New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP000730 895785 =62 (0.680)27 (0.340) 15/226 NT 32.6% coding (806/822 nt) USA300HOU_0849 ABC superfamily ATP binding cassette transporter, binding protein
?CP000730 = 909740 58 (0.730)intergenic (‑663/‑371) ear/USA300HOU_0868 Ear protein/hypothetical protein

CGCTCAAATCTGAGCGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP000730/895941‑895785
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttatttagcaggaataaTTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGCCCTTGAAAACAACC  <  CP000730/909740‑909601
                                                                                                                                                                                                                                                                                                         
tgtttAAATCTGAGCGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTTCCCCTTTTGTGCCTTTTTTTATTGAAAAAAAAAAAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTAT                                                                                                                                                              <  2:819495/136‑1
 GCTCAAATCTGAGCGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTAT                                                                                                                                                              >  2:844461/1‑140
 GCTCAAATCTGAGCGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTAT                                                                                                                                                              >  1:987266/1‑140
 GCTCAAATCTGAGCGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTAT                                                                                                                                                              <  2:987266/140‑1
 GCTCAAATCTGAGCGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTAT                                                                                                                                                              <  1:844461/140‑1
   TCAAATCTGAGCTTATTTTTTTGTTTAAAAGTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATAACACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTAT                                                                                                                                                           <  2:699413/141‑1
   TCAAATCTGAGCGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTAT                                                                                                                                                           <  2:959106/141‑1
        TCTGAGCGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGC                                                                                                                                                      >  1:828033/1‑141
            AGCGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCCGGA                                                                                                                                                  <  2:927553/141‑1
            AGCGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGA                                                                                                                                                  <  1:191388/141‑1
                cATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCGCTTTTTTATTTTAAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTGTTTAGCAGGAATAA                                                                                                                                              <  2:756776/140‑1
                 ATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAAT                                                                                                                                             >  1:1048767/1‑141
                            TAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATTCCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTA                                                                                                                                  <  1:108960/141‑1
                              AAATTCGATAATTTGCATATACTGCCCCTTTGGGGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATC                                                                                                                                <  2:76502/141‑1
                               AATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCA                                                                                                                               <  2:483025/141‑1
                               AATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCA                                                                                                                               <  2:819493/141‑1
                               AATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTCTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCA                                                                                                                               <  1:758207/141‑1
                               AATTCGATAATTTACATATACCGCCCCTTTTTTGCCCTTTTTTATTTAAAAAACAAAAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCA                                                                                                                               <  2:819598/141‑1
                               AATTCAATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGTTATGTTTATATAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCA                                                                                                                               <  1:757611/141‑1
                                ATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTATTTGGTATTATTTAGCAGGAATACTTgcacgcttggatct                                                                                                                              >  2:866281/1‑127
                                         TTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCA                                                                                                                     <  1:782082/141‑1
                                            GCATATACTGCCCCTTTGGTGCCCTTTTTTCTTTTCAATACCACAAGAATAACCCCTTAATCGGTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGACTAAGTGGCCAGATTATCCAGACAGTTAAAGG                                                                                                                  >  2:337282/1‑141
                                              ATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTTGCCAGATTATCAAGGAAGTTCAAGGGC                                                                                                                >  1:230556/1‑141
                                              ATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGC                                                                                                                >  2:385106/1‑141
                                              ATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTAATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAGGGGAGTTCAAGGac                                                                                                                >  2:379795/1‑139
                                                          TTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATT                                                                                                    >  1:267032/1‑141
                                                            TTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCACGGAAGTTCAAGGGCAGTCAAAACATTtt                                                                                                  >  2:247870/1‑139
                                                                                     ccCAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCA                                                                         <  1:876774/139‑1
                                                                                     caacAAAATAACGCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCA                                                                         <  1:641015/137‑1
                                                                                         AAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATCTTGCGCGAAGATGGAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGAT                                                                     <  1:255555/141‑1
                                                                                                             GTTATTACAGGGTATTTTTAATTAATGGGGATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTT                                                 <  2:546314/141‑1
                                                                                                             GTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACACTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTT                                                 <  1:211703/141‑1
                                                                                                             GTTAATAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTT                                                 <  1:391788/141‑1
                                                                                                                 aTAAAGGTGATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCC                                             <  1:103161/140‑1
                                                                                                                 TTAAAGGGTATTTTTATTTTATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCC                                             <  2:938499/141‑1
                                                                                                                 TTAAAGGGTAATTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTGAAGATAATTTATTATTCATACCCTTGCCC                                             <  2:407744/141‑1
                                                                                                                 TTAAAGGGGATTTGTAGTTAATTGGTATTATTTGGCGGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACAGTTGGATATGTGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCC                                             <  2:1005077/141‑1
                                                                                                                            TTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGATCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATATATACTCTTGCCATTTGTTTCAAA                                  >  2:788579/1‑141
                                                                                                                                 TTTAATTGGTATTATTTAGCAGGAATAATTAGCACGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTAT                             <  1:256899/141‑1
                                                                                                                                      TTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCT                        <  2:12238/141‑1
                                                                                                                                             TATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTt                 <  2:131152/141‑2
                                                                                                                                             TATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTt                 >  1:987607/1‑140
                                                                                                                                              ATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGC                >  2:40219/1‑141
                                                                                                                                                 TAGCAGGAATAATTGGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGCCCT             >  1:721788/1‑141
                                                                                                                                                 TAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTTCCCT             >  2:88505/1‑141
                                                                                                                                                 TAGCACGAATAATTAGCCAGATTATCACGGAAGTTCAAGGGCAATCACAACATCGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTAAAAATTATGCCCTTTTTTTGCCCT             <  1:705925/141‑1
                                                                                                                                                       GAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGCCCTTGAAAA       <  2:535290/141‑1
                                                                                                                                                          TAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAGTTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGCCCTTGAAAACAA    <  1:1042500/141‑1
                                                                                                                                                            ATTAGCCCGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGCCCTTGAAAACAACC  <  2:15293/141‑1
                                                                                                                                                            ATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAGAATTATGCCCTTTTTTTGCCCTTGAAAACAACC  >  2:1057843/1‑141
                                                                                                                                                            ATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGCCCTTGAAAGCAACC  >  2:803102/1‑141
                                                                                                                                                            ATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTCCCCTTGAAAACAACC  >  2:393602/1‑141
                                                                                                                                                            ATTAGCCAGATTAGCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATACAATTTTCAAGATAATTTATTATTCATACCCGTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGGCCTTGATAACAACC  <  2:367719/141‑1
                                                                                                                                                                                                                                                                                                         
CGCTCAAATCTGAGCGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP000730/895941‑895785
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttatttagcaggaataaTTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGCCCTTGAAAACAACC  <  CP000730/909740‑909601

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ 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.