Skip to content

Update normal allele range #309

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Draft
strchive-bot wants to merge 2 commits into
base: main
Choose a base branch
from
Draft

Update normal allele range #309

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
71850f9
Update normal allele range
strchive-bot Dec 9, 2025
ade4011
Update data
strchive-bot Dec 9, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion data/STRchive-citations.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand Down
16 changes: 8 additions & 8 deletions data/STRchive-loci.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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].",
Expand All @@ -98,8 +98,8 @@
"unknown_motif_gene_orientation": [],
"locus_structure": [],
"benign_min": 4,
"benign_max": 39,
"intermediate_min": 40,
"benign_max": 69,
Copy link

@dnil dnil Dec 9, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Suggested change
"benign_max": 69,
"benign_max": 39,

"intermediate_min": 70,
Copy link

@dnil dnil Dec 9, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Suggested change
"intermediate_min": 70,
"intermediate_min": 40,

"intermediate_max": 200,
"pathogenic_min": 201,
"pathogenic_max": 2000,
Expand Down
2 changes: 1 addition & 1 deletion data/catalogs/STRchive-disease-loci.T2T-chm13.TRGT.bed
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -72,4 +72,4 @@ chrX 69887153 69887230 ID=XDP_TAF1;MOTIFS=AGAGGG;STRUC=<TR>
chrX 135876774 135876804 ID=VACTERLX_ZIC3;MOTIFS=GCN;STRUC=<TR>
chrX 138816203 138816248 ID=XLMR_SOX3;MOTIFS=NGC;STRUC=<TR>
chrX 146176677 146176769 ID=FXS_FMR1;MOTIFS=CGG;STRUC=<TR>
chrX 146765190 146765342 ID=FRAXE_AFF2;MOTIFS=GCC;STRUC=<TR>
chrX 146765223 146765271 ID=FRAXE_AFF2;MOTIFS=GCC;STRUC=<TR>
2 changes: 1 addition & 1 deletion data/catalogs/STRchive-disease-loci.T2T-chm13.atarva.bed
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Binary file modified data/catalogs/STRchive-disease-loci.T2T-chm13.atarva.bed.gz
View file
Open in desktop
Binary file not shown.
Binary file modified data/catalogs/STRchive-disease-loci.T2T-chm13.atarva.bed.gz.tbi
View file
Open in desktop
Binary file not shown.
2 changes: 1 addition & 1 deletion data/catalogs/STRchive-disease-loci.T2T-chm13.general.bed
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
2 changes: 1 addition & 1 deletion data/catalogs/STRchive-disease-loci.T2T-chm13.longTR.bed
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
2 changes: 1 addition & 1 deletion data/catalogs/STRchive-disease-loci.T2T-chm13.straglr.bed
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
4 changes: 2 additions & 2 deletions data/catalogs/STRchive-disease-loci.T2T-chm13.stranger.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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,
Copy link

@dnil dnil Dec 9, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Suggested change
"NormalMax": 69,
"NormalMax": 39,

"PathologicMin": 201,
"Gene": "AFF2"
}]
2 changes: 1 addition & 1 deletion data/catalogs/STRchive-disease-loci.hg19.TRGT.bed
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -72,4 +72,4 @@ chrX 70672904 70672981 ID=XDP_TAF1;MOTIFS=AGAGGG;STRUC=<TR>
chrX 136648985 136649015 ID=VACTERLX_ZIC3;MOTIFS=GCN;STRUC=<TR>
chrX 139586481 139586526 ID=XLMR_SOX3;MOTIFS=NGC;STRUC=<TR>
chrX 146993567 146993629 ID=FXS_FMR1;MOTIFS=CGG;STRUC=<TR>
chrX 147582124 147582273 ID=FRAXE_AFF2;MOTIFS=GCC;STRUC=<TR>
chrX 147582157 147582202 ID=FRAXE_AFF2;MOTIFS=GCC;STRUC=<TR>
2 changes: 1 addition & 1 deletion data/catalogs/STRchive-disease-loci.hg19.atarva.bed
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Binary file modified data/catalogs/STRchive-disease-loci.hg19.atarva.bed.gz
View file
Open in desktop
Binary file not shown.
Binary file modified data/catalogs/STRchive-disease-loci.hg19.atarva.bed.gz.tbi
View file
Open in desktop
Binary file not shown.
2 changes: 1 addition & 1 deletion data/catalogs/STRchive-disease-loci.hg19.general.bed
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
2 changes: 1 addition & 1 deletion data/catalogs/STRchive-disease-loci.hg19.longTR.bed
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
2 changes: 1 addition & 1 deletion data/catalogs/STRchive-disease-loci.hg19.straglr.bed
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
4 changes: 2 additions & 2 deletions data/catalogs/STRchive-disease-loci.hg19.stranger.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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"
}]
2 changes: 1 addition & 1 deletion data/catalogs/STRchive-disease-loci.hg38.TRGT.bed
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -72,4 +72,4 @@ chrX 71453054 71453131 ID=XDP_TAF1;MOTIFS=AGAGGG;STRUC=<TR>
chrX 137566826 137566856 ID=VACTERLX_ZIC3;MOTIFS=GCN;STRUC=<TR>
chrX 140504316 140504361 ID=XLMR_SOX3;MOTIFS=NGC;STRUC=<TR>
chrX 147912049 147912111 ID=FXS_FMR1;MOTIFS=CGG;STRUC=<TR>
chrX 148500604 148500753 ID=FRAXE_AFF2;MOTIFS=GCC;STRUC=<TR>
chrX 148500637 148500682 ID=FRAXE_AFF2;MOTIFS=GCC;STRUC=<TR>
2 changes: 1 addition & 1 deletion data/catalogs/STRchive-disease-loci.hg38.atarva.bed
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Binary file modified data/catalogs/STRchive-disease-loci.hg38.atarva.bed.gz
View file
Open in desktop
Binary file not shown.
2 changes: 1 addition & 1 deletion data/catalogs/STRchive-disease-loci.hg38.general.bed
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
2 changes: 1 addition & 1 deletion data/catalogs/STRchive-disease-loci.hg38.longTR.bed
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
2 changes: 1 addition & 1 deletion data/catalogs/STRchive-disease-loci.hg38.straglr.bed
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
4 changes: 2 additions & 2 deletions data/catalogs/STRchive-disease-loci.hg38.stranger.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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,
Copy link

@dnil dnil Dec 9, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

And this appears to have transferred from the previous PR. Kind bot, but not as intended.

Suggested change
"NormalMax": 69,
"NormalMax": 39,

"PathologicMin": 201,
"Gene": "AFF2"
}]
8 changes: 4 additions & 4 deletions data/plots/path-size.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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":
Expand All @@ -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"
},
Expand Down Expand Up @@ -278,7 +278,7 @@
},
"mode": "lines",
"showlegend": false,
"x": [117, 120],
"x": [207, 210],
"y": ["FRAXE", "FRAXE"],
"type": "scatter"
},
Expand Down
8 changes: 4 additions & 4 deletions data/ref-alleles/ref-alleles.T2T-chm13.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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

8 changes: 4 additions & 4 deletions data/ref-alleles/ref-alleles.hg19.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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

8 changes: 4 additions & 4 deletions data/ref-alleles/ref-alleles.hg38.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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