New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP009273 964816 =129 (0.370)10 (0.030) 7/94 NT 7.4% intergenic (+8/‑29) lpxK/ycaQ lipid A 4'kinase/DUF1006 family protein with C‑terminal wHTH domain
?CP009273 964858 = 143 (0.480)coding (14/1233 nt) ycaQ DUF1006 family protein with C‑terminal wHTH domain

Only 100 of 227 total aligned reads displayed.

CAGGTGATGAACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATGCGCGTAAT  >  CP009273/964750‑964883
                                                                  |                                                                   
cAGGTGATGAACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTAcgccgc                                                                    >  1:1276804/1‑68 (MQ=255)
 gcggggtttgtttaacaggccttgtgcggcaaggtgaagattacgcgcatcagcaagggagaggtGCg                                                                   <  1:33217‑M1/3‑1 (MQ=255)
  ggTGATGAACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCcgcg                                                                   >  1:25756726/1‑67 (MQ=255)
  ggTGATGAACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCcgcg                                                                   >  1:5330581/1‑67 (MQ=255)
  ggTGATGAACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCcgcg                                                                   >  1:19075195/1‑67 (MQ=255)
  ggTGATGAACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCcgcg                                                                   >  1:18720248/1‑67 (MQ=255)
  ggTGATGAACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCcgcg                                                                   >  1:17920747/1‑67 (MQ=255)
  ggTGATGAACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCcgcg                                                                   >  1:6526817/1‑67 (MQ=255)
  ggTGATGAACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCcgcg                                                                   >  1:2455853/1‑67 (MQ=255)
  ggTGATGAACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCcgcg                                                                   >  1:12439160/1‑67 (MQ=255)
   ggggtttgtttaacaggccttgtgcggcaaggtgaagattacgcgcatcagcaagggagaggtGCGGc                                                                 <  1:8124914‑M1/5‑1 (MQ=255)
     ggtttgtttaacaggccttgtgcggcaaggtgaagattacgcgcatcagcaagggagaggtGCGGCa                                                                <  1:7627061‑M1/6‑1 (MQ=255)
     ggtttgtttaacaggccttgtgcggcaaggtgaagattacgcgcatcagcaagggagaggtGCGGCa                                                                <  1:14970777‑M1/6‑1 (MQ=255)
     gatgaACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCa                                                                >  1:15241414/1‑67 (MQ=255)
       tttgtttaacaggccttgtgcggcaaggtgaagattacgcgcatcagcaagggagaggtGCGGCAGc                                                              >  1:19237362‑M1/60‑67 (MQ=255)
         aaCCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGt                                                            >  1:28924730/1‑67 (MQ=255)
          aCCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTc                                                          >  1:27738567/1‑68 (MQ=255)
          aCCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTc                                                          >  1:21392783/1‑68 (MQ=255)
             aGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGAt                                                       >  1:19981892/1‑68 (MQ=255)
                gAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGAtt                                                      <  1:13073784/66‑1 (MQ=255)
                 aaaCTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGAt                                                   >  1:1247599/1‑68 (MQ=255)
                  aaCTGCTTACGCAACTCACCTTGCTGGCTTCTGGCACCTAGTTACGCCGCGGCAGCGTTCGATTGAt                                                   <  1:6448393/67‑1 (MQ=255)
                    cTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGa                                                <  1:25466731/68‑1 (MQ=255)
                    cTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGa                                                <  1:9543181/68‑1 (MQ=255)
                     tGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAg                                               <  1:21130403/68‑1 (MQ=255)
                      gCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGt                                              <  1:17696791/68‑1 (MQ=255)
                      gCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGt                                              <  1:4878154/68‑1 (MQ=255)
                        ttACGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCa                                            <  1:11559730/68‑1 (MQ=255)
                           cGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGa                                         >  1:26254274/1‑68 (MQ=255)
                           cGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGa                                         <  1:11977916/68‑1 (MQ=255)
                           cGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGa                                         >  1:18950725/1‑68 (MQ=255)
                            gCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGaa                                        >  1:3769679/1‑68 (MQ=255)
                             cAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAAt                                       >  1:29244783/1‑68 (MQ=255)
                             cAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAAt                                       >  1:4700963/1‑68 (MQ=255)
                             cAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAAt                                       >  1:1844660/1‑68 (MQ=255)
                             cAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAAt                                       >  1:5496665/1‑68 (MQ=255)
                               aCTAACCTTGCTGGCTTCTGGCAACTAGTTACGCCCCGGCAGCGTTCGATTGATGGAGTCAAGAATg                                      >  1:3181295/1‑67 (MQ=255)
                                   aCCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCt                                 <  1:1436302/68‑1 (MQ=255)
                                   aCCTTGCTGGCTGCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCt                                 <  1:6885008/68‑1 (MQ=255)
                                    ccTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCt                                 >  1:25671241/1‑67 (MQ=255)
                                         cTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGc                            >  1:226764/1‑67 (MQ=255)
                                          tGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCa                           <  1:24362283/67‑1 (MQ=255)
                                          tGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCa                           <  1:18931514/67‑1 (MQ=255)
                                          tGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCa                           <  1:19660418/67‑1 (MQ=255)
                                          tGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCa                           <  1:15320929/67‑1 (MQ=255)
                                          tGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCAc                          <  1:116229/68‑1 (MQ=255)
                                           ggCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCAcc                         <  1:5796722/68‑1 (MQ=255)
                                           ggCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCAcc                         <  1:29034429/68‑1 (MQ=255)
                                           ggCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCAcc                         <  1:14688896/68‑1 (MQ=255)
                                           ggCTTCGGGAACCTAGAGACGCCGCGGCAGCGTGCGATTGATGGAGTCATGAATGTCGCTGCCGcggc                         <  1:11908228/68‑4 (MQ=255)
                                              ttCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACctct                      <  1:6386871/68‑1 (MQ=255)
                                              ttCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACctct                      <  1:24961193/68‑1 (MQ=255)
                                              cgcatcagcaagggagaggtGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACctc                       <  1:20100929‑M1/47‑1 (MQ=255)
                                               tCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACctct                      >  1:27157310/1‑67 (MQ=255)
                                                  ggCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCt                  >  1:28046485/1‑68 (MQ=255)
                                                    cAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCtt                 <  1:4301494/67‑1 (MQ=255)
                                                    cAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCtt                 <  1:7236139/67‑1 (MQ=255)
                                                    cAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCtt                 <  1:24004496/67‑1 (MQ=255)
                                                    cAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCtt                 <  1:17507907/67‑1 (MQ=255)
                                                    cAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCtt                 <  1:2088711/67‑1 (MQ=255)
                                                     aaCTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGc               <  1:8976978/68‑1 (MQ=255)
                                                     aaCTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGc               <  1:10216403/68‑1 (MQ=255)
                                                       aagggagaggtGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTg             <  1:10964454‑M1/57‑1 (MQ=255)
                                                         aGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGAt           >  1:20315886/1‑68 (MQ=255)
                                                         aGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGAt           >  1:8782585/1‑68 (MQ=255)
                                                         aGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGAt           >  1:25592261/1‑68 (MQ=255)
                                                         aGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGAt           >  1:25299517/1‑68 (MQ=255)
                                                         aGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGAt           >  1:13969436/1‑68 (MQ=255)
                                                          ggagaggtGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGctgct           <  1:6251616‑M1/59‑3 (MQ=255)
                                                           ttACGCCGCGGCAGCGATCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGAttc         >  1:26410042/1‑66 (MQ=255)
                                                           gagaggtGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATgc         <  1:22841119‑M1/61‑1 (MQ=255)
                                                            tACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATgcg        <  1:23925686/68‑1 (MQ=255)
                                                            tACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATgcg        <  1:16389146/68‑1 (MQ=255)
                                                            tACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATgcg        <  1:20430775/68‑1 (MQ=255)
                                                            agaggtGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATgc         <  1:178868‑M1/61‑1 (MQ=255)
                                                             aCGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATgcgc       <  1:2822139/68‑1 (MQ=255)
                                                             aCGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATgcgc       >  1:16439996/1‑68 (MQ=255)
                                                              cgccgcGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATGcgcg      <  1:21783566/68‑1 (MQ=255)
                                                               ggtGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATGCGCGt     <  1:13392614‑M1/65‑1 (MQ=255)
                                                               gccgcGGCTGCGTTCGATTGATGGAGTCATGATTGTCGCGGCCGCCCCTCTCCCTTGCTGAGGCGCGt     >  1:5979186/1‑68 (MQ=255)
                                                               gccgcGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATGCGCGt     >  1:14609371/1‑68 (MQ=255)
                                                               gccgcGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATGCGCGt     >  1:16056819/1‑68 (MQ=255)
                                                               gccgcGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATGCGCGt     >  1:25102158/1‑68 (MQ=255)
                                                               gccgcGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATGCGCGt     >  1:27656892/1‑68 (MQ=255)
                                                                ccgcGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATGCGCGTa    >  1:4994558/1‑68 (MQ=255)
                                                                ccgcGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATGCGCGTa    >  1:11843279/1‑68 (MQ=255)
                                                                ccgcGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATGCGCGTa    >  1:5426558/1‑68 (MQ=255)
                                                                ccgcGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATGCGCGTa    >  1:20337751/1‑68 (MQ=255)
                                                                ccgcGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATGCGCGTa    >  1:23450162/1‑68 (MQ=255)
                                                                ccgcGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATGCGCGTa    >  1:26954551/1‑68 (MQ=255)
                                                                 tGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTTCTGATGCGCGTaa   <  1:3248604‑M1/67‑1 (MQ=255)
                                                                 cgcgGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATGCGCGTaa   >  1:14738715/1‑68 (MQ=255)
                                                                 cgcgGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATGCGCGTaa   >  1:24773013/1‑68 (MQ=255)
                                                                  GCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATGCGCGTAAt  >  1:6215190‑M1/1‑68 (MQ=255)
                                                                  GCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATGCGCGTAAt  >  1:21980922‑M1/1‑68 (MQ=255)
                                                                  GCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATGCGCGTAAt  >  1:22067653‑M1/1‑68 (MQ=255)
                                                                  GCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATGCGCGTAAt  >  1:15740045‑M1/1‑68 (MQ=255)
                                                                  GCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATGCGCGTAAt  >  1:7847147‑M1/1‑68 (MQ=255)
                                                                  GCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATGCGCGTAAt  >  1:25415203‑M1/1‑68 (MQ=255)
                                                                  GCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATGCGCGTAAt  >  1:11424643‑M1/1‑68 (MQ=255)
                                                                  |                                                                   
CAGGTGATGAACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATGCGCGTAAT  >  CP009273/964750‑964883

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ 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.