New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? REL606 = 2883502NA (NA)22 (0.270) 4/38 NT 28.1% noncoding (791/1255 nt) IS3 repeat region
?REL606 3001880 = 71 (0.690)coding (2317/2847 nt) flu antigen 43 (Ag43) phase‑variable biofilm formation autotransporter

Only 100 of 288 total aligned reads displayed.

AGCGTCATCGGACAATAACGACTTCCGCGCCCGGGGCTGGGGCTGGCTGGGCTCACTGGAAACCGGTCT  >  REL606/3001846‑3001914
                                  |                                  
ggagacatcacgtgcttacgtacagatgaaggctg                                    <  1:9549776‑M2/1‑1 (MQ=255)
ggagacatcacgtacttacgtacagatgaaggctg                                    >  1:16270318‑M2/35‑35 (MQ=255)
ggagacatcacgtacttacgtacagatgaaggctg                                    >  1:16456075‑M2/35‑35 (MQ=255)
ggagacatcacgtacttacgtacagatgaaggctg                                    <  1:18263018‑M2/1‑1 (MQ=255)
ggagacatcacgtacttacgtacagatgaaggctg                                    >  1:11536525‑M2/35‑35 (MQ=255)
ggagacatcacgtacttacgtacagatgaaggctg                                    >  1:20265846‑M2/35‑35 (MQ=255)
ggagacatcacgtacttacgtacagatgaaggctg                                    <  1:3533475‑M2/1‑1 (MQ=255)
ggagacatcacgtacttacgtacagatgaaggctg                                    >  1:5313558‑M2/35‑35 (MQ=255)
ggagacatcacgtacttacgtacagatgaaggctg                                    <  1:10036336‑M2/1‑1 (MQ=255)
aGCGTCATCGGACAATAACGACTTCCGCGCCCggg                                    >  1:8672907/1‑35 (MQ=255)
aGCGTCATCGGACAATAACGACTTCCGCGCCCggg                                    >  1:20044422/1‑35 (MQ=255)
aGCGTCATCGGACAATAACGACTTCCGCGCCCggg                                    >  1:19728862/1‑35 (MQ=255)
aGCGTCATCGGACAATAACGACTTCCGCGCCCggg                                    >  1:16839958/1‑35 (MQ=255)
 gagacatcacgtacttacgtacagatgaaggctgg                                   >  1:5266242‑M2/34‑35 (MQ=255)
 gagacatcacgtacttacgtacagatgaaggctgg                                   <  1:2660259‑M2/2‑1 (MQ=255)
 gagacatcacgtacttacgtacagatgaaggctgg                                   <  1:19990734‑M2/2‑1 (MQ=255)
 gagacatcacgtacttacgtacagatgaaggctgg                                   >  1:894970‑M2/34‑35 (MQ=255)
 gagacatcacgtacttacgtacagatgaaggctgg                                   <  1:9479080‑M2/2‑1 (MQ=255)
 gagacatcacgtacttacggacagatgaaggctgg                                   <  1:7742078‑M2/2‑1 (MQ=255)
 gCGTCATCGGACAATAACGACTTCCGCGCCCgggg                                   >  1:14049451/1‑35 (MQ=255)
  cGTCATCGGACAATAACGACTTCCGCGCCCggggc                                  >  1:6998144/1‑35 (MQ=255)
  agacatcacgtacttacgtacagatgaaggctggc                                  >  1:6127861‑M2/33‑35 (MQ=255)
  agacatcacgtacttacgtacagatgaaggctggc                                  <  1:5774863‑M2/3‑1 (MQ=255)
  agacatcacgtacttacgtacagatgaaggctggc                                  <  1:3808562‑M2/3‑1 (MQ=255)
  agacatcacgtacttacgtacagatgaaggctggc                                  >  1:15084700‑M2/33‑35 (MQ=255)
  agacatcacgtacttacgtacagatgaaggctggc                                  >  1:4498490‑M2/33‑35 (MQ=255)
   gacatcacgtacttacgtacagatgaaggctggct                                 <  1:6956594‑M2/4‑1 (MQ=255)
   gacatcacgtacttacgtacagatgaaggctggct                                 <  1:8134167‑M2/4‑1 (MQ=255)
   gacatcacgtacttacgtacagatgaaggctggct                                 <  1:8422818‑M2/4‑1 (MQ=255)
   gacatcacgtacttacgtacagatgaaggctggct                                 >  1:10409709‑M2/32‑35 (MQ=255)
   gacatcacgtacttacgtacagatgaaggctggct                                 >  1:9067311‑M2/32‑35 (MQ=255)
   gacatcacgtacttacgtacagatgaaggctggct                                 <  1:11269830‑M2/4‑1 (MQ=255)
   gacatcacgtacttacgtacagatgaaggctggct                                 <  1:15306033‑M2/4‑1 (MQ=255)
   gacatcacgtacttacgtacagatgaaggctggct                                 <  1:14897149‑M2/4‑1 (MQ=255)
    acatcacgtacttacgtacagatgaaggctggctg                                >  1:6213108‑M2/31‑35 (MQ=255)
    acatcacgtacttacgtacagatgaaggctggctg                                >  1:978822‑M2/31‑35 (MQ=255)
    acatcacgtacttacgtacagatgaaggctggctg                                <  1:7555987‑M2/5‑1 (MQ=255)
    acatcacgtacttacgtacagatgaaggctggctg                                <  1:4963961‑M2/5‑1 (MQ=255)
    acatcacgtacttacgtacagatgaaggctggctg                                >  1:17989407‑M2/31‑35 (MQ=255)
    acatcacgtacttacgtacagatgaaggctggctg                                <  1:17851490‑M2/5‑1 (MQ=255)
    acatcacgtacttacgtacagatgaaggctggctg                                <  1:12920650‑M2/5‑1 (MQ=255)
    acatcacgtacttacgtacagatgaaggctggctg                                <  1:15571840‑M2/5‑1 (MQ=255)
    acatcacgtacttacgtacagatgaaggctggctg                                <  1:16070062‑M2/5‑1 (MQ=255)
     catcacgtacttacgtacagatgaaggctggctgg                               >  1:17160972‑M2/30‑35 (MQ=255)
     catcacgtacttacgtacagatgaaggctggctgg                               >  1:11875176‑M2/30‑35 (MQ=255)
     catcacgtacttacgtacagatgaaggctggctgg                               >  1:14230180‑M2/30‑35 (MQ=255)
     cATCGGACAATAACGACTTCCGCGCCCggggctgg                               >  1:14672738/1‑35 (MQ=255)
      atcacgtacttacgtacagatgaaggctggctggg                              >  1:3614348‑M2/29‑35 (MQ=255)
      atcacgtacttacgtacagatgaaggctggctggg                              >  1:11183888‑M2/29‑35 (MQ=255)
      aTCGGACAATAACGACTTCCGCGCCCggggctggg                              <  1:11986136/35‑1 (MQ=255)
      aTCGGACAATAACGACTTCCGCGCCCggggctggg                              >  1:4080110/1‑35 (MQ=255)
       tcacgtacttacgtacagatgaaggctggctgggt                             >  1:15991258‑M2/28‑34 (MQ=255)
       tcacgtacttacgtacagatgaaggctggctgggt                             >  1:10189500‑M2/28‑34 (MQ=255)
       tCGGACAATAACGACTTCCGCGCCCggggctgggg                             >  1:5636349/1‑35 (MQ=255)
        ccgACAATATCGACTTCCGCGCCCggggctggggc                            <  1:766631/33‑1 (MQ=38)
        cacgtacttacgtacagatgaatgctggctggggg                            >  1:17052146‑M2/27‑34 (MQ=255)
        cacgtacttacgtacagatgaaggctggctggtgc                            >  1:13978160‑M2/27‑35 (MQ=255)
        cacgtacttacgtacagatgaaggctggctgggtc                            >  1:3355642‑M2/27‑33 (MQ=255)
        cacgtacttacgtacagatgaaggctggctggggc                            >  1:9951162‑M2/27‑35 (MQ=255)
        aggACAATAACGACTTCCGCGCCCggggctggggc                            <  1:3159612/34‑1 (MQ=255)
         ggACAATAACGACTTCCGCGCCCggggctggggct                           >  1:18178103/1‑35 (MQ=255)
         acgtacttacgtacagatgaaggctggctgggtgc                           >  1:7064001‑M2/26‑32 (MQ=255)
         acgtacttacgtacagatgaaggctggctgggtct                           >  1:13490322‑M2/26‑35 (MQ=255)
         acgtacttacgtacagatgaaggctggctggggct                           >  1:3034021‑M2/26‑35 (MQ=255)
         acgtacttacgtacagatgaaggctggctgggcgc                           >  1:5892755‑M2/26‑32 (MQ=255)
          cgtacttacgtacagatgaaggctggctgggtctg                          >  1:14138947‑M2/25‑35 (MQ=255)
          cgtacttacgtacagatgaaggctggctggggttg                          >  1:7493801‑M2/25‑35 (MQ=255)
           gtacttacgtacagatgaaggctggctgggtctgg                         >  1:6593183‑M2/24‑35 (MQ=255)
           aCAATAACGACTTCCGCGCCCGGggctggggctgg                         >  1:2832426/1‑35 (MQ=255)
           aCAATAACGACTTCCGCGCCCGGggctggggctgg                         >  1:12423798/1‑35 (MQ=255)
            tacttacgtacagatgaaggctggctgggtctggc                        >  1:13046958‑M2/23‑35 (MQ=255)
            tacttacgtacagatgaaggctggctggggttggg                        >  1:507992‑M2/23‑34 (MQ=255)
             aaTAACGCCTTCCGCGCCCGGGGCTGGggctggct                       <  1:13072156/35‑1 (MQ=255)
             aaTAACGCCTTCCGCGCCCGGGGCTGGggctggct                       <  1:19632632/35‑1 (MQ=255)
             aaTAACGACTTCCGCGCCCGGggctggggctgggt                       >  1:8841151/1‑33 (MQ=255)
             aaTAACGACTTCCGCGCCCGGGGCTGGggctggct                       <  1:7357662/35‑1 (MQ=255)
              aTAACGACTTCCGCGCCCGGGGCTGGGgctggctg                      >  1:12614422/1‑35 (MQ=255)
                aaCGACTTCCGCGCCCGGGGCTGGGGCTGGCTggg                    >  1:1874490/1‑35 (MQ=255)
                aaCGACTTCCGCGCCCGGGGCTGGGGCTGGCTggg                    <  1:3182164/35‑1 (MQ=255)
                 aCGACTTCCGCGCCCGGGGCTGGGGCTGGCTgggg                   >  1:10278260/1‑34 (MQ=255)
                  cGACTTCCGCGCCCGGGGCTGGGGCTGGCTggggt                  >  1:10891105/1‑33 (MQ=255)
                   gACTTCCGCGCCCGGGGCTGGGGCTGGGTggggtg                 >  1:19822600/1‑32 (MQ=25)
                   gACCTCCGCGCCCGGGGCTGGGGCTGGCTGGGGTc                 >  1:6638543/1‑35 (MQ=37)
                    aCTTCCGCGCCCGGGGCTGGGGCTGGCTGGGCTCa                <  1:4379568/35‑1 (MQ=255)
                     cTTCCGCGCCCGGGGCTGGGGCTGGCTGGGCTCAc               >  1:14427534/1‑35 (MQ=255)
                      ttCCGCGCCCGGGGCTGGGGCTGGCTGGGGTCACt              >  1:603035/1‑35 (MQ=255)
                      ttCCGCGCCCGGGGCTGGGGCTGGCTGGGCTCACt              <  1:19103912/35‑1 (MQ=255)
                        tctcgcCCGGGGCTGGGGCTGGCTGGGCTCACTgg            <  1:241035/32‑1 (MQ=255)
                        ccGCGCCCGGGGCTGGGGCTGGCTGGGCTCACTgg            >  1:4746404/1‑35 (MQ=255)
                         cgcgCCCGGGGCTGGGGCTGGCTGGGCTCCCTggg           >  1:5601677/1‑34 (MQ=255)
                          gcgcCCGGGGCTGGGGCTGGCTGGGCTCACTggga          >  1:10061469/1‑33 (MQ=255)
                          gcgcCCGGGGCTGGGGCTGGCTGGGCTCACTGGaa          <  1:17332603/35‑1 (MQ=255)
                             tctggggctggggctGGCTGGGCTCACTGGAAAcc       <  1:105917/32‑1 (MQ=255)
                             cccGGGGCTGGGGCTGGCTGGGGTCACTGGgaaac       >  1:16816363/1‑33 (MQ=25)
                             cccGGGGCTGGGGCTGGCTGGGCTCACTGGAAAcc       <  1:17564274/35‑1 (MQ=255)
                              ccGGGGCTGGGGCTGGCTGGGCTCACTGGaaaacc      >  1:9178516/1‑32 (MQ=255)
                              ccGGGGCTGGGGCTGGCTGGGCTCACTGGAAACCg      <  1:11425605/35‑1 (MQ=255)
                               cGGGGCTGGGGCTGGCTGGGCTCACTGGAAACCgg     <  1:18298833/35‑1 (MQ=255)
                                ggggctggggctGGCTGGGCTCACTGGAAACCGGt    <  1:194642/35‑1 (MQ=255)
                                 gggctggggctgGCTGGGCTCACTGGAAACCGGTc   >  1:20539191/1‑35 (MQ=255)
                                  |                                  
AGCGTCATCGGACAATAACGACTTCCGCGCCCGGGGCTGGGGCTGGCTGGGCTCACTGGAAACCGGTCT  >  REL606/3001846‑3001914

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.