New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1962618 =	22 (0.430)	28 (0.540)	24/284	1.4	56.0%	coding (355/393 nt)	flhE	proton seal during flagellar secretion
	?	NC_000913	= 2290111	NA (NA)					intergenic (‑32/+1)	insH1/yejO	IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system

AATCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTACAGAAAATACCCATAGCTCCATACCCGGA  >  NC_000913/2289975‑2290253                                                                                                                                         |                                                                                                                                               aagctcgTTTCTGGTCGGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACg                                                                                                                                          <  2:303583/140‑1 (MQ=255)     tctTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGGACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGt                                                                                                                                      <  1:707714/143‑1 (MQ=38)            tGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGAGGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGccacc                                                                                                                               <  2:168347/143‑1 (MQ=255)                       cgcTTACTGCTGAATTCACTGTCGGCGAATGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGatat                                                                                                                    >  2:107464/1‑143 (MQ=255)                         gttggtggtgATTTCACTGTCGGGGAGGGGAAGTTGATGACGCATGATGAACCCTGTGCTATGGCGCCGGATGACAAACATGATCTCATATCAGGGACTTGTTCGCAGCTGCCATAACGCTGTAGCCACCAGAACAGATATTg                                                                                                                  <  2:236090/135‑1 (MQ=17)                              tgctgAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGaa                                                                                                             >  1:714657/1‑143 (MQ=255)                              tgctgAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTACCATAACGCTGTAGCCACCAGAACAGATATTGCGGaa                                                                                                             >  2:483880/1‑143 (MQ=255)                               gcttAATTCACTGTCTGCGAAGGTAACTTAATGACTCCTGATCAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATCGCAGGGACTTTTTCGCACCTTCCATATCGCTGTAGCCACCAGAACAGATATTGCGGAAc                                                                                                            <  2:240075/143‑1 (MQ=18)                                 tgAATTCACTGTCGGCGAACGTAAGTTGATGACTCATGATGAACCCTGTGCTATCGCTCCAGATGACAAACATGATCGCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGa                                                                                                          <  2:162105/143‑1 (MQ=255)                                               gCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGCTGTGCCCGAACGACAAAGAGAAACAGa                                                                                            >  2:675033/1‑143 (MQ=18)                                                 gAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGCACGACAAAGAGAAACAGAAc                                                                                          >  1:448341/1‑143 (MQ=255)                                                     gTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCTTATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGa                                                                                      >  1:739016/1‑143 (MQ=255)                                                          ttGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGCACGACAAAGAGAAACAGAACCAGATTGAt                                                                                 >  1:894008/1‑143 (MQ=255)                                                          ttGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGAt                                                                                 >  2:276642/1‑143 (MQ=255)                                                            gatggCTCATGTTGAACGCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGc                                                                               <  2:555535/143‑1 (MQ=255)                                                               gaCTCATGATGAACCCTGTGCTATGGCTCCAGATGACCAACATGATCTCATATCAGGGACTTGTTAGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCAtt                                                                            <  2:70453/143‑1 (MQ=255)                                                                  tCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCCATGAg                                                                         >  2:872299/1‑143 (MQ=255)                                                                          aaCCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATc                                                                 >  1:251706/1‑143 (MQ=255)                                                                            cgcTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCTACTAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACAAGATTCATGCATAGAGCTTTCATCCt                                                               >  2:492606/3‑143 (MQ=25)                                                                            cccTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCt                                                               >  2:56509/1‑143 (MQ=255)                                                                                gTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGa                                                           <  1:179760/143‑1 (MQ=255)                                                                                  tCTATGTCTCCAGATGACAAACACGATCTCATATCAGGGACGTGTTCGCACCTTCCATAACGCTGTAGCCAACAGAACAGATATTGCGGAACTACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGaaa                                                         <  2:44848/143‑1 (MQ=255)                                                                                             acaTGACACACAGGATCTCATATCCGTGACTTTTTCTCTCCTTCCATAACGCTGTAGCCACCAGAACAGTTATTGCGGAACGACAAAGAGATACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGt                                              <  2:254319/141‑1 (MQ=255)                                                                                             aGATGACAACCATGCTCTCATATCAGGGACGTGGTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGt                                              <  1:502076/143‑1 (MQ=255)                                                                                                    aaaCATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGc                                       >  1:15859/1‑143 (MQ=255)                                                                                                      aCATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCAt                                     >  1:707618/1‑143 (MQ=255)                                                                                                        aTGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGACACAGAACCAGATTGATGCATTGAGCTTTCCTCCTATGAAATTAATTACTGTTAAAAGCAttt                                   >  2:827660/1‑142 (MQ=255)                                                                                                         cgctcccATATCACGGACTTCGTCGCACCTTCCATAACGCTGTAGCAACCAGAACACATATTGCGGAACCACAAAGAGAAACAGAACCAGACTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTgg                                  <  1:462988/137‑1 (MQ=255)                                                                                                          ggtgccATATCAGGGATGTCTTCGCCCCTTCCATAACGCTGAAGACGAGTTGATATTTCTTGCGAGAGGACAAAGAGAGACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTggg                                 <  2:190443/138‑1 (MQ=255)                                                                                                            tctcATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAAAGACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCAATGAAAATAATTGCTGTGAAAAGCATTGGGTa                               >  2:71725/1‑143 (MQ=255)                                                                                                             ctcATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTCTCGTGCTATGAAGTTAATTGCGGTTAAAAGCATTGGATAc                              >  2:511982/1‑143 (MQ=255)                                                                                                                   tCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTACAGaaaa                        >  1:739199/1‑143 (MQ=255)                                                                                                                      gggACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTACAGAAAATAc                     <  1:543939/143‑1 (MQ=255)                                                                                                                          gttGTTCGCACCTTCCATAACGCTGTAGCCAACAGAAAAGATATTGCGGAACGACAAATAGAAACAGAATCAGATTTATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTACAGAAAATACCCAt                 <  2:372350/142‑1 (MQ=255)                                                                                                                           ttGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTACAGAAAATACCCATa                >  2:72134/1‑143 (MQ=255)                                                                                                                           ttGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCACCCAATGAAAAAAATTGCTGTTAAAAGCATTGGGTACAGAAAATACCAATa                >  2:267546/1‑143 (MQ=255)                                                                                                                                 gCACCTTCCATAACGCTGTAGCCACCCGAACAGATATCGCGTAACGACAAAGAGAAACAGAACCAGCTTGATGCATTGAGCTTTCATCCTATGAAAGGAATAACCGTTAAAAGCAACGTCTACAGAAAATACCCAGAGCACCa          >  2:108834/1‑143 (MQ=255)                                                                                                                                     cTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCATTGCGCTTATATCCTAGGAAATTAATTGCTGTTAAAAGCATTGGGTACAGAAAATACCCATAGCTCCATAcc      >  2:316530/1‑143 (MQ=255)                                                                                                                                      ttCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTACAGAAAATACCCATAGCTCCATAccc     <  1:532712/143‑1 (MQ=255)                                                                                                                                      ttCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTACAGAAAATACCCATAGCTCCATAccc     >  1:367333/1‑143 (MQ=255)                                                                                                                                       tCCATAACGCTGTAGCCACCAGAACAGATATTGCGGCACGACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTACAGAAAATACCCATCGCTCCATACCCg    >  2:110180/1‑143 (MQ=255)                                                                                                                                        ccATAACGCTGTAGGCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTACAGAAAATACCCATAGCTCCATACCCgg   <  2:577714/143‑1 (MQ=255)                                                                                                                                         cATCACGCTGTAGCCAACAGATCAGATATTGCGGAACGATAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTACAGAAAATACCCATAGCTCCATACCCGGa  <  2:906322/143‑1 (MQ=255)                                                                                                                                         cATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGTCTCCACAAAATCCCCATAGCTCCCTACCCgca  >  2:347818/1‑141 (MQ=255)                                                                                                                                         cATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTACAGAAAATACCCATAGCTCCATACCCGGa  <  2:448341/143‑1 (MQ=255)                                                                                                                                         |                                                                                                                                               AATCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTACAGAAAATACCCATAGCTCCATACCCGGA  >  NC_000913/2289975‑2290253

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.