New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913_3_vch_pgi = 446637217 (0.880)3 (0.160) 3/274 2.5 17.1% coding (878/948 nt) treR trehalose 6‑phosphate‑inducible trehalose regulon transcriptional repressor
?NC_000913_3_vch_pgi = 4466464 13 (0.710)coding (786/948 nt) treR trehalose 6‑phosphate‑inducible trehalose regulon transcriptional repressor
Rejected: Frequency below/above cutoff threshold.

GAATATATTGCGCGGAAAAATTTAAAAACGGGAACGTTCCCGAAACGCAGCGAAGATCACAATTTATCGTTCAGGAAACGATCAGGACAGGGTGGCGGGGATGATGATTTGTTGCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913_3_vch_pgi/4466221‑4466372
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑caactggcGAGCGTCGGTAATACGCCGTTAATGAAATTCCTCCATCCGGAGATCGTAACCGTAGATCCCGGTTACGCCGAAGCTGGACGCCAGGCGGCTTGCCAGTTGATCGCGCAGGTAACCGGGCGCAGCGAACCGCAACAAATCATCATCCC  <  NC_000913_3_vch_pgi/4466464‑4466318
                                                                                                                                                                                                                                                                                                           
GAATATATTGCGCGGAAAAATTTAAAAACGGGAACGTTCCCGAAACGCAGCGAAGATCACAATTTATCGTTCAGGAAACGATCAAAACAGGGTGGCGGGTTTGATGATTTTTTGCGGTACGCTTCTCCCGGTTACCTTCGCGATCAACT                                                                                                                                                        >  1:70764/1‑149
                                                    AAGATCACAATTTATCGTTCAGGAAACGATCAGGACAGGGTGGCGGGGATGATGATTTGTTGCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGCGAGCGTCGGTAATACGCCGTTAATGAAATTCCTCCATCCGGAGATCGTA                                                                                                    >  1:261320/1‑149
                                                                                                          ATTTGTTGCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGCGAGCGTCGGTAATACGCCGTTAATGAAATTCCTCCATCCGGAGATCGTAACCGTAGATCCCGGTTACGCCGAAGCTGGACGCCAGGCGGCTTGCCAGTTGATC                                              <  2:261320/149‑1
                                                                                                                                        accccttTCAACTGGCGAGCGTCGGTAATTCGCCGTTAATGAAATTCCTCCATCCGGAGATCGTAACCGTAGATCCCGGTTACGCCGAAGCTGGACGCCAGGCGGCTTGCCAGTTGATCGCGCAGGTAACCGGGCGCAGCGAACCGCAA                <  1:176834/142‑1
                                                                                                                                                 AACTGGCGAGCGTCGGTAATACGCCGTTAATGAAATTCCTCCATCCGGAGATCGTAACCGTAGATCCCGGTTACGCCGAAGCTGGACGCCAGGCGGCTTGCCAGTTGATCGCGCAGGTAACCGGGCGCAGCGAACCGCAACAAATCATC       <  1:140450/149‑1
                                                                                                                                                 AACGGGCGGGCGTCGGAAATGCGCCGGTACTGAAATTCCTCCATCCCGAGATCGGAGCCGTAGATCCCGTTTACGCCGAAGCTGGACGCCAGGCGGCTTGCCAGTGGATCGCGCAGGTAACCGGGCGTAGCCAACCGCAACAAATCATC       <  2:18533/149‑1
                                                                                                                                                      GCGAGCGTCGCGAACACGCCGCTAATTAAATTCCTCCATCCGGAGATCGTAACCGTAGATCCCGGTTACGCCGAAGCTGGACGCCAGGCGGCTTGCCAGTTGATCTCGCAGGTAACCGTGCGCAGCGAACCTCAACAAATCATCATCCC  <  1:92580/149‑1
                                                                                                                                                                                                                                                                                                           
GAATATATTGCGCGGAAAAATTTAAAAACGGGAACGTTCCCGAAACGCAGCGAAGATCACAATTTATCGTTCAGGAAACGATCAGGACAGGGTGGCGGGGATGATGATTTGTTGCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913_3_vch_pgi/4466221‑4466372
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑caactggcGAGCGTCGGTAATACGCCGTTAATGAAATTCCTCCATCCGGAGATCGTAACCGTAGATCCCGGTTACGCCGAAGCTGGACGCCAGGCGGCTTGCCAGTTGATCGCGCAGGTAACCGGGCGCAGCGAACCGCAACAAATCATCATCCC  <  NC_000913_3_vch_pgi/4466464‑4466318

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ 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.