New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? REL606 = 3744020103 (1.000)12 (0.160) 5/36 NT 18.0% coding (300/807 nt) waaP kinase that phosphorylates core heptose of lipopolysaccharide
?REL606 = 3861481 32 (0.420)coding (1109/1617 nt) yieC carbohydrate‑specific outer membrane porin, cryptic

AAATGGACTTGCGCCAGCATAACGGCCAAAGTTACTGGCGATAGAGTTATTCGCAACCAGGAAGGAGAA  >  REL606/3861447‑3861515
                                  |                                  
aaaTGGACTTGCGCCAGCATAACGGCCAAAGTTAc                                    >  1:19690124/1‑35 (MQ=255)
aaaTGGACTTGCGCCAGCATAACGGCCAAAGTTAc                                    >  1:9709309/1‑35 (MQ=255)
aaaTGGACTTGCGCCAGCATAACGGCCAAAGTTAc                                    >  1:87505/1‑35 (MQ=255)
aaaTGGACTTGCGCCAGCATAACGGCCAAAGTTAc                                    >  1:8250793/1‑35 (MQ=255)
aaaTGGACTTGCGCCAGCATAACGGCCAAAGTTAc                                    >  1:14748443/1‑35 (MQ=255)
 aaTGGACTTGCGCCAGCATAACGGCCAAAGTTACt                                   <  1:10525088‑M2/35‑2 (MQ=255)
 aaTGGACTTGCGCCAGCATAACGGCCAAAGTTACt                                   <  1:11470161‑M2/35‑2 (MQ=255)
 aaTGGACTTGCGCCAGCATAACGGCCAAAGTTACt                                   <  1:16946738‑M2/35‑2 (MQ=255)
 aaTGGACTTGCGCCAGCATAACGGCCAAAGTTACt                                   <  1:13255478‑M2/35‑2 (MQ=255)
  aTGGACTTGCGCCAGCATAACGGCCAAAGTTACtg                                  <  1:9198563‑M2/35‑3 (MQ=255)
  aTGGACTTGCGCCAGCATAACGGCCAAAGTTACtg                                  <  1:3366782‑M2/35‑3 (MQ=255)
    ggACTTGCGCCAGCATAACGGCCAAAGTTACtggc                                <  1:7624693‑M2/35‑5 (MQ=255)
     gACTTGCGCCAGCATAACGGCCAAAGTTACtggcg                               <  1:15704406‑M2/35‑6 (MQ=255)
     gACTTGCGCCAGCATAACGGCCAAAGTTACtggcg                               <  1:12886206‑M2/35‑6 (MQ=255)
     gACTTGCGCCAGCATAACGGCCAAAGTTACtggcg                               <  1:9992224‑M2/35‑6 (MQ=255)
      aCTTGCGCCAGCATAACGGCCAAAGTTACtggcga                              <  1:5336511‑M2/35‑7 (MQ=255)
      aCTTGCGCCAGCATAACGGCCAAAGTTACtggcga                              <  1:4016063‑M2/35‑7 (MQ=255)
      aCTTGCGCCAGCATAACGGCCAAAGTTACtggcga                              <  1:12984081‑M2/35‑7 (MQ=255)
       cTTGCGCCAGCATAACGGCCAAGGTTACtggcgaa                             <  1:19984311‑M2/35‑8 (MQ=255)
       cTTGCGCCAGCATAACGGCCAAAGTTACtggcgaa                             <  1:19282223‑M2/35‑8 (MQ=255)
        ttGCGCCAGCATAACGGCCAAAGTTACtggcgaaa                            <  1:13961320‑M2/35‑9 (MQ=255)
        ttGCGCCAGCATAACGGCCAAAGTTACtggcgaaa                            <  1:13106335‑M2/35‑9 (MQ=255)
         tGCGCCAGCATAACGGCCAAAGTTACtggcgaaaa                           <  1:17317863‑M2/35‑10 (MQ=255)
         tGCGACAGAAAACCGGCCAAAGTTACTGGCGATag                           <  1:8173119/35‑1 (MQ=19)
         tGCCCCACCAAACCGGCCAAAGTTACTGGCGATag                           <  1:7775159/35‑1 (MQ=19)
          gcgcCAGCATAACGGCCAAAGTTACtggcgaaaaa                          <  1:16228844‑M2/35‑11 (MQ=255)
          gcgcCAGCATAACGGCAAAAGTTACTGGCGATaga                          <  1:20049748/35‑1 (MQ=255)
           cgcCAGCATAACGGCCAAAGTTACtggcgaaagag                         <  1:10199160‑M2/35‑12 (MQ=255)
           cgcCAGCATAACGGCCAAAGTTACtggcgaaaaag                         <  1:7147422‑M2/35‑12 (MQ=255)
           cgcCAGCATAACGGCCAAAGTTACtggcgaaaaag                         <  1:6257711‑M2/35‑12 (MQ=255)
            gcCAGCATACCGGCCAAAGTTACTGGCGATAGAGt                        <  1:15357031/35‑1 (MQ=255)
            gcCAGCATAACGGCCAAAGTTACtggcgaaagagg                        <  1:1746938‑M2/35‑13 (MQ=255)
            cccAGCATACCGGCCAAAGTTACTGGCGATAGAGt                        <  1:15368686/34‑1 (MQ=255)
            cccAGCATACCGGCCAAAGTTACTGGCGATAGAGt                        <  1:2633277/34‑1 (MQ=255)
             ccAGCATAACGGCCAAAGTTACtggcgaaagaggt                       <  1:9666948‑M2/35‑14 (MQ=255)
             ccAGCATAACGGCCAAAGTTACtggcgaaaaagtt                       <  1:17470844‑M2/35‑14 (MQ=255)
             ccAGCATAACGGCCAAAGTTACtggcgaaaaaggt                       <  1:6103116‑M2/35‑14 (MQ=255)
              cAGCATACCGGCCAAAGTTACTGGCGATAGAGTTa                      <  1:9473297/35‑1 (MQ=255)
              cAGCATACCGGCCAAAGTTACTGGCGATAGAGTTa                      <  1:4538669/35‑1 (MQ=255)
              cAGCATAACGGCCAAAGTTACtggcgaaagaggta                      <  1:5926643‑M2/35‑15 (MQ=255)
              cAGCATAACGGCCAAAGTTACtggcgaaaaaggta                      <  1:16702662‑M2/35‑15 (MQ=255)
              cAGCATAACGGCCAAAGTTACTGGCGATAGAGGTa                      >  1:6429199/1‑35 (MQ=255)
              cAGCATAACGGCCAAAGTTACTGGCGATAAAGCTa                      >  1:4455240/1‑35 (MQ=37)
               agaaTACCGGCCAAAGTTACTGGCGATAGAGTTAt                     <  1:17557385/32‑1 (MQ=37)
               agaaTAACGGACAAAGTTACTGGCGATAGAGTTAt                     <  1:19634841/32‑1 (MQ=37)
               aGCATAACGGCCAAAGTTACtggcgaaaaaggtat                     <  1:2366219‑M2/35‑16 (MQ=255)
               aGCATAACGGCCAAAGTTACtggcgaaaaaggtat                     <  1:5219984‑M2/35‑16 (MQ=255)
               aGCAAACCGGCCAAAGTTACTGGCGATAGAGTTAt                     <  1:17191587/35‑1 (MQ=37)
                gCATAACGGCCAAAGTTACtggcgaaaaaggtatt                    <  1:8202667‑M2/35‑17 (MQ=255)
                gCATAACGGCCAAAGTTACtggcgaaaaaagtatt                    <  1:8569694‑M2/35‑17 (MQ=255)
                 cATACCGGCCAAAGTTACTGGCGATAGAGTTATTc                   <  1:11530613/35‑1 (MQ=255)
                 cATAACGGCCAAAGTTACtggcgaaaaagttattt                   <  1:3771477‑M2/35‑18 (MQ=255)
                 cATAACGGCCAAAGTTACtggcgaaaaaggtattt                   <  1:19699406‑M2/35‑18 (MQ=255)
                  aTAACGGCCAAAGTTACtggcgaaaaaggtatttg                  <  1:18448402‑M2/35‑19 (MQ=255)
                   tAACGGCCAAAGTTACTGGCGAAAGAGGTAttttc                 >  1:956949/1‑32 (MQ=25)
                   tAACGGCCAAAGTTACTGGCGAAAAAGATAttttc                 >  1:10441143/1‑32 (MQ=16)
                   caccGGCCAAAGTTACTGGCGATAGAGTTATTCGc                 <  1:16197776/32‑1 (MQ=255)
                    accGGCCAAAGTTACTGGCGATAGAGTTATTCGCa                <  1:15311667/33‑1 (MQ=255)
                    accGGCCAAAGTTACTGGCGATAGAGTTATTCGCa                <  1:13066086/33‑1 (MQ=255)
                    accGGCCAAAGTTACTGGCGATAGAGTTATTCGCa                <  1:12038192/33‑1 (MQ=255)
                    aaCGGCCAAAGTTACTGGCGAAAAAGATATTTGCa                >  1:17662308/1‑35 (MQ=19)
                     ccGGCCAAAGTTACTGGCGATAGAGTTATTCGCaa               <  1:19519249/34‑1 (MQ=255)
                     aCGGCCAAAGTTACTGGCGAAAAAGGTTTTTGCaa               >  1:769415/1‑35 (MQ=12)
                      cGGCCAAAGTTACTGGCGATAGAGTTATTCGCAAc              <  1:13084863/35‑1 (MQ=255)
                      cGGCCAAAGTTACTGGCGATAGAGTTATTCGCAAc              <  1:7610841/35‑1 (MQ=255)
                        gCCAAAGTTACTGGCGATAGAGTTATTCGCAACCa            <  1:8322125/35‑1 (MQ=255)
                         ccAAAGTTACTGGCGATAGAGTTATTCGCAACCag           <  1:2302088/35‑1 (MQ=255)
                         ccAAAGTTACTGGCGATAGAGTTATTCGCAACCag           <  1:7926384/35‑1 (MQ=255)
                          cAAAGTTACTGGCGATAGAGTTATTCGCAACCagg          <  1:1542927/35‑1 (MQ=255)
                          cAAAGTTACTGGCGATAGAGTTATTCGCAACCagg          <  1:18563997/35‑1 (MQ=255)
                          cAAAGTTACTGGCGATAGAGTTATTCGCAACCagg          <  1:5536852/35‑1 (MQ=255)
                           aaaGTTACTGGCGATAGAGTTATTCGCAACCagga         <  1:19440710/35‑1 (MQ=255)
                            aaGTTACTGGCGATAGAGTTATTCGCAACCaggaa        <  1:3161966/35‑1 (MQ=255)
                            aaGTTACTGGCGATAGAGTTATTCGCAACCaggaa        <  1:4915724/35‑1 (MQ=255)
                             aGTTACTGGCGATAGAGTTATTCGCAACCaggaag       <  1:17999081/35‑1 (MQ=255)
                               ttACTGGCGATAGAGTTATTCGCAACCaggaagga     <  1:3523994/35‑1 (MQ=255)
                               ttACTGGCGATAGAGTTATTCGCAACCaggaagga     <  1:5691619/35‑1 (MQ=255)
                               ttACTGGCGATAGAGTTATTCGCAACCaggaagga     <  1:7094520/35‑1 (MQ=255)
                               ttACTGGCGATAGAGTTATTCGCAACCaggaagga     <  1:7344407/35‑1 (MQ=255)
                                 aCTGGCGATAGAGTTATTCGCAACCAGGAAGgaga   <  1:2274135/35‑1 (MQ=255)
                                  cTGGCGATAGAGTTATTCTCAACCAGGAAGGAGaa  >  1:6295654/1‑35 (MQ=255)
                                  cTGGCGATAGAGTTATTCGCAACCAGGAAGGAGaa  >  1:19337009/1‑35 (MQ=255)
                                  cTGGCGATAGAGTTATTCGCAACCAGGAAGGAGaa  >  1:4333200/1‑35 (MQ=255)
                                  cTGGCGATAGAGTTATTCGCAACCAGGAAGGAGaa  <  1:18491383/35‑1 (MQ=255)
                                  cTGGCGATAGAGTTATTCGCAACCAGGAAGGAGaa  <  1:7217706/35‑1 (MQ=255)
                                  cTGGCGATAGAGTTATTCGCAACCAGGAAGGAGaa  <  1:218788/35‑1 (MQ=255)
                                  |                                  
AAATGGACTTGCGCCAGCATAACGGCCAAAGTTACTGGCGATAGAGTTATTCGCAACCAGGAAGGAGAA  >  REL606/3861447‑3861515

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ 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.