aTGGATGTAAATTCCAATTGTTTATGGGATTTGCCCCTATCTTTCAAGACATCTGTTATCTCTTACCCCATTGCAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATTACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCt                      <  2:203129/149‑1 (MQ=14)                                                                                                                            aaGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGaa                  <  2:1689/149‑1 (MQ=255)                                                                                                                            aaGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATAACTTACCCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCCaa                  >  2:102421/1‑149 (MQ=255)                                                                                                                               tAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGc               >  2:147787/1‑149 (MQ=255)                                                                                                                                 agttCCAATTGTTTATTGGATTTGCCCCGATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCct             <  2:332206/147‑1 (MQ=255)                                                                                                                                     ccAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAAAACAGCGCCCTATGTTCATGCCATTCGTTCTAATGCTCGAACACCTCTGc         >  2:364933/1‑149 (MQ=11)                                                                                                                                         ttGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAgg     <  1:385057/149‑1 (MQ=34)                                                                                                                                           gTTTATTGGATTTGCCCCTATATTTCCGGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCACGGtt   >  1:758027/1‑149 (MQ=17)                                                                                                                                            tttATTGGATTTGCCTCTAGATTTCCAGACATCTGGTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTAGGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTc  <  1:26633/149‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                               ATTTATTTCCAGCGGTATAGCTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTC  >  NC_000913/2996215‑2996502

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ 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.