Primary allele | Genotyping summary |
---|---|
CAG repeats | {A1_CAG} |
CCG repeats | {A1_CCG} |
Intervening status | {A1_STRUCTURELABEL} |
Intervening structure | {A1_STRUCTURE} |
Intervening sequence | {A1_INTERVENING} |
Backwards slippage ratio | {A1_SLIPPAGE} |
Somatic mosaicism score | {A1_MOSAICISM} |
ScaleHD confidence | {A1_CONFIDENCE} |
Secondary allele | Genotyping summary |
---|---|
CAG repeats | {A2_CAG} |
CCG repeats | {A2_CCG} |
Intervening status | {A2_STRUCTURELABEL} |
Intervening structure | {A2_STRUCTURE} |
Intervening sequence | {A2_INTERVENING} |
Backwards slippage ratio | {A2_SLIPPAGE} |
Somatic mosaicism score | {A2_MOSAICISM} |
ScaleHD confidence | {A2_CONFIDENCE} |
SNP Calling | Value |
---|---|
Primary allele call | {A1_SNP} |
Primary call score | {A1_CALLSCORE} |
Secondary allele call | {A2_SNP} |
Secondary call score | {A2_CALLSCORE} |
Flag title | Value |
---|---|
Exception raised | {SHDFLAG_EXCEPTION} |
Homozygous haplotype | {SHDFLAG_HZYG} |
Neighbouring peaks | {SHDFLAG_NEIGHBOUR} |
Diminished peak presence | {SHDFLAG_DIMINISH} |
Novel atypical allele structure | {SHDFLAG_NOVELATYP} |
Alignment warning | {SHDFLAG_ALNWARN} |
Atypical alignment warning | {SHDFLAG_ATYPALIGNWARN} |
CCG Rewritten | {SHDFLAG_CCGREWR} |
CCG Zygosity rewritten | {SHDFLAG_CCGZYG_REWR} |
CCG Uncertainty | {SHDFLAG_CCGUNCERTAIN} |
CCT Uncertainty | {SHDFLAG_CCTUNCERTAIN} |
SVM Failure | {SHDFLAG_SVMFAIL} |
Differential confusion | {SHDFLAG_DIFFCONFUSE} |
Missed expansion | {SHDFLAG_MISSEDEXP} |
Heuristic filter success | {SHDFLAG_FILTERPASS} |
Peak inspection warning | {SHDFLAG_PEAKINSPECT} |
Low distribution reads | {SHDFLAG_LOWDISTREADS} |
Low allele-peak reads | {SHDFLAG_LOWPEAKREADS} |