New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP009273 = 20563NA (NA)24 (0.930) 20/294 NT 100% noncoding (1/768 nt) IS1 repeat region
?CP009273 = 879039 0 (0.000)intergenic (‑195/‑90) ybjG/mdfA undecaprenyl pyrophosphate phosphatase/multidrug efflux system protein

CCCGGCATCCAACGCCATTCATGGCCATATCAATGATTTTCTGGTGCGTACCGGGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  CP009273/20307‑20563
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CACATTCTTACATTATTACGAGTATAGCTACGCTTTCTTTAAGTTTTATTTAACCTATGCCCGTTACAATCACCCACCGTAAACAGGCCGCTTGAGGGAAATAAGACGATGCCGCTTTACCCAGTTTAACCTGCACTTTATTCTCAACGACTTGCCTGTATTGGCTCCCTTTTAATCACTTTGCGTCGGGAAGTTATGCTGGAAAATTTGAATCTCTCTCTATTCTCTCTTATTAACG  <  CP009273/879039‑878802
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
gCCGGCATCCAACGCCATTCATGGCTATATTAATGATTTTCTGGGGCGTACCGGGTTGTGAAGCGGTGTGAGTTAACTGCAGTTTCCATGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTAAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCACATTCTTACATTATT                                                                                                                                                                                                                               <  2:465545/273‑1
  CGGCATCCAACGCCATTCATGGCCATATCAATGATTTTCTGGTGCGTACCGGGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACGCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTAAAAAACACCATCATACACTAAATAAGTAAGTTGGAAGCATCACCCACATTCTTAAAT                                                                                                                                                                                                                                   >  1:465558/1‑268
                 TTCATGGCCATATCAATGATTTTCTGGTGCGTACCGGGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCACATTCTTACATTATTACGAGTATAGCTACGCTT                                                                                                                                                                                                             >  1:397542/1‑275
                                                        gGAGAAGGGGTGTTAGTGAGCTGAAGTGGCCATGTTTTACGGCAGTGAGCGCAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCACATTCTTACATTATTACGAGTATAGCTACGCTTTCTTTAAGTTTTATTTAACCTATGCCCGTTACAATCAC                                                                                                                                                                       <  2:399649/273‑1
                                                          AGAAGCGGTGTAAGTGAACTGCAGTTGCCATGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCACATTCTTACATTATTACGAGTATAGCTACGCTTTCTTTAAGTTTTATTTAACCTATGCCCGTTACAATCACac                                                                                                                                                                     >  1:399662/1‑272
                                                                      agggaaaggaAGTTGCTATGTTGTAAGGCAGTGAGAGCAGAGAGAGCGCTGAGGTCCGGCGGTGCTGTTGCCGTTACGCACCACCCCGTAAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCACATTCTTACATTATTACGAGTATAGCTACGCTTTCTTTAAGTTTTATTTAACCTATGCCCGTTACAATCACCCACCGTAAACAGG                                                                                                                                                         <  2:397529/264‑1
                                                                                                                              CGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCACATTCTTACATTATTACGAGTATAGCTACGCTTTCTTTAAGTTTTATTTANCCTATGCCCGTTACAATCACCCACCGTAAACAGGCCGCTTGAGGGAAATAAGACGATGCCGCTTTACCCATTTTAACCTGCACTTTA                                                                                                    >  1:385355/1‑271
                                                                                                                                                         CCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCACATTCT                                                                                                                                                                                                                                        >  2:72133/1‑112
                                                                                                                                                             GTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCACATTCTTACATTATTACGAGT                                                                                                                                                                                                                         <  1:134202/123‑1
                                                                                                                                                             GTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCACATTCTTACA                                                                                                                                                                                                                                    <  1:72135/112‑1
                                                                                                                                                                        AACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCACATTCTTACATTATTACGAGTATAGCTACGCTTTCTTT                                                                                                                                                                                                        >  1:297707/1‑129
                                                                                                                                                                            GGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCACATTCTTACATTATTACGAGTATAGCTACGCTTTCTTTAAGT                                                                                                                                                                                                    <  2:297698/129‑1
                                                                                                                                                                                  ACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCACATTCTTACAT                                                                                                                                                                                                                                   >  2:488451/1‑92
                                                                                                                                                                                      CTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCACATTCTTACATTATT                                                                                                                                                                                                                               <  1:488464/92‑1
                                                                                                                                                                                                        ACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCACATTCTTACATTATTACGAGTATAGCTACGCTTTCTTTAAGTTTTATTTAACCTATGCCCGTTACAA                                                                                                                                                                           >  2:198305/1‑126
                                                                                                                                                                                                            GAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCACATTCTTACATTATTACGAGTATAGCTACGCTTTCTTTAAGTTTTATTTAACCTATGCCCGTTACAATCAC                                                                                                                                                                       <  1:198311/126‑1
                                                                                                                                                                                                                  CTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCACAT                                                                                                                                                                                                                                           >  2:217907/1‑52
                                                                                                                                                                                                                   TCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCA                                                                                                                                                                                                                                              <  2:34985/48‑1
                                                                                                                                                                                                                      AAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCACATTCTT                                                                                                                                                                                                                                       <  1:217914/52‑1
                                                                                                                                                                                                                            CCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCACATTCTTACATTATTACGAGTATAGCTACGCTTTCTTTA                                                                                                                                                                                                       >  2:281283/1‑78
                                                                                                                                                                                                                              ATCATACACTAAATCAGTAAGTTGGCAGCATCACCCACATTCTTACATTATTACGAGTATAGCTACGCTTTCTTTAACTTTTATTTAACCTATGCCCGTTACAATCACCCACCGTAAACAGGCCGCTTGAGGGAAATAAGACGATGCCGCTTTACCCAGTTTAACCTGCACTTTATTCTCAACGACTTGCCTGTATTGGCTCCCTTTTAATCACTTTGCGTCGGGAAGTTATGCTGGAAAATTTGAATCTCTCTCTATTCTCTCTTATTAACG  <  1:488157/273‑1
                                                                                                                                                                                                                                CATACACTAAATCAGTAAGTTGGCAGCATCACCCACATTCTTACATTATTACGAGTATAGCTACGCTTTCTTTAAGTT                                                                                                                                                                                                   <  1:281291/78‑1
                                                                                                                                                                                                                                       TAAATCAGTAAGTTGGCAGCATCACCCACATTCTTACAT                                                                                                                                                                                                                                   >  1:260190/1‑39
                                                                                                                                                                                                                                           TCAGTAAGTTGGCAGCATCACCCACATTCTTACATTATT                                                                                                                                                                                                                               <  2:260182/39‑1
                                                                                                                                                                                                                                               TAAGTTGGCAGCATCACCCACATTCTTACATTATTACGAGTATAGCTACGCTTTCTTTAAGTTTTATTTAACCTATGCCCGTTACAA                                                                                                                                                                           >  2:48044/1‑87
                                                                                                                                                                                                                                                   TTGGCAGCATCACCCACATTCTTACATTATTACGAGTATAGCTACGCTTTCTTTAAGTTTTATTTAACCTATGCCCGTTACAATCAC                                                                                                                                                                       <  1:48046/87‑1
                                                                                                                                                                                                                                                             CACCCACATTCTTACATTATTACGAGTATAGCTACGCTTTCTTTAAGTTTTATTTAACCT                                                                                                                                                                                        >  1:129567/1‑60
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
CCCGGCATCCAACGCCATTCATGGCCATATCAATGATTTTCTGGTGCGTACCGGGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  CP009273/20307‑20563
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CACATTCTTACATTATTACGAGTATAGCTACGCTTTCTTTAAGTTTTATTTAACCTATGCCCGTTACAATCACCCACCGTAAACAGGCCGCTTGAGGGAAATAAGACGATGCCGCTTTACCCAGTTTAACCTGCACTTTATTCTCAACGACTTGCCTGTATTGGCTCCCTTTTAATCACTTTGCGTCGGGAAGTTATGCTGGAAAATTTGAATCTCTCTCTATTCTCTCTTATTAACG  <  CP009273/879039‑878802

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ 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.