diff --git a/data/STRchive-citations.json b/data/STRchive-citations.json index 6cb68489..ddff0185 100644 --- a/data/STRchive-citations.json +++ b/data/STRchive-citations.json @@ -155534,7 +155534,7 @@ "id": "pmid:25101480", "manubot_success": false, "link": "https://pubmed.ncbi.nlm.nih.gov/25101480", - "note": "WARNING: Couldn't parse Manubot response: list index out of range" + "note": "WARNING: Manubot could not generate citation: Command '['manubot', 'cite', 'pmid:25101480']' timed out after 3 seconds" }, { "id": "pmid:29939637", diff --git a/data/STRchive-loci.json b/data/STRchive-loci.json index bf0c5861..7d2fbf71 100644 --- a/data/STRchive-loci.json +++ b/data/STRchive-loci.json @@ -66,12 +66,12 @@ "disease_id": "FRAXE", "gene": "AFF2", "chrom": "chrX", - "start_hg38": 148500604, - "stop_hg38": 148500753, - "start_hg19": 147582124, - "stop_hg19": 147582273, - "start_t2t": 146765190, - "stop_t2t": 146765342, + "start_hg38": 148500637, + "stop_hg38": 148500682, + "start_hg19": 147582157, + "stop_hg19": 147582202, + "start_t2t": 146765223, + "stop_t2t": 146765271, "disease": "Fragile X syndrome, FRAXE type", "inheritance": ["XR"], "disease_description": "A nonsyndromic X-linked mental retardation (NS-XLMR) characterized by mild intellectual deficit. FRAXE is the most common form of NS-XLMR [@mondo:0010659].", @@ -98,8 +98,8 @@ "unknown_motif_gene_orientation": [], "locus_structure": [], "benign_min": 4, - "benign_max": 39, - "intermediate_min": 40, + "benign_max": 69, + "intermediate_min": 70, "intermediate_max": 200, "pathogenic_min": 201, "pathogenic_max": 2000, diff --git a/data/catalogs/STRchive-disease-loci.T2T-chm13.TRGT.bed b/data/catalogs/STRchive-disease-loci.T2T-chm13.TRGT.bed index 192ac6d9..85c663da 100644 --- a/data/catalogs/STRchive-disease-loci.T2T-chm13.TRGT.bed +++ b/data/catalogs/STRchive-disease-loci.T2T-chm13.TRGT.bed @@ -72,4 +72,4 @@ chrX 69887153 69887230 ID=XDP_TAF1;MOTIFS=AGAGGG;STRUC= chrX 135876774 135876804 ID=VACTERLX_ZIC3;MOTIFS=GCN;STRUC= chrX 138816203 138816248 ID=XLMR_SOX3;MOTIFS=NGC;STRUC= chrX 146176677 146176769 ID=FXS_FMR1;MOTIFS=CGG;STRUC= -chrX 146765190 146765342 ID=FRAXE_AFF2;MOTIFS=GCC;STRUC= +chrX 146765223 146765271 ID=FRAXE_AFF2;MOTIFS=GCC;STRUC= diff --git a/data/catalogs/STRchive-disease-loci.T2T-chm13.atarva.bed b/data/catalogs/STRchive-disease-loci.T2T-chm13.atarva.bed index 86e42039..96b95974 100644 --- a/data/catalogs/STRchive-disease-loci.T2T-chm13.atarva.bed +++ b/data/catalogs/STRchive-disease-loci.T2T-chm13.atarva.bed @@ -84,4 +84,4 @@ chrX 69887153 69887230 AGAGGG 6 XDP_TAF1 chrX 135876774 135876804 GCN 3 VACTERLX_ZIC3 chrX 138816203 138816248 NGC 3 XLMR_SOX3 chrX 146176677 146176769 CGG 3 FXS_FMR1 -chrX 146765190 146765342 GCC 3 FRAXE_AFF2 +chrX 146765223 146765271 GCC 3 FRAXE_AFF2 diff --git a/data/catalogs/STRchive-disease-loci.T2T-chm13.atarva.bed.gz b/data/catalogs/STRchive-disease-loci.T2T-chm13.atarva.bed.gz index abee0b5a..7f1c237f 100644 Binary files a/data/catalogs/STRchive-disease-loci.T2T-chm13.atarva.bed.gz and b/data/catalogs/STRchive-disease-loci.T2T-chm13.atarva.bed.gz differ diff --git a/data/catalogs/STRchive-disease-loci.T2T-chm13.atarva.bed.gz.tbi b/data/catalogs/STRchive-disease-loci.T2T-chm13.atarva.bed.gz.tbi index abae9bfb..4ff9e353 100644 Binary files a/data/catalogs/STRchive-disease-loci.T2T-chm13.atarva.bed.gz.tbi and b/data/catalogs/STRchive-disease-loci.T2T-chm13.atarva.bed.gz.tbi differ diff --git a/data/catalogs/STRchive-disease-loci.T2T-chm13.general.bed b/data/catalogs/STRchive-disease-loci.T2T-chm13.general.bed index 49877b6f..1eaa6eeb 100644 --- a/data/catalogs/STRchive-disease-loci.T2T-chm13.general.bed +++ b/data/catalogs/STRchive-disease-loci.T2T-chm13.general.bed @@ -73,4 +73,4 @@ chrX 69887153 69887230 XDP_TAF1 TAF1 AGAGGG AGAGGG 35 XR X-linked dystonia-parki chrX 135876774 135876804 VACTERLX_ZIC3 ZIC3 GCN GCN 12 XR X-linked VACTERL syndrome chrX 138816203 138816248 XLMR_SOX3 SOX3 NGC NGC 22 XR X-linked panhypopituitarism ; X-linked mental retardation with isolated growth hormone chrX 146176677 146176769 FXS_FMR1 FMR1 CGG CGG 201 XD Fragile X syndrome (FXS), fragile X-associated tremor/ataxia syndrome (FXTAS), and fragile X-associated primary ovarian insufficiency FXPOI/POF1 -chrX 146765190 146765342 FRAXE_AFF2 AFF2 GCC GCC 201 XR Fragile X syndrome, FRAXE type +chrX 146765223 146765271 FRAXE_AFF2 AFF2 GCC GCC 201 XR Fragile X syndrome, FRAXE type diff --git a/data/catalogs/STRchive-disease-loci.T2T-chm13.longTR.bed b/data/catalogs/STRchive-disease-loci.T2T-chm13.longTR.bed index c36c8a4d..6b2ddf41 100644 --- a/data/catalogs/STRchive-disease-loci.T2T-chm13.longTR.bed +++ b/data/catalogs/STRchive-disease-loci.T2T-chm13.longTR.bed @@ -72,4 +72,4 @@ chrX 69887154 69887230 AGAGGG XDP_TAF1 chrX 135876775 135876804 GCN VACTERLX_ZIC3 chrX 138816204 138816248 NGC XLMR_SOX3 chrX 146176678 146176769 CGG FXS_FMR1 -chrX 146765191 146765342 GCC FRAXE_AFF2 +chrX 146765224 146765271 GCC FRAXE_AFF2 diff --git a/data/catalogs/STRchive-disease-loci.T2T-chm13.straglr.bed b/data/catalogs/STRchive-disease-loci.T2T-chm13.straglr.bed index 2f601147..d756440b 100644 --- a/data/catalogs/STRchive-disease-loci.T2T-chm13.straglr.bed +++ b/data/catalogs/STRchive-disease-loci.T2T-chm13.straglr.bed @@ -82,4 +82,4 @@ chrX 69887153 69887230 AGAGGG XDP_TAF1 XDP_TAF1 chrX 135876774 135876804 GCN VACTERLX_ZIC3 VACTERLX_ZIC3 chrX 138816203 138816248 NGC XLMR_SOX3 XLMR_SOX3 chrX 146176677 146176769 CGG FXS_FMR1 FXS_FMR1 -chrX 146765190 146765342 GCC FRAXE_AFF2 FRAXE_AFF2 +chrX 146765223 146765271 GCC FRAXE_AFF2 FRAXE_AFF2 diff --git a/data/catalogs/STRchive-disease-loci.T2T-chm13.stranger.json b/data/catalogs/STRchive-disease-loci.T2T-chm13.stranger.json index c24a0a9d..80a5babd 100644 --- a/data/catalogs/STRchive-disease-loci.T2T-chm13.stranger.json +++ b/data/catalogs/STRchive-disease-loci.T2T-chm13.stranger.json @@ -988,14 +988,14 @@ }, { "LocusId": "FRAXE_AFF2", - "ReferenceRegion": "chrX:146765190-146765342", + "ReferenceRegion": "chrX:146765223-146765271", "LocusStructure": "(GCC)*", "VariantType": "Repeat", "HGNCId": null, "InheritanceMode": ["XR"], "DisplayRU": "GCC", "Disease": "FRAXE", - "NormalMax": 39, + "NormalMax": 69, "PathologicMin": 201, "Gene": "AFF2" }] diff --git a/data/catalogs/STRchive-disease-loci.hg19.TRGT.bed b/data/catalogs/STRchive-disease-loci.hg19.TRGT.bed index ab47340c..2008dba2 100644 --- a/data/catalogs/STRchive-disease-loci.hg19.TRGT.bed +++ b/data/catalogs/STRchive-disease-loci.hg19.TRGT.bed @@ -72,4 +72,4 @@ chrX 70672904 70672981 ID=XDP_TAF1;MOTIFS=AGAGGG;STRUC= chrX 136648985 136649015 ID=VACTERLX_ZIC3;MOTIFS=GCN;STRUC= chrX 139586481 139586526 ID=XLMR_SOX3;MOTIFS=NGC;STRUC= chrX 146993567 146993629 ID=FXS_FMR1;MOTIFS=CGG;STRUC= -chrX 147582124 147582273 ID=FRAXE_AFF2;MOTIFS=GCC;STRUC= +chrX 147582157 147582202 ID=FRAXE_AFF2;MOTIFS=GCC;STRUC= diff --git a/data/catalogs/STRchive-disease-loci.hg19.atarva.bed b/data/catalogs/STRchive-disease-loci.hg19.atarva.bed index 78f66ecc..892c020b 100644 --- a/data/catalogs/STRchive-disease-loci.hg19.atarva.bed +++ b/data/catalogs/STRchive-disease-loci.hg19.atarva.bed @@ -84,4 +84,4 @@ chrX 70672904 70672981 AGAGGG 6 XDP_TAF1 chrX 136648985 136649015 GCN 3 VACTERLX_ZIC3 chrX 139586481 139586526 NGC 3 XLMR_SOX3 chrX 146993567 146993629 CGG 3 FXS_FMR1 -chrX 147582124 147582273 GCC 3 FRAXE_AFF2 +chrX 147582157 147582202 GCC 3 FRAXE_AFF2 diff --git a/data/catalogs/STRchive-disease-loci.hg19.atarva.bed.gz b/data/catalogs/STRchive-disease-loci.hg19.atarva.bed.gz index 98a3a488..1e071475 100644 Binary files a/data/catalogs/STRchive-disease-loci.hg19.atarva.bed.gz and b/data/catalogs/STRchive-disease-loci.hg19.atarva.bed.gz differ diff --git a/data/catalogs/STRchive-disease-loci.hg19.atarva.bed.gz.tbi b/data/catalogs/STRchive-disease-loci.hg19.atarva.bed.gz.tbi index a3f690d9..2e28ad6f 100644 Binary files a/data/catalogs/STRchive-disease-loci.hg19.atarva.bed.gz.tbi and b/data/catalogs/STRchive-disease-loci.hg19.atarva.bed.gz.tbi differ diff --git a/data/catalogs/STRchive-disease-loci.hg19.general.bed b/data/catalogs/STRchive-disease-loci.hg19.general.bed index a44fe09d..d8ef114c 100644 --- a/data/catalogs/STRchive-disease-loci.hg19.general.bed +++ b/data/catalogs/STRchive-disease-loci.hg19.general.bed @@ -73,4 +73,4 @@ chrX 70672904 70672981 XDP_TAF1 TAF1 AGAGGG AGAGGG 35 XR X-linked dystonia-parki chrX 136648985 136649015 VACTERLX_ZIC3 ZIC3 GCN GCN 12 XR X-linked VACTERL syndrome chrX 139586481 139586526 XLMR_SOX3 SOX3 NGC NGC 22 XR X-linked panhypopituitarism ; X-linked mental retardation with isolated growth hormone chrX 146993567 146993629 FXS_FMR1 FMR1 CGG CGG 201 XD Fragile X syndrome (FXS), fragile X-associated tremor/ataxia syndrome (FXTAS), and fragile X-associated primary ovarian insufficiency FXPOI/POF1 -chrX 147582124 147582273 FRAXE_AFF2 AFF2 GCC GCC 201 XR Fragile X syndrome, FRAXE type +chrX 147582157 147582202 FRAXE_AFF2 AFF2 GCC GCC 201 XR Fragile X syndrome, FRAXE type diff --git a/data/catalogs/STRchive-disease-loci.hg19.longTR.bed b/data/catalogs/STRchive-disease-loci.hg19.longTR.bed index 3ba18238..9d91e5f7 100644 --- a/data/catalogs/STRchive-disease-loci.hg19.longTR.bed +++ b/data/catalogs/STRchive-disease-loci.hg19.longTR.bed @@ -72,4 +72,4 @@ chrX 70672905 70672981 AGAGGG XDP_TAF1 chrX 136648986 136649015 GCN VACTERLX_ZIC3 chrX 139586482 139586526 NGC XLMR_SOX3 chrX 146993568 146993629 CGG FXS_FMR1 -chrX 147582125 147582273 GCC FRAXE_AFF2 +chrX 147582158 147582202 GCC FRAXE_AFF2 diff --git a/data/catalogs/STRchive-disease-loci.hg19.straglr.bed b/data/catalogs/STRchive-disease-loci.hg19.straglr.bed index 9e52fca2..c251405c 100644 --- a/data/catalogs/STRchive-disease-loci.hg19.straglr.bed +++ b/data/catalogs/STRchive-disease-loci.hg19.straglr.bed @@ -82,4 +82,4 @@ chrX 70672904 70672981 AGAGGG XDP_TAF1 XDP_TAF1 chrX 136648985 136649015 GCN VACTERLX_ZIC3 VACTERLX_ZIC3 chrX 139586481 139586526 NGC XLMR_SOX3 XLMR_SOX3 chrX 146993567 146993629 CGG FXS_FMR1 FXS_FMR1 -chrX 147582124 147582273 GCC FRAXE_AFF2 FRAXE_AFF2 +chrX 147582157 147582202 GCC FRAXE_AFF2 FRAXE_AFF2 diff --git a/data/catalogs/STRchive-disease-loci.hg19.stranger.json b/data/catalogs/STRchive-disease-loci.hg19.stranger.json index 9da2ed04..2a854ee1 100644 --- a/data/catalogs/STRchive-disease-loci.hg19.stranger.json +++ b/data/catalogs/STRchive-disease-loci.hg19.stranger.json @@ -988,14 +988,14 @@ }, { "LocusId": "FRAXE_AFF2", - "ReferenceRegion": "chrX:147582124-147582273", + "ReferenceRegion": "chrX:147582157-147582202", "LocusStructure": "(GCC)*", "VariantType": "Repeat", "HGNCId": null, "InheritanceMode": ["XR"], "DisplayRU": "GCC", "Disease": "FRAXE", - "NormalMax": 39, + "NormalMax": 69, "PathologicMin": 201, "Gene": "AFF2" }] diff --git a/data/catalogs/STRchive-disease-loci.hg38.TRGT.bed b/data/catalogs/STRchive-disease-loci.hg38.TRGT.bed index 75c81b02..e99632c3 100644 --- a/data/catalogs/STRchive-disease-loci.hg38.TRGT.bed +++ b/data/catalogs/STRchive-disease-loci.hg38.TRGT.bed @@ -72,4 +72,4 @@ chrX 71453054 71453131 ID=XDP_TAF1;MOTIFS=AGAGGG;STRUC= chrX 137566826 137566856 ID=VACTERLX_ZIC3;MOTIFS=GCN;STRUC= chrX 140504316 140504361 ID=XLMR_SOX3;MOTIFS=NGC;STRUC= chrX 147912049 147912111 ID=FXS_FMR1;MOTIFS=CGG;STRUC= -chrX 148500604 148500753 ID=FRAXE_AFF2;MOTIFS=GCC;STRUC= +chrX 148500637 148500682 ID=FRAXE_AFF2;MOTIFS=GCC;STRUC= diff --git a/data/catalogs/STRchive-disease-loci.hg38.atarva.bed b/data/catalogs/STRchive-disease-loci.hg38.atarva.bed index 8311febd..6d88e9d9 100644 --- a/data/catalogs/STRchive-disease-loci.hg38.atarva.bed +++ b/data/catalogs/STRchive-disease-loci.hg38.atarva.bed @@ -84,4 +84,4 @@ chrX 71453054 71453131 AGAGGG 6 XDP_TAF1 chrX 137566826 137566856 GCN 3 VACTERLX_ZIC3 chrX 140504316 140504361 NGC 3 XLMR_SOX3 chrX 147912049 147912111 CGG 3 FXS_FMR1 -chrX 148500604 148500753 GCC 3 FRAXE_AFF2 +chrX 148500637 148500682 GCC 3 FRAXE_AFF2 diff --git a/data/catalogs/STRchive-disease-loci.hg38.atarva.bed.gz b/data/catalogs/STRchive-disease-loci.hg38.atarva.bed.gz index 23164d4e..0567b3f8 100644 Binary files a/data/catalogs/STRchive-disease-loci.hg38.atarva.bed.gz and b/data/catalogs/STRchive-disease-loci.hg38.atarva.bed.gz differ diff --git a/data/catalogs/STRchive-disease-loci.hg38.general.bed b/data/catalogs/STRchive-disease-loci.hg38.general.bed index b77e7175..eb2efd46 100644 --- a/data/catalogs/STRchive-disease-loci.hg38.general.bed +++ b/data/catalogs/STRchive-disease-loci.hg38.general.bed @@ -73,4 +73,4 @@ chrX 71453054 71453131 XDP_TAF1 TAF1 AGAGGG AGAGGG 35 XR X-linked dystonia-parki chrX 137566826 137566856 VACTERLX_ZIC3 ZIC3 GCN GCN 12 XR X-linked VACTERL syndrome chrX 140504316 140504361 XLMR_SOX3 SOX3 NGC NGC 22 XR X-linked panhypopituitarism ; X-linked mental retardation with isolated growth hormone chrX 147912049 147912111 FXS_FMR1 FMR1 CGG CGG 201 XD Fragile X syndrome (FXS), fragile X-associated tremor/ataxia syndrome (FXTAS), and fragile X-associated primary ovarian insufficiency FXPOI/POF1 -chrX 148500604 148500753 FRAXE_AFF2 AFF2 GCC GCC 201 XR Fragile X syndrome, FRAXE type +chrX 148500637 148500682 FRAXE_AFF2 AFF2 GCC GCC 201 XR Fragile X syndrome, FRAXE type diff --git a/data/catalogs/STRchive-disease-loci.hg38.longTR.bed b/data/catalogs/STRchive-disease-loci.hg38.longTR.bed index 8a36b988..d62b6c55 100644 --- a/data/catalogs/STRchive-disease-loci.hg38.longTR.bed +++ b/data/catalogs/STRchive-disease-loci.hg38.longTR.bed @@ -72,4 +72,4 @@ chrX 71453055 71453131 AGAGGG XDP_TAF1 chrX 137566827 137566856 GCN VACTERLX_ZIC3 chrX 140504317 140504361 NGC XLMR_SOX3 chrX 147912050 147912111 CGG FXS_FMR1 -chrX 148500605 148500753 GCC FRAXE_AFF2 +chrX 148500638 148500682 GCC FRAXE_AFF2 diff --git a/data/catalogs/STRchive-disease-loci.hg38.straglr.bed b/data/catalogs/STRchive-disease-loci.hg38.straglr.bed index 6b4a89c4..537af7b6 100644 --- a/data/catalogs/STRchive-disease-loci.hg38.straglr.bed +++ b/data/catalogs/STRchive-disease-loci.hg38.straglr.bed @@ -82,4 +82,4 @@ chrX 71453054 71453131 AGAGGG XDP_TAF1 XDP_TAF1 chrX 137566826 137566856 GCN VACTERLX_ZIC3 VACTERLX_ZIC3 chrX 140504316 140504361 NGC XLMR_SOX3 XLMR_SOX3 chrX 147912049 147912111 CGG FXS_FMR1 FXS_FMR1 -chrX 148500604 148500753 GCC FRAXE_AFF2 FRAXE_AFF2 +chrX 148500637 148500682 GCC FRAXE_AFF2 FRAXE_AFF2 diff --git a/data/catalogs/STRchive-disease-loci.hg38.stranger.json b/data/catalogs/STRchive-disease-loci.hg38.stranger.json index 3231f70c..f8fd39c0 100644 --- a/data/catalogs/STRchive-disease-loci.hg38.stranger.json +++ b/data/catalogs/STRchive-disease-loci.hg38.stranger.json @@ -988,14 +988,14 @@ }, { "LocusId": "FRAXE_AFF2", - "ReferenceRegion": "chrX:148500604-148500753", + "ReferenceRegion": "chrX:148500637-148500682", "LocusStructure": "(GCC)*", "VariantType": "Repeat", "HGNCId": null, "InheritanceMode": ["XR"], "DisplayRU": "GCC", "Disease": "FRAXE", - "NormalMax": 39, + "NormalMax": 69, "PathologicMin": 201, "Gene": "AFF2" }] diff --git a/data/plots/path-size.json b/data/plots/path-size.json index 825f367b..289d0a5e 100644 --- a/data/plots/path-size.json +++ b/data/plots/path-size.json @@ -12,12 +12,12 @@ "offset": -0.3, "orientation": "h", "width": 0.6, - "x": [0, 110, 66, 198, 0, 0, 99, 54, 126, 0, 51, 780, 25, 513, 51, 51, 105, 117, 0, 0, 39, 12, 30, 123, 222, 60, 0, 220, 96, 95, 59, 105, 0, 90, 99, 51, 84, 149, 78, 87, 87, 45, 87, 36, 54, 66, 0, 87, 75, 69, 60, 48, 33, 0, 0, 0, 30, 0, 0, 42, 0, 39, 0, 21, 18, 0, 0, 0, 0, 12, 0, 0, 0, 0], + "x": [0, 110, 66, 198, 0, 0, 99, 54, 126, 0, 51, 780, 25, 513, 51, 51, 195, 117, 0, 0, 39, 12, 30, 123, 222, 60, 0, 220, 96, 95, 59, 105, 0, 90, 99, 51, 84, 149, 78, 87, 87, 45, 87, 36, 54, 66, 0, 87, 75, 69, 60, 48, 33, 0, 0, 0, 30, 0, 0, 42, 0, 39, 0, 21, 18, 0, 0, 0, 0, 12, 0, 0, 0, 0], "y": ["FAME4", "SCA10", "SCA36", "MRUPAV", "FAME6", "FAME3", "GDPAG", "CANVAS", "FTDALS1", "FAME2", "FRA7A", "CPUM", "NME", "SCA27B", "FRA2A", "FRA12A", "FRAXE", "FXS, FXTAS, POF1", "SCA31", "FAME1", "OPML1", "EPM1", "OPDM4", "OPDM5", "JBS", "DM2", "FAME7", "RCPS", "OPDM1", "OPDM2", "DBQD2, BSS", "SCA8", "XDP", "NIID", "SCA3, MJD", "DMD", "FRDA", "SCA37", "SCA12", "FECD3", "DM1", "SCA17", "DRPLA", "SCA4", "SCA51", "HDL2", "CJD", "SCA1", "SBMA", "SCA7", "HD", "SCA2", "CCHS", "TOF", "HPE5", "HFG-I", "HFG-III", "SD5", "XLMR", "SCA6", "PRTS", "CCD", "HFG-II", "HSAN VIII", "EIEE1", "BPES", "FAME8", "OPMD", "VACTERLX", "ALS1", "EDM1, PSACH", "CHNG3", "HMNR7", "CPEO"], "type": "bar" }, { - "base": [0, 165, 90, 0, 0, 0, 0, 55, 144, 0, 126, 0, 0, 540, 0, 417, 120, 135, 0, 0, 0, 0, 0, 0, 240, 108, 0, 260, 0, 0, 0, 150, 0, 114, 135, 0, 102, 0, 120, 120, 105, 123, 108, 81, 0, 87, 0, 108, 108, 84, 81, 93, 63, 0, 0, 0, 0, 0, 0, 57, 0, 0, 0, 0, 0, 0, 0, 33, 33, 0, 0, 0, 0, 0], + "base": [0, 165, 90, 0, 0, 0, 0, 55, 144, 0, 126, 0, 0, 540, 0, 417, 210, 135, 0, 0, 0, 0, 0, 0, 240, 108, 0, 260, 0, 0, 0, 150, 0, 114, 135, 0, 102, 0, 120, 120, 105, 123, 108, 81, 0, 87, 0, 108, 108, 84, 81, 93, 63, 0, 0, 0, 0, 0, 0, 57, 0, 0, 0, 0, 0, 0, 0, 33, 33, 0, 0, 0, 0, 0], "hovertemplate": "Disease: %{y} \u003cbr\u003e Range: %{base} - %{x} bp", "legendgroup": "Intermediate", "marker": @@ -28,7 +28,7 @@ "offset": -0.3, "orientation": "h", "width": 0.6, - "x": [0, 4085, 3804, 0, 0, 0, 0, 945, 216, 0, 129, 0, 0, 417, 0, 201, 480, 465, 0, 0, 0, 0, 0, 0, 60, 188, 0, 0, 0, 0, 0, 60, 0, 81, 42, 0, 63, 0, 27, 30, 42, 21, 33, 54, 0, 30, 0, 6, 3, 21, 24, 9, 12, 0, 0, 0, 0, 0, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], + "x": [0, 4085, 3804, 0, 0, 0, 0, 945, 216, 0, 129, 0, 0, 417, 0, 201, 390, 465, 0, 0, 0, 0, 0, 0, 60, 188, 0, 0, 0, 0, 0, 60, 0, 81, 42, 0, 63, 0, 27, 30, 42, 21, 33, 54, 0, 30, 0, 6, 3, 21, 24, 9, 12, 0, 0, 0, 0, 0, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], "y": ["FAME4", "SCA10", "SCA36", "MRUPAV", "FAME6", "FAME3", "GDPAG", "CANVAS", "FTDALS1", "FAME2", "FRA7A", "CPUM", "NME", "SCA27B", "FRA2A", "FRA12A", "FRAXE", "FXS, FXTAS, POF1", "SCA31", "FAME1", "OPML1", "EPM1", "OPDM4", "OPDM5", "JBS", "DM2", "FAME7", "RCPS", "OPDM1", "OPDM2", "DBQD2, BSS", "SCA8", "XDP", "NIID", "SCA3, MJD", "DMD", "FRDA", "SCA37", "SCA12", "FECD3", "DM1", "SCA17", "DRPLA", "SCA4", "SCA51", "HDL2", "CJD", "SCA1", "SBMA", "SCA7", "HD", "SCA2", "CCHS", "TOF", "HPE5", "HFG-I", "HFG-III", "SD5", "XLMR", "SCA6", "PRTS", "CCD", "HFG-II", "HSAN VIII", "EIEE1", "BPES", "FAME8", "OPMD", "VACTERLX", "ALS1", "EDM1, PSACH", "CHNG3", "HMNR7", "CPEO"], "type": "bar" }, @@ -278,7 +278,7 @@ }, "mode": "lines", "showlegend": false, - "x": [117, 120], + "x": [207, 210], "y": ["FRAXE", "FRAXE"], "type": "scatter" }, diff --git a/data/ref-alleles/ref-alleles.T2T-chm13.txt b/data/ref-alleles/ref-alleles.T2T-chm13.txt index 1ce62e6a..70ecf7fe 100644 --- a/data/ref-alleles/ref-alleles.T2T-chm13.txt +++ b/data/ref-alleles/ref-alleles.T2T-chm13.txt @@ -443,8 +443,8 @@ GTGCGGCAGC G CGG CGG CGG CGG CGG CGG CGG CGG CGG CGG AGG CGG CGG CGG CGG CGG CGG GTGCGGCAGC G CGG CGG CGG CGG CGG CGG CGG CGG CGG CGG AGG CGG CGG CGG CGG CGG CGG CGG CGG CGG AGG CGG CGG CGG CGG CGG CGG CGG CGG CGG C TGGGCCTCGA FRAXE_AFF2 -chrX 146765190 146765342 GCC STRchive -chrX 146765190 146765342 GCC TRGT -GTGTGATGCT GCC GCG GCC GCC GCC GCC GCC TGTGCA GCC GCT GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCT GCC GCC CCGGCT GCC GC GCC GC GCC GCT GCC TCT GCC CCG GCC GCC CCC GCC GCC GCT GCC GCC GCC G GCCCGCAGCC -GTGTGATGCT GCC GCG GCC GCC GCC GCC GCC TGTGCA GCC GCT GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCT GCC GCC CCGGCT GCC GC GCC GC GCC GCT GCC TCT GCC CCG GCC GCC CCC GCC GCC GCT GCC GCC GCC G GCCCGCAGCC +chrX 146765223 146765271 GCC STRchive +chrX 146765223 146765271 GCC TRGT +TGCAGCCGCT GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCTGCCGCCC +TGCAGCCGCT GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCTGCCGCCC diff --git a/data/ref-alleles/ref-alleles.hg19.txt b/data/ref-alleles/ref-alleles.hg19.txt index 4571380e..da49d6dc 100644 --- a/data/ref-alleles/ref-alleles.hg19.txt +++ b/data/ref-alleles/ref-alleles.hg19.txt @@ -443,8 +443,8 @@ GTGCGGCAGC G CGG CGG CGG CGG CGG CGG CGG CGG CGG CGG AGG CGG CGG CGG CGG CGG CGG GTGCGGCAGC G CGG CGG CGG CGG CGG CGG CGG CGG CGG CGG AGG CGG CGG CGG CGG CGG CGG CGG CGG CGG C TGGGCCTCGA FRAXE_AFF2 -chrX 147582124 147582273 GCC STRchive -chrX 147582124 147582273 GCC TRGT -GTGTGATGCT GCC GCG GCC GCC GCC GCC GCC TGTGCA GCC GCT GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCT GCC GCC CCGGCT GCC GC GCC GC GCC GCT GCC TCT GCC CCG GCC GCC CCC GCC GCC GCT GCC GCC GCC G GCCCGCAGCC -GTGTGATGCT GCC GCG GCC GCC GCC GCC GCC TGTGCA GCC GCT GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCT GCC GCC CCGGCT GCC GC GCC GC GCC GCT GCC TCT GCC CCG GCC GCC CCC GCC GCC GCT GCC GCC GCC G GCCCGCAGCC +chrX 147582157 147582202 GCC STRchive +chrX 147582157 147582202 GCC TRGT +TGCAGCCGCT GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCTGCCGCCC +TGCAGCCGCT GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCTGCCGCCC diff --git a/data/ref-alleles/ref-alleles.hg38.txt b/data/ref-alleles/ref-alleles.hg38.txt index a7875038..4524cd3d 100644 --- a/data/ref-alleles/ref-alleles.hg38.txt +++ b/data/ref-alleles/ref-alleles.hg38.txt @@ -443,8 +443,8 @@ GTGCGGCAGC G CGG CGG CGG CGG CGG CGG CGG CGG CGG CGG AGG CGG CGG CGG CGG CGG CGG GTGCGGCAGC G CGG CGG CGG CGG CGG CGG CGG CGG CGG CGG AGG CGG CGG CGG CGG CGG CGG CGG CGG CGG C TGGGCCTCGA FRAXE_AFF2 -chrX 148500604 148500753 GCC STRchive -chrX 148500604 148500753 GCC TRGT -GTGTGATGCT GCC GCG GCC GCC GCC GCC GCC TGTGCA GCC GCT GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCT GCC GCC CCGGCT GCC GC GCC GC GCC GCT GCC TCT GCC CCG GCC GCC CCC GCC GCC GCT GCC GCC GCC G GCCCGCAGCC -GTGTGATGCT GCC GCG GCC GCC GCC GCC GCC TGTGCA GCC GCT GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCT GCC GCC CCGGCT GCC GC GCC GC GCC GCT GCC TCT GCC CCG GCC GCC CCC GCC GCC GCT GCC GCC GCC G GCCCGCAGCC +chrX 148500637 148500682 GCC STRchive +chrX 148500637 148500682 GCC TRGT +TGCAGCCGCT GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCTGCCGCCC +TGCAGCCGCT GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCTGCCGCCC