FORMAT (per-sample): GT:AD:DP:SR:DR:GQ:PL:LO:LO_n:KC — SV uses DR=disc, INDEL uses DR=cigar; KC=kmer-spanning reads excluded from assembly/r2c. To inline the per-read alignment plot below this panel, also load the .r2c.db in the upload row above.
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Genotype (GT)
0/0homozygous reference (no alt allele)
0/1heterozygous (one alt allele)
1/1homozygous alt (both alleles are alt)
./.no call / insufficient coverage
Per-sample FORMAT fields GT:AD:DP:SR:DR:GQ:PL:LO:LO_n:KC
ADallelic depth (# reads supporting the alt allele)
DPtotal read depth at this site
SRsplit-read support (reads spanning the breakpoint)
DRdiscordant-pair support for SVs; CIGAR-indel support for INDELs
GQgenotype quality (Phred)
PLPhred-scaled genotype likelihoods (0/0, 0/1, 1/1)
LOlog-odds variant vs. error at this sample (see CLAUDE.md)
LO_nlog-odds variant vs. error, normal-model only
KCkmer-spanning reads: unique reads carrying the breakend junction kmer (≥19/20bp, either strand) that were excluded from assembly/r2c (adapter/blacklist), folded into the normal alt count for somatic scoring
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