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 191 total aligned reads displayed.

GGAGACATCACGTACTTACGTACAGATGAAGGCTggctg‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  REL606/2883469‑2883502
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGCTGGGGCTGGCTGGGCTCACTGGAAACCGGTCTGCCC  >  REL606/3001880‑3001918
                                                                         
GGAGACATCACGTACTTACGTACAGATGAAGGCTG                                        >  1:9623695/1‑35
GGAGACATCACGTACTTACGTACAGATGAAGGCTG                                        <  1:9040532/35‑1
GGAGACATCACGTACTTACGTACAGATGAAGGCTG                                        <  1:7985771/35‑1
GGAGACATCACGTACTTACGTACAGATGAAGGCTG                                        >  1:5313558/1‑35
GGAGACATCACGTACTTACGTACAGATGAAGGCTG                                        >  1:20265846/1‑35
GGAGACATCACGTACTTACGTACAGATGAAGGCTG                                        <  1:18263018/35‑1
GGAGACATCACGTACTTACGTACAGATGAAGGCTG                                        <  1:1703409/35‑1
GGAGACATCACGTACTTACGTACAGATGAAGGCTG                                        >  1:16270318/1‑35
GGAGACATCACGTACTTACGTACAGATGAAGGCTG                                        >  1:14040692/1‑35
GGAGACATCACGTACTTACGTACAGATGAAGGCTG                                        <  1:11473126/35‑1
GGAGACATCACGTACTTACGTACAGATGAAGGCTG                                        <  1:10036336/35‑1
GGAGACATCACGTACTTACGTACAGATGAAGGCTG                                        <  1:11264848/35‑1
GGAGACATCACGTACTTACGTAAAGATGAAGGCTG                                        >  1:3977098/1‑35
GGAGACATCACGTACTTACATACAGATGAAGGCTG                                        >  1:15430165/1‑35
 GAGACATCACGTACTTACGTACAGATGAAGGCTGG                                       <  1:1905526/35‑1
 GAGACATCACGTACTTACGTACAGATGAAGGCTGG                                       <  1:9479080/35‑1
 GAGACATCACGTACTTACGTACAGATGAAGGCTGG                                       <  1:10040114/35‑1
 GAGACATCACGTACTTACGTACAGATGAAGGCTGG                                       >  1:894970/1‑35
 GAGACATCACGTACTTACGTACAGATGAAGGCTGG                                       <  1:12941521/35‑1
 GAGACATCACGTACTTACGTACAGATGAAGGCTGG                                       <  1:19990734/35‑1
 GAGACATCACGTACTTACGTACAGATGAAGGCTGG                                       <  1:2660259/35‑1
 GAGACATCACGTACTTACGTACAGATGAAGGCTGG                                       >  1:6623103/1‑35
 GAGACATCACGTACTTACGTACAGATGAAGGCTGG                                       >  1:14104458/1‑35
 GAGACATCACGTACTTACGTACAGATGAAGGCTGG                                       <  1:14551561/35‑1
  AGACATCACGTACTTACGTACAGATGAAGGCTGtc                                      >  1:5671554/1‑33
  AGACATCACGTACTTACGTACAGATGAAGGCTGGC                                      >  1:10275610/1‑35
  AGACATCACGTACTTACGTACAGATGAAGGCTGGC                                      >  1:4498490/1‑35
  AGACATCACGTACTTACGTACAGATGAAGGCTGGC                                      >  1:6127861/1‑35
  AGACATCACGTACTTACGTACAGATGAAGGCTGGC                                      <  1:14143493/35‑1
  AGACATCACGTACTTACGTACAGATGAAGGCTGGC                                      >  1:10332828/1‑35
  AGACATCACGTACTTACGTACAGATGAAGGCTGGC                                      >  1:9540928/1‑35
  AGACATCACGTACTTACGTACAGATGAAGGCTGGC                                      >  1:17252092/1‑35
   GACATCACGTACTTACGTACAGATTAAGGCTGGCT                                     >  1:16180397/1‑35
   GACATCACGTACTTACGTACAGATGAAGGCTGGCT                                     >  1:2945112/1‑35
   GACATCACGTACTTACGTACAGATGAAGGCTGGCT                                     <  1:7479435/35‑1
   GACATCACGTACTTACGTACAGATGAAGGCTGGCT                                     >  1:2192333/1‑35
   GACATCACGTACTTACGTACAGATGAAGGCTGGCT                                     <  1:8422818/35‑1
   GACATCACGTACTTACGTACAGATGAAGGCTGGCT                                     <  1:1845026/35‑1
   GACATCACGTACTTACGTACAGATGAAGGCTGGCT                                     <  1:10446574/35‑1
   GACATCACGTACTTACGTACAGATGAAGGCTGGCT                                     <  1:14897149/35‑1
   GACATCACGTACTTACGTACAGATGAAGGCTGGCT                                     >  1:1571196/1‑35
   GACATCACGTACTTACGTACAGATGAAGGCTGGCT                                     >  1:1639399/1‑35
    ACATCACGTACTTACGTACAGATGAAGGCTGGCTG                                    <  1:6097935/35‑1
    ACATCACGTACTTACGTACAGATGAAGGCTGGCTG                                    >  1:6213108/1‑35
    ACATCACGTACTTACGTACAGATGAAGGCTGGCTG                                    >  1:7002903/1‑35
    ACATCACGTACTTACGTACAGATGAAGGCTGGCTG                                    <  1:4963961/35‑1
    ACATCACGTACTTACGTACAGATGAAGGCTGGCTG                                    <  1:13257873/35‑1
    ACATCACGTACTTACGTACAGATGAAGGCTGGCTG                                    >  1:3511041/1‑35
    ACATCACGTACTTACGTACAGATGAAGGCTGGCTG                                    <  1:7555987/35‑1
    ACATCACGTACTTACGTACAGATGAAGGCTGGCTG                                    >  1:17989407/1‑35
    ACATCACGTACTTACGTACAGATGAAGGCTGGCTG                                    >  1:978822/1‑35
    ACATCACGTACTTACGTACAGATGAAGGCTGGCTG                                    >  1:12781689/1‑35
     CATCACGTACTTACGTACAGATGAAGGCTGGCTGG                                   >  1:5817635/1‑35
     CATCACGTACTTACGTACAGATGAAGGCTGGCTGG                                   >  1:14230180/1‑35
     CATCACGTACTTACGTACAGATGAAGGCTGGCTGG                                   >  1:17623015/1‑35
     CATCACGTACTTACGTACAGATGAAGGCTGGCTGG                                   >  1:11875176/1‑35
     CATCACGTACTTACGTACAGATGAAGGCTGGCTGG                                   >  1:17160972/1‑35
      ATCACGTACTTACGTACAGATGAAGGCTGGCTGGa                                  >  1:14748049/1‑34
      ATCACGTACTTACGTACAGATGAAGGCTGGCTGGG                                  >  1:11183888/1‑35
      ATCACGTACTTACGTACAGATGAAGGCTGGCTGGG                                  >  1:3732121/1‑35
      ATCACGTACTTACGTACAGATGAAGGCTGGCTGGG                                  >  1:3614348/1‑35
       TCACGTACTTACGTACAGATGAAGGCTGGCTGGGt                                 >  1:3566303/1‑34
       TCACGTACTTACGTACAGATGAAGGCTGGCTGGGt                                 >  1:15991258/1‑34
       TCACGTACTTACGTACAGATGAAGGCTGGCTGGGt                                 >  1:10189500/1‑34
       TCACGTACTTACGTACAGATGAAGGCTGGCTGGGG                                 >  1:4294221/1‑35
        CACGTACTTACGTACAGATGAAGGCTGGCTGGatt                                >  1:9116692/1‑32
        CACGTACTTACGTACAGATGAAGGCTGGCTGGTGC                                >  1:13978160/1‑35
        CACGTACTTACGTACAGATGAAGGCTGGCTGGGtt                                >  1:7650232/1‑33
        CACGTACTTACGTACAGATGAAGGCTGGCTGGGtt                                >  1:6489095/1‑33
        CACGTACTTACGTACAGATGAAGGCTGGCTGGGtt                                >  1:8728552/1‑33
        CACGTACTTACGTACAGATGAAGGCTGGCTGGGtg                                >  1:19709310/1‑33
        CACGTACTTACGTACAGATGAAGGCTGGCTGGGtc                                >  1:19518934/1‑33
        CACGTACTTACGTACAGATGAAGGCTGGCTGGGtc                                >  1:11690451/1‑33
        CACGTACTTACGTACAGATGAAGGCTGGCTGGGtc                                >  1:3355642/1‑33
        CACGTACTTACGTACAGATGAAGGCTGGCTGGGtc                                >  1:783479/1‑33
        CACGTACTTACGTACAGATGAAGGCTGGCTGGGGC                                >  1:9951162/1‑35
         ACGTACTTACGTACAGATGAAGGCTGGCTGGGttc                               >  1:6899855/1‑32
         ACGTACTTACGTACAGATGAAGGCTGGCTGGGttc                               >  1:1197214/1‑32
         ACGTACTTACGTACAGATGAAGGCTGGCTGGGtgt                               >  1:12438694/1‑32
         ACGTACTTACGTACAGATGAAGGCTGGCTGGGtgc                               >  1:7064001/1‑32
         ACGTACTTACGTACAGATGAAGGCTGGCTGGGTCT                               >  1:20066025/1‑35
         ACGTACTTACGTACAGATGAAGGCTGGCTGGGGtt                               >  1:1829076/1‑33
         ACGTACTTACGTACAGATGAAGGCTGGCTGGGGCT                               >  1:3034021/1‑35
          CGTACTTACGTACAGATGAAGGCTGGCTGGGTCTG                              >  1:1105926/1‑35
          CGTACTTACGTACAGATGAAGGCTGGCTGGGTCTG                              >  1:6210812/1‑35
          CGTACTTACGTACAGATGAAGGCTGGCTGGGTCTG                              >  1:499723/1‑35
          CGTACTTACGTACAGATGAAGGCTGGCTGGGGTTG                              >  1:7493801/1‑35
           GTACTTACGTACAGATGAAGGCTGGCTGGGGGTGt                             >  1:5276197/1‑34
            TACTTACGTACAGATGAAGGCTGGCTGGGTCTGGg                            >  1:19458312/1‑34
            TACTTACGTACAGATGAAGGCTGGCTGGGTCTGGC                            >  1:13046958/1‑35
            TACTTACGTACAGATGAAGGCTGGCTGGGGTTGGC                            >  1:20490417/1‑35
            TACTTACGTACAGATGAAGGCTGGCTGGGGCTGGg                            >  1:3090465/1‑34
            TACTTACGTACAGATGAAGGCTGGCTGGGGCTGGC                            >  1:5218797/1‑35
             ACTTACGTACAGATGAAGGCTGGCTGGGTCTGGCa                           >  1:16751839/1‑34
                                  GGCTGGGGCTGGCTGGGCTCACTGGAAACCGGTCT      <  1:17856769/35‑1
                                    CTGGGGCTGGCTGGGCTCACTGGAAACCGGTCTGC    <  1:3229114/35‑1
                                    CTGGGGCTGGCTGGGCTCACTGGAAACCGGTCTGC    <  1:1521837/35‑1
                                     gGGGGCTGGCGGGGCTCACTGGAAACCGGTCTGCC   <  1:5026499/34‑1
                                     TGGGGCTGGCTGGGCTCACTGGAAACCGGTCTGCC   <  1:19801304/35‑1
                                      GGGGCTGGCTGGGCTGACTGGAAACCGGTCTGCCC  <  1:5583409/35‑1
                                                                         
GGAGACATCACGTACTTACGTACAGATGAAGGCTggctg‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  REL606/2883469‑2883502
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGCTGGGGCTGGCTGGGCTCACTGGAAACCGGTCTGCCC  >  REL606/3001880‑3001918

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 33 ≤ 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.