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.