New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? REL606 558248 =18 (0.180)6 (0.090) 4/32 NT 19.7% coding (185/294 nt) ECB_00516 conserved hypothetical protein
?REL606 3001100 = 37 (0.540)coding (1537/2847 nt) flu antigen 43 (Ag43) phase‑variable biofilm formation autotransporter

Only 100 of 113 total aligned reads displayed.

CTCCCCGGTAACGTTCCATAAACTGACCACCACGAACCTCACCGGCCAGGGCGGCACCATCAATATGCG  >  REL606/3001066‑3001134
                                  |                                  
cTCCCCGGTAACGTTCCATAAACTGACCACCACGa                                    >  1:14818137/1‑35 (MQ=255)
cTCCCCGGTAACGTTCCATAAACTGACCACCACGa                                    >  1:12077466/1‑35 (MQ=255)
 tCCCCGGTAACGTTCCATAAACTGACCACCACGaa                                   >  1:16492844/1‑35 (MQ=255)
 tCCCCGGTAACGTTCCATAAACTGACCACCACGaa                                   >  1:17740758/1‑35 (MQ=255)
   cccGGTAACGTTCCATAAACTGACCACCACGAAcc                                 >  1:16341773/1‑35 (MQ=255)
    ccGGTAACGTTCCATAAACTGACCACCACGAACCt                                >  1:14744651/1‑35 (MQ=255)
    ccGGTAACGTTCCATAAACTGACCACCACGAACCt                                >  1:17317935/1‑35 (MQ=255)
     cGGTAACGTTCCATAAACTGACCACCACGAACCTc                               >  1:3657033/1‑35 (MQ=255)
     cGGTAACGTTCCATAAACTGACCACCACGAACCTc                               >  1:16982495/1‑35 (MQ=255)
     cGGTAACGTTCCATAAACTGACCACCACGAACCTc                               >  1:8797762/1‑35 (MQ=255)
       gTAACGTTCCATAAACTGACCACCACGAACCTCAc                             >  1:5423611/1‑35 (MQ=255)
        tAACGTTCCATAAACTGACCACCACGAACCTCAcc                            >  1:17902577/1‑35 (MQ=255)
        tAACGTTCCATAAACTGACCACCACGAACCTCAcc                            >  1:13355656/1‑35 (MQ=255)
        tAACGTTCCAAAAACTGCCCACCACGAACCTCAcc                            <  1:7768449/35‑1 (MQ=37)
         aaCGTTCCATAAACTGACCACCACGAACCTCACCg                           >  1:1232267/1‑35 (MQ=255)
         aaCGTTCCATAAACTGACCACCACGAACCTCACCg                           >  1:15991677/1‑35 (MQ=255)
         aaCGTTCCATAAACTGACCACCACGAACCTCACCg                           >  1:6087118/1‑35 (MQ=255)
          aCGTTCCATAAACTGACCACCACGAACCTCACCgg                          >  1:19282953/1‑35 (MQ=255)
          aCGTTCCATAAACTGACCACCACGAACCTCACCgg                          >  1:265035/1‑35 (MQ=255)
          aCGTTCCATAAACTGACCACCACGAACCTCACCgg                          >  1:16744464/1‑35 (MQ=255)
          aCGTTCCATAAACTGACCACCACGAACCTCACCgg                          >  1:1106792/1‑35 (MQ=255)
           cGTTCCATAAACTGACCACCACGAACCTCACCGGc                         >  1:10795748/1‑35 (MQ=255)
           cGTTCCATAAACTGACCACCACGAACCTCACCGGc                         >  1:11832571/1‑35 (MQ=255)
            gTTCCATAAACTGACCACCACGAACCTCACCGGcc                        >  1:457745/1‑35 (MQ=255)
            gTTCCATAAACTGACCACCACGAACCTCACCGGcc                        >  1:13584160/1‑35 (MQ=255)
             ttCCATAAACTGACCACCACGAACCTCACCGGCCa                       >  1:19060300/1‑35 (MQ=255)
             ttCCATAAACTGACCACCACGAACCTCACCGGCCa                       >  1:14181162/1‑35 (MQ=255)
             ttCCATAAACTGACCACCACGAACCTCACCGGCCa                       >  1:18549380/1‑35 (MQ=255)
             ttCCATAAACTGACCACCACGAACCTCACCGGCCa                       >  1:4836500/1‑35 (MQ=255)
              tCCATAAACTGACCACCACGAACCTCACCTGCCAg                      >  1:11331865/1‑35 (MQ=255)
              tCCATAAACTGACCACCACGAACCTCACCGGCCAg                      >  1:14530670/1‑35 (MQ=255)
               ccATAAACTGACCACCACGAACCTCACCGGCCAgg                     >  1:17029098/1‑35 (MQ=255)
               caaaaaccgccccaccacgAACCTCACCGGCCAgg                     <  1:6977799‑M2/16‑1 (MQ=255)
                caaaacctccccaccacgAACCTCACCGGCCAggg                    <  1:6061973‑M2/17‑1 (MQ=255)
                caaaaacgccccaccacgAACCTCACCGGCCAggg                    <  1:15085725‑M2/17‑1 (MQ=255)
                caaaaaCTGCCCACCACGAACCTCACCGGCCAggg                    <  1:8443833/32‑1 (MQ=37)
                cATAAACTGACCACCACGAACCTCACCGGCCAggg                    >  1:1296088/1‑35 (MQ=255)
                 aaaaacgccccaccacgAACCTCACCGGCCAGggc                   <  1:1951617‑M2/18‑1 (MQ=255)
                 aaaaaCTCCCCACCACGAACCTCACCGGCCAGggc                   <  1:13450850/33‑1 (MQ=37)
                  tAAACTGACCACCACGAACCTCACCGGCCAGggcg                  >  1:3782629/1‑35 (MQ=255)
                   aacctccccaccacgAACCTCACCGGCCAGggcgg                 <  1:4845574‑M2/20‑1 (MQ=255)
                   aaacgccccaccacgAACCTCACCGGCCAGggcgg                 <  1:12257482‑M2/20‑1 (MQ=255)
                   aaaCTGACCACCACGAACCTCACCGGCCAGggcgg                 >  1:562561/1‑35 (MQ=255)
                   aaaCTGACCACCACGAACCTCACCGGCCAGggcgg                 >  1:7737980/1‑35 (MQ=255)
                    aaCTGCCCACCACGAACCTCACCGGCCAGggcggc                <  1:18984821/35‑1 (MQ=255)
                    aaCTGCCCACCACGAACCTCACCGGCCAGggcggc                <  1:7787740/35‑1 (MQ=255)
                    aaCTGACCACCACGAACCTCACCGGCCAGggcggc                >  1:10311667/1‑35 (MQ=255)
                    aaCTGACCACCACCAACCTCACCGGCCAGggcggc                >  1:13462557/1‑35 (MQ=255)
                     actccccaccacgAACCTCACCGGCCAGGGCGGCa               <  1:5399816‑M2/22‑1 (MQ=255)
                     aCTGACCACCACGAACCTCACCGGCCAGggcgggc               >  1:3863966/1‑33 (MQ=255)
                     aCTGACCACCACGAACCTCACCGGCCAGGGCGGCa               >  1:6828994/1‑35 (MQ=255)
                      ccgcccaccacgAACCTCACCGGCCAGGGCGGCAc              <  1:2694370‑M2/23‑1 (MQ=255)
                       tacccaccaCGAACCTAACCGGCCAGGGCGGCAcc             <  1:15006587/32‑1 (MQ=37)
                       tGACCACCACGAACCTCACCTGCCAGGGCGGCAcc             >  1:15816177/1‑35 (MQ=255)
                       tGACCACCACGAACCTCACCGGCCAGGGCGGCAcc             >  1:10499598/1‑35 (MQ=255)
                        gACCACCACGAACCTCACCGGCCAGGGCGGCACCa            >  1:10966158/1‑35 (MQ=255)
                        gACCACCACGAACCTCACCGGCCAGGGCGGCACCa            >  1:3228978/1‑35 (MQ=255)
                        gACCACCACGAACCTCACCGGCCAGGGCGGCACCa            >  1:17866543/1‑35 (MQ=255)
                        gACCACCACGAACCTCACCGGCCAGGGCGGCACCa            >  1:18979205/1‑35 (MQ=255)
                        ccccaccacgAACCTCACCGGCCAGGGCGGCACCa            <  1:11020646‑M2/25‑1 (MQ=255)
                         accaccACGAACCTCACCGGCCAGGGCGGCACCAt           >  1:12154269/1‑35 (MQ=255)
                          ccaccacgAACCTCACCGGCCAGGGCGGCACCATc          >  1:12920923‑M2/9‑35 (MQ=255)
                          ccaccacgAACCTCACCGGCCAGGGCGGCACCATc          >  1:18939566‑M2/9‑35 (MQ=255)
                          ccaccacgAACCTCACCGGCCAGGGCGGCACCATc          <  1:3791107‑M2/27‑1 (MQ=255)
                           caccacgAACCTCACCGGCCAGGGCGGCACCATCa         <  1:8260426‑M2/28‑1 (MQ=255)
                           caccacgAACCTCACCGGCCAGGGCGGCACCATCa         <  1:4214927‑M2/28‑1 (MQ=255)
                           caccacgAACCTCACCGGCCAGGGCGGCACCATCa         <  1:412958‑M2/28‑1 (MQ=255)
                           caccacgAACCTCACCGGCCAGGGCGGCACCATCa         >  1:3885779‑M2/8‑35 (MQ=255)
                            accacgAACCTCACCGGCCAGGGCGGCACCATCaa        >  1:9861478‑M2/7‑35 (MQ=255)
                            accacgAACCTCACCGGCCAGGGCGGCACCATCaa        <  1:12744747‑M2/29‑1 (MQ=255)
                            accacgAACCTCACCGGCCAGGGCGGCACCATCaa        <  1:197425‑M2/29‑1 (MQ=255)
                             ccacgAACCTCACCGGCCAGGGCGGCACCATCAat       >  1:2879783‑M2/6‑35 (MQ=255)
                             ccacgAACCTCACCGGCCAGGGCGGCACCATCAat       <  1:1454657‑M2/30‑1 (MQ=255)
                             ccacgAACCTCACCGGCCAGGGCGGCACCATCAat       >  1:629482‑M2/6‑35 (MQ=255)
                             ccacgAACCTCACCGGCCAGGGCGGCACCATCAat       <  1:15315935‑M2/30‑1 (MQ=255)
                              cacgAACCTCACCGGCCAGGGCGGCACCATCAata      >  1:13376837‑M2/5‑35 (MQ=255)
                              cacgAACCTCACCGGCCAGGGCGGCACCATCAata      >  1:14039183‑M2/5‑35 (MQ=255)
                              cacgAACCTCACCGGCCAGGGCGGCACCATCAata      >  1:8114716‑M2/5‑35 (MQ=255)
                              cacgAACCTCACCGGCCAGGGCGGCACCATCAata      >  1:6059037‑M2/5‑35 (MQ=255)
                              cacgAACCTCACCGGCCAGGGCGGCACCATCAata      >  1:2570527‑M2/5‑35 (MQ=255)
                              cacgAACCTCACCGGCCAGGGCGGCACCATCAata      >  1:2736372‑M2/5‑35 (MQ=255)
                              cacgAACCTCACCGGCCAGGGCGGCACCATCAata      >  1:11838075‑M2/5‑35 (MQ=255)
                              cacgAACCTCACCGGCCAGGGCGGCACCATCAata      >  1:3290798‑M2/5‑35 (MQ=255)
                              aacgAACCTCACCGGCCAGGGCGGCACCATCAata      <  1:12566762‑M2/31‑1 (MQ=255)
                               acgAACCTCACCGGCCAGGGCGGCACCATCAatat     <  1:20171631‑M2/32‑1 (MQ=255)
                               acgAACCTCACCGGCCAGGGCGGCACCATCAatat     >  1:12338401‑M2/4‑35 (MQ=255)
                               acgAACCTCACCGGCCAGGGCGGCACCATCAatat     >  1:2190732‑M2/4‑35 (MQ=255)
                               acgAACCTCACCGGCCAGGGCGGCACCATCAatat     >  1:15227045‑M2/4‑35 (MQ=255)
                               acgAACCTCACCGGCCAGGGCGGCACCATCAatat     >  1:8667352‑M2/4‑35 (MQ=255)
                               acgAACCTCACCGGCCAGGGCGGCACCATCAatat     <  1:8018887‑M2/32‑1 (MQ=255)
                                cgAACCTCACCGGCCAGGGCGGCACCATCAATATg    >  1:9392529‑M2/3‑35 (MQ=255)
                                cgAACCTCACCGGCCAGGGCGGCACCATCAATATg    <  1:14778570‑M2/33‑1 (MQ=255)
                                cgAACCTCACCGGCCAGGGCGGCACCATCAATATg    >  1:6303750‑M2/3‑35 (MQ=255)
                                cgAACCTCACCGGCCAGGGCGGCACCATCAATATg    >  1:20534432‑M2/3‑35 (MQ=255)
                                cgAACCTCACCGGCCAGGGCGGCACCATCAATATg    >  1:3115348‑M2/3‑35 (MQ=255)
                                 gAACCTCACCGGCCAGGGCGGCACCATCAATATGc   >  1:4659178‑M2/2‑35 (MQ=255)
                                 gAACCTCACCGGCCAGGGCGGCACCATCAATATGc   <  1:4079007‑M2/34‑1 (MQ=255)
                                 gAACCTCACCGGCCAGGGCGGCACCATCAATATGc   >  1:1002043‑M2/2‑35 (MQ=255)
                                  aaCCTCACCGGCCAGGGCGGCACCATCAATATGCg  >  1:9512718/1‑35 (MQ=255)
                                  aaCCTCACCGGACAGGGCGGCACCATCAATATGCg  <  1:9124366/35‑1 (MQ=255)
                                  |                                  
CTCCCCGGTAACGTTCCATAAACTGACCACCACGAACCTCACCGGCCAGGGCGGCACCATCAATATGCG  >  REL606/3001066‑3001134

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ 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.