New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP009273 4557863 =562 (1.070)4 (0.010) 4/98 NT 0.85% coding (474/1233 nt) mdtM multidrug efflux system protein
?CP009273 4557894 = 444 (0.960)coding (443/1233 nt) mdtM multidrug efflux system protein
Rejected: Frequency below/above cutoff threshold.

Only 100 of 755 total aligned reads displayed.

AAAAAGGACTTTCCAGTGCATAAAGTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATCGCCATCAACTTGATCCCTTTTGTCTGTCCGAACGCCTCCTGCAC  >  CP009273/4557827‑4557961
                                                                   |                                                                   
caagttgatggcgattatcacctccatcgtactgattgcgccgattatcggcccgctttccggcgcaa                                                                     <  1:41449995‑M2/1‑1 (MQ=255)
aaaaaGGACTTTCCAGTGCATAAAGTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCaa                                                                     <  1:10613985/68‑1 (MQ=255)
aaaaaGGACTTTCCAGTGCATAAAGTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCaa                                                                     <  1:26405396/68‑1 (MQ=255)
aaaaaGGACTTTCCAGTGCATAAAGTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCaa                                                                     <  1:14893690/68‑1 (MQ=255)
aaaaaGGACTTTCCAGTGCATAAAGTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCaa                                                                     <  1:39390819/68‑1 (MQ=255)
aaaaaGGACTTTCCAGTGCATAAAGTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCaa                                                                     <  1:41118598/68‑1 (MQ=255)
aaaaaGGACTTTCCAGTGCATAAAGTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCaa                                                                     <  1:4768503/68‑1 (MQ=255)
 aaaaGGACTTTCCAGTGCATAAAGTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCaa                                                                     >  1:12499470/1‑67 (MQ=255)
 aaaaGGACTTTCCAGTGCATAAAGTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAAt                                                                    <  1:4445608/68‑1 (MQ=255)
   aaGGACTTTCCAGTGCATAAAGTGCATCAGAGCTGCGCGTGAAAGCGGGCCGATAATCGGCGCAATCa                                                                  <  1:8414234/68‑1 (MQ=255)
   aaGGACTTTCCAGTGCATAAAGTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCa                                                                  <  1:19816855/68‑1 (MQ=255)
     ggACTTTCCAGTGCATAAAGTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGt                                                                >  1:39062352/1‑68 (MQ=255)
      gACTTTCCAGTGCATAAAGTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGt                                                                >  1:8570425/1‑67 (MQ=255)
       aCTTTCCAGTGCATAAAGTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGt                                                                <  1:10874109/66‑1 (MQ=255)
       aCTTTCCAGTGCATAAAGTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGt                                                                <  1:21423999/66‑1 (MQ=255)
       aCTTTCCAGTGCATAAAGTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGt                                                                <  1:20069786/66‑1 (MQ=255)
        cTTTCCAGTGCATAAAGTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCaa                                                                     <  1:9829611/60‑1 (MQ=255)
        cTTTCCAGTGCATAAAGTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACg                                                             <  1:38268445/68‑1 (MQ=255)
          ttCCAGTGCATAAAGTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGAt                                                           <  1:28298977/68‑1 (MQ=255)
          ttCCAGTGCATAAAGTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGAt                                                           <  1:37301745/68‑1 (MQ=255)
            ccAGTGCATAAAGTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATgg                                                         >  1:27924592/1‑68 (MQ=255)
            ccAGTGCATAAAGTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATgg                                                         <  1:31267733/68‑1 (MQ=255)
            ccAGTGCATAAAGTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATgg                                                         >  1:38706164/1‑68 (MQ=255)
            ccAGTGCATAAAGTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATgg                                                         >  1:19208222/1‑68 (MQ=255)
             cAGTGCATAAAGTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGa                                                        >  1:30380374/1‑68 (MQ=255)
             cAGTGCATAAAGTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGa                                                        <  1:18323680/68‑1 (MQ=255)
                 gCATAAAGTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAgg                                                      <  1:25523303/66‑1 (MQ=255)
                 gCATAAAGTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAgg                                                      <  1:6738540/66‑1 (MQ=255)
                 gCATAAAGTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTg                                                    >  1:9122338/1‑68 (MQ=255)
                   aTAAAGTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGa                                                   <  1:40232060/67‑1 (MQ=255)
                      aaGTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATaa                                                >  1:36457584/1‑67 (MQ=255)
                      aaGTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATaa                                                >  1:11660062/1‑67 (MQ=255)
                      aaGTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATaa                                                >  1:8089257/1‑67 (MQ=255)
                      aaGTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATaa                                                >  1:41898145/1‑67 (MQ=255)
                      aaGTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATaa                                                >  1:21644871/1‑67 (MQ=255)
                      aaGTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATaa                                                >  1:20444177/1‑67 (MQ=255)
                       aGTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATc                                              >  1:28967924/1‑68 (MQ=255)
                       aGTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATc                                              >  1:2719088/1‑68 (MQ=255)
                        gTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATc                                              >  1:3526948/1‑67 (MQ=255)
                        gTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATc                                              >  1:42520981/1‑67 (MQ=255)
                        gTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATc                                              >  1:17804605/1‑67 (MQ=255)
                        gTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATc                                              >  1:7296394/1‑67 (MQ=255)
                        gTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATc                                              >  1:13288049/1‑67 (MQ=255)
                        gTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATc                                              >  1:14637712/1‑67 (MQ=255)
                        gTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATc                                              >  1:39842138/1‑67 (MQ=255)
                        gTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATc                                              >  1:22418722/1‑67 (MQ=255)
                        gTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATc                                              >  1:18911198/1‑67 (MQ=255)
                          gCATAAGAGCTGCTCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATCGc                                            <  1:38516804/67‑1 (MQ=255)
                             tCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATCGCCATc                                        >  1:23554600/1‑68 (MQ=255)
                               agagCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATCGCCATCa                                       >  1:24543842/1‑67 (MQ=255)
                               agagCTGCGCCGGAAAGCGGGCCGATAATCCGCGCAATCTGTACGATGGAGGGGATAATCGCCAtga                                       >  1:31706458/1‑65 (MQ=255)
                                  tcTGCGCCGGAAAGCGGTCCGATAATCGGCGCAATAATTAATATGGAGGTGATAATCGCAATCAAc                                     <  1:37625917/65‑1 (MQ=255)
                                  gCTGCGCCGGAAAGCGGGCCGATAATCTGCGCAATCAGTAATATGGAGGTGATAATAGCCATCAAcat                                   >  1:23775419/1‑66 (MQ=255)
                                  gCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATCGCCATCaa                                      <  1:33274456/65‑1 (MQ=255)
                                  gCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATCGCCATCAAcat                                   >  1:29209835/1‑66 (MQ=255)
                                  gCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATCGCCATCAAc                                     <  1:15898332/66‑1 (MQ=255)
                                  gCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATCGCCATCAACtt                                   >  1:22893561/1‑68 (MQ=255)
                                  gCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATCGCCATCAACtt                                   >  1:27565796/1‑68 (MQ=255)
                                  gCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATCGCCATCAACtt                                   >  1:2082329/1‑68 (MQ=255)
                                  gCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATCGCCATCAACtt                                   >  1:16737541/1‑68 (MQ=255)
                                  gCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATCGCCATCAACtt                                   >  1:14220702/1‑68 (MQ=255)
                                  gCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATCGCCATCAACtt                                   >  1:19706294/1‑68 (MQ=255)
                                  gCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATCGCCATCAACtt                                   >  1:1713749/1‑68 (MQ=255)
                                  gCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATCGCCATCAACtt                                   >  1:3368534/1‑68 (MQ=255)
                                  gCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATCGCCATCAACtt                                   >  1:30812170/1‑68 (MQ=255)
                                  gCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATCGCCATCAACtt                                   >  1:2980430/1‑68 (MQ=255)
                                    TGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATCGCCATCAACTTGa                                 >  1:5638266‑M1/1‑68 (MQ=255)
                                       GCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATCGCCATCATCTTGATc                               <  1:25938078‑M1/67‑1 (MQ=255)
                                       GCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATCGCCATCAACTTGATc                               <  1:18660166‑M1/67‑1 (MQ=255)
                                       GCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATCGCCATCAACTTGATc                               <  1:7487024‑M1/67‑1 (MQ=255)
                                       GCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATCGCCATCAACTTGATc                               <  1:40776312‑M1/67‑1 (MQ=255)
                                       GCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATCGCCATCAACTGgatac                              <  1:35738491‑M1/68‑3 (MQ=255)
                                       GCCGGAAAGCGGGCCGATAATCGGCGCAATCAGGACGATGGAGGTGATAATCGCCATCAACTTGATc                               <  1:32879817‑M1/67‑1 (MQ=255)
                                         CGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATCGCCATCAACTTGATccc                             >  1:5353675‑M1/1‑67 (MQ=255)
                                         CGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATCGCCATCAACTTGATccc                             >  1:12774129‑M1/1‑67 (MQ=255)
                                         CGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATCGCCATCAACTTGATccc                             >  1:5962410‑M1/1‑67 (MQ=255)
                                         CGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATCGCCATCAACTTGATccc                             >  1:16463603‑M1/1‑67 (MQ=255)
                                         CGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATCGCCATCAACTTGATccc                             >  1:34628224‑M1/1‑67 (MQ=255)
                                         CGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATCGCCATCAACTTGATccc                             >  1:15393095‑M1/1‑67 (MQ=255)
                                            aaaGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATCGCCATCACCTTGATCCCtttt                         >  1:1947638/1‑68 (MQ=255)
                                              aGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATCGCCATCAACTTGATCCCTTTtgt                       <  1:8851029/68‑1 (MQ=255)
                                                    ccGATAATCGGCGCAATCAGTACGATGGAGGTGATAATCGCCATCAACTTGATCCCTTTtgtctgtc                  <  1:41690656/67‑1 (MQ=255)
                                                    ccGATAATCGGCGCAATCAGTACGATGGAGGTGATAATCGCCATCAACTTGATCCCTTTTGTCTGTcc                 >  1:13848979/1‑68 (MQ=255)
                                                         aaTCGGCGCAATCAGTACGATGGAGGTGATAATCGCCATCAACTTGATCCCTTTTGTCTGTCCGAAc             >  1:37006116/1‑67 (MQ=255)
                                                          aTCGGCGCAATCAGTACGATGGAGGTGATAATCGCCATCAACTTGATCCCTTTTGTCTGTCCGAACGc           <  1:10040094/68‑1 (MQ=255)
                                                           tCGGCGCAATCAGTACGATGGAGGTGTTAATCGCCATCAACTTGATCCCTTTTGTCTGTCCGAACg            >  1:24065112/1‑66 (MQ=255)
                                                           tCGGCGCAATCAGTACGATGGAGGTGATAATCGCCATCAACTTGATCCCTTTTGTCTGTCCGAACg            >  1:43361589/1‑66 (MQ=255)
                                                            cgtcgcaATCAGTACGATGGAGGTGTTAATCGCCATCAACTTGATCCCTTTTGTCTGTCCGAACGcct         <  1:42111509‑M2/61‑1 (MQ=255)
                                                            cggcgcaATCAGTACGATGGATGTGATAATCGCCATCAACTTGATCCCTTTTGTCTGTCCGAACGcct         <  1:43029367‑M2/61‑1 (MQ=255)
                                                            cggcgcaATCAGTACGATGGAGGTGATAATCGCCATCAACTTGATCCCTTTTGTCTGTCCGAACGcct         <  1:12139820‑M2/61‑1 (MQ=255)
                                                            cggcgcaATCAGTACGATGGAGGTGATAATCGCCATCAACTTGATCCCTTTTGTCTGTCCGAACGcct         <  1:40441022‑M2/61‑1 (MQ=255)
                                                            cggcgcaATCAGTACGATGGAGGTGATAATCGCCATCAACTTGATCCCTTTTGTCTGTCCGAACGcct         <  1:37881330‑M2/61‑1 (MQ=255)
                                                            cggcgcaATCAGTACGATGGAGGTGATAATCGCCATCAACTTGATCCCTTTTGTCTGTCCGAACGcct         <  1:36104429‑M2/61‑1 (MQ=255)
                                                            cggcgcaATCAGTACGATGGAGGTGATAATCGCCATCAACTTGATCCCTTTTGTCTGTCCGAACGcct         <  1:34153478‑M2/61‑1 (MQ=255)
                                                            cggcgcaATCAGTACGATGGAGGTGATAATCGCCATCAACTTGATCCCTTTTGTCTGTCCGAACGcct         <  1:25013059‑M2/61‑1 (MQ=255)
                                                            cggcgcaATCAGTACGATGGAGGTGATAATCGCCATCAACTTGATCCCTTTTGTCTGTCCGAACGcct         <  1:9387648‑M2/61‑1 (MQ=255)
                                                            cggcgcaATCAGTACGATGGAGGTGATAATCGCCATCAACTTGATCCCTTTTGTCTGTCCGAACGcct         <  1:23204092‑M2/61‑1 (MQ=255)
                                                            cggcgaaATCAGTACGATGGAGGTGATAATCGCCATCAACTTGATCCCTTTTGTCTGTCCGAACGcct         <  1:31045157‑M2/61‑1 (MQ=255)
                                                             ggcgcaATCAGTACGATGGAGGTGATAATCGCCATCAACTTGATCCCTTTTGTCTGTCCGAACGcct         >  1:32325931‑M2/7‑67 (MQ=255)
                                                               cgcaATCAGTACGATGGAGGTGATAATCGCCATCAACTTGATCCCTTTTGTCTGTCCGAACGcctcc       <  1:11252938‑M2/63‑1 (MQ=255)
                                                                   |                                                                   
AAAAAGGACTTTCCAGTGCATAAAGTGCATCAGAGCTGCGCCGGAAAGCGGGCCGATAATCGGCGCAATCAGTACGATGGAGGTGATAATCGCCATCAACTTGATCCCTTTTGTCTGTCCGAACGCCTCCTGCAC  >  CP009273/4557827‑4557961

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.