ABC
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Annotation NameExample ValuesDescription
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LocusId1-86580219-86580243-CCTACT;
9-69037286-69037304-GAA		Unique id for this locus in the format "chrom-start0based-end-motif"
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CanonicalMotifACTCCT;
AAG		The reference repeat motif, normalized by computing all cyclic shifts (ie. CAG, AGC, GAC, CTG, TGC, GCT)
and taking the one that's alphabetically first
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NumRepeatsInReference4; 6Locus interval size divided by motif size, rounded down to the nearest integer. Range: 1 to 300
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ReferenceRepeatPurity1; 1Fraction of bases within the locus interval that exactly match perfect repeats of the given motif. Range: 0.43 to 1
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NsInFlanks0; 0Number of "N" bases in the reference genome within +/-1000bp of the TR locus. ExpansionHunter reports an error is this exceeds 5
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TRsInRegion1; 2Number of TRs in the vicinity of this locus that are separated from each other by no more than 6bp of spacer sequence. Range: 1 to 13 TRs
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SourceIllumina174kPolymorphicTRs;
KnownDiseaseAssociatedLoci		The source catalog (Table 2) that contributed this locus definition. Possible values:
KnownDiseaseAssociatedLoci, Illumina174kPolymorphicTRs, PerfectRepeatsInReference, PolymorphicTRsInT2TAssemblies
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LeftFlankMappability1; 0.29UCSC 36-mer mappability track per-base mappability scores averaged across a
150bp window of flanking sequence immmediately to the left of the TR locus. Range: 0 to 1
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RightFlankMappability1; 0.17UCSC 36-mer mappability track per-base mappability scores averaged across a
150bp window of flanking sequence immmediately to the right of the TR locus. Range: 0 to 1
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FlanksAndLocusMappability1; 0.26UCSC 36-mer mappability track per-base mappability scores averaged across the TR locus +/- 150bp of flanking sequence. Range: 0 to 1
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VariationClusterTypeThe variation cluster type: Isolated; VC; ComplexVC; Unannotated
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VariationCluster1:86580213-86580243; NoneThe chrom:start-end of coordinates of the variation cluster that contains this TR locus
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VariationClusterSizeDiff6; NoneThe difference in size between the original TR locus and the region spanned by the variation cluster. Range: 6 to 8,308 bp
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KnownDiseaseAssociatedLocusNone; FXNWhether this locus is known to cause a monogenic disease
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KnownDiseaseAssociatedMotifNone; AAGWhether this locus has the same canonical motif as a locus that is known to cause a monogenic disease
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GencodeGeneRegionCDS;
intron		The most significant gene region that this locus overlaps based on Gencode v46 gene annotations. Possible values in order from least to
most significant are: intergenic, promoter, intron, exon, 3' UTR, 5' UTR, CDS. Here, "exon" means an exon of a non-coding transcript
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GencodeGeneNameCLCA4; FXNThe first gene whose reported GencodeGeneRegion overlaps this locus based on Gencode v46 annotations
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GencodeGeneIdENSG00000016602; ENSG00000165060ENSG gene id of the first gene whose reported GencodeGeneRegion overlaps this locus based on Gencode v46 annotations
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GencodeTranscriptIdENST00000370563; ENST00000377270ENST transcript id of the first transcript whose reported GencodeGeneRegion overlaps this locus based on Gencode v46 annotations
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RefseqGeneRegionCDS; intron[RefSeq annotations. See description of GencodeGeneRegion]
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RefseqGeneNameCLCA4; FXN[RefSeq annotations. See description of GencodeGeneName]
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RefseqGeneIdCLCA4; FXN[RefSeq annotations. See description of GencodeGeneId]
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RefseqTranscriptIdNM_012128; NM_000144[RefSeq annotations. See description of GencodeTranscriptId]
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ManeGeneRegionCDS; intron[MANE v1.3 annotations. See description of GencodeGeneRegion]
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ManeGeneNameCLCA4; FXN[MANE v1.3 annotations. See description of GencodeGeneName]
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ManeGeneIdENSG00000016602; ENSG00000165060[MANE v1.3 annotations. See description of GencodeGeneId]
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ManeTranscriptIdENST00000370563; ENST00000484259[MANE v1.3 annotations. See description of GencodeTranscriptId]
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LPSLengthStdevFromHPRC1000.353;
3.329		Standard deviation of the number of repeats in the longest pure segment (LPS) detected at this tandem repeat locus in
100 high-coverage long-read (LR) samples from the HPRC. Range: 0 to 123.0
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LPSMotifFractionFromHPRC100CCTACT: 200/200;
GAA: 194/200		The fraction of alleles at this tandem repeat locus in which the given motif composed the longest pure segment (LPS) among
100 high-coverage long-read (LR) samples from the HPRC.
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AlleleFrequenciesFromIllumina174k1x:1,2x:2,3x:3786,4x:1147,5x:72;
None		Allele frequencies based on short read data from 2,504 1kGP samples (source: https://github.com/Illumina/RepeatCatalogs).
Only available for the 174k loci taken from the Illumina174kPolymorphicTRs catalog
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StdevFromIllumina174k0.471; NoneStandard deviation of the allele frequency distribution represented by AlleleFrequenciesFromIllumina174k. Range: 0 to 31.5
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AlleleFrequenciesFromT2TAssemblies3x:18,4x:136,5x:2; 6x:137,8x:11,9x:8Allele frequencies from analyzing 78 diploid T2T assemblies.
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StdevFromT2TAssemblies0.343; 0.810Standard deviation of the allele frequency distribution represented by AlleleFrequenciesFromT2TAssemblies. Range: 0 to 1267.3
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AoU1027_StdevStandard deviation of the repeat counts in the allele frequency distribution from 1,027 African American individuals in the AoU PacBio HiFi dataset
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AoU1027_MedianMedian repeat count derived from the allele frequency distribution in 1,027 African American individuals in the AoU PacBio HiFi dataset
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AoU1027_99thPercentile99th Precentile repeat count derived from the allele frequency distribution in 1,027 African American individuals in the AoU PacBio HiFi dataset
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AoU1027_ModeAlleleMode repeat count derived from the allele frequency distribution in 1,027 African American individuals in the AoU PacBio HiFi dataset
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AoU1027_OE_LengthObserved / Expected length derived from the constraint metric described in [Danzi 2024]
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AoU1027_OE_LengthPercentileObserved / Expected length percentile derived from the constraint metric described in [Danzi 2024]
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HPRC100_StdevStandard deviation of the repeat counts in the allele frequency distribution from 100 PacBio HiFi samples of diverse ancestries in the HPRC dataset.
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HPRC100_Median" "
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HPRC100_99thPercentile" "
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HPRC100_ModeAllele" "
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HPRC100_AlleleHistogram" "
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TenK10K_StdevStandard deviation of the repeat counts in the allele frequency distribution from the TenK10K Phase 1 short read dataset generated using ExpansionHunter v5
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TenK10K_Median" "
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TenK10K_99thPercentile" "
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TenK10K_ModeAllele" "
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TenK10K_AlleleHistogram" "
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