Detection and small corrections

data/STRchive-citations.json

@@ -165894,10 +165894,10 @@
   "note": "WARNING: Manubot does not support url:https://omim.org/entry/300123. Skipping"
 },
 {
-  "id": "omim:607136,@pmid:35053321,@genereviews:NBK1438,@pmid:12805114,@genereviews:NBK1438",
+  "id": "omim:607136",
   "manubot_success": false,
-  "link": "https://omim.org/entry/607136,@pmid:35053321,@genereviews:NBK1438,@pmid:12805114,@genereviews:NBK1438",
-  "note": "WARNING: Manubot does not support url:https://omim.org/entry/607136,@pmid:35053321,@genereviews:NBK1438,@pmid:12805114,@genereviews:NBK1438. Skipping"
+  "link": "https://omim.org/entry/607136",
+  "note": "WARNING: Manubot does not support url:https://omim.org/entry/607136. Skipping"
 },
 {
   "id": "omim:187500",
@@ -165965,6 +165965,12 @@
   "link": "https://www.ncbi.nlm.nih.gov/books/NBK1229",
   "note": "WARNING: Manubot could not generate citation: Command '['manubot', 'cite', 'url:https://www.ncbi.nlm.nih.gov/books/NBK1229']' timed out after 3 seconds"
 },
+{
+  "id": "genereviews:NBK1438",
+  "manubot_success": false,
+  "link": "https://www.ncbi.nlm.nih.gov/books/NBK1438",
+  "note": "WARNING: Manubot could not generate citation: Command '['manubot', 'cite', 'url:https://www.ncbi.nlm.nih.gov/books/NBK1438']' timed out after 3 seconds"
+},
 {
   "id": "isbn:978-3-031-66932-3",
   "manubot_success": false,
@@ -165982,12 +165988,6 @@
   "link": "https://pubmed.ncbi.nlm.nih.gov/29939637",
   "note": "WARNING: Couldn't parse Manubot response: list index out of range"
 },
-{
-  "id": "pmid:35245110,@genereviews:NBK1438,@pmid:29100084,@pmid:10484774,@mondo:0011781",
-  "manubot_success": false,
-  "link": "https://pubmed.ncbi.nlm.nih.gov/35245110,@genereviews:NBK1438,@pmid:29100084,@pmid:10484774,@mondo:0011781",
-  "note": "WARNING: Couldn't parse Manubot response: list index out of range"
-},
 {
   "id": "pmid:39666847",
   "manubot_success": false,

data/STRchive-loci.json

@@ -1443,12 +1443,12 @@
   "orphanet": [],
   "gnomad": ["CSNK1E"],
   "stripy": [],
-  "tr_atlas": ["TR344468"],
+  "tr_atlas": ["TR344466"],
   "webstr_hg38": [],
   "webstr_hg19": [],
   "locus_tags": [],
   "disease_tags": ["epilepsy"],
-  "references": ["pmid:40751262", "pmid:39107278", "pmid: 39107278"],
+  "references": ["pmid:40751262", "pmid:39107278"],
   "additional_literature": []
 },
 {
@@ -2099,7 +2099,7 @@
   "typ_age_onset_min": 0.0,
   "typ_age_onset_max": 0.0,
   "details": "14 repeats appears highly constrained in humans: homozygous expansions from 14 polyalanines to 19 leads to disease, which can be limited to isolated palpebral defects [@pmid:15591279]. Heterozygous expansions to 24 polyalanines also lead to disease [@pmid:15591279]. Locus start can differ between catalogs, which can affect genotyping.",
-  "detection": null,
+  "detection": "These expansions are generally within the standard short-read sequencing flanking region and show up with dedicated STR callers, though allelic dropout has been reported [@pmid:42100494]. PCR based assays with subsequent capillary have accurately detected this expansion when used with a GC-enhancing co solvent [@pmid:31077882].",
   "mechanism": "GoF/LoF",
   "mechanism_detail": "Polyalanine expansion leads to haploinsufficiency, likely due to decreased protein availability due to mislocalization following nuclear inclusion [@genereviews:NBK1441; @pmid:15591279]",
   "year": "2003 [@pmid:12529855]",
@@ -3082,10 +3082,10 @@
   "mechanism_detail": "Toxic protein product accumulates in kidneys [@genereviews:NBK153723]",
   "year": "2013 [@pmid:23396133]",
   "location_in_gene": "Coding Exon 2",
-  "gene_strand": "+",
+  "gene_strand": "-",
   "reference_motif_reference_orientation": ["GGCTNNGGGNGCGGTGGAGCCCGGGGCNGGNCTGNTNTCCGGGGCCGAGGTGACANCNTG"],
-  "pathogenic_motif_reference_orientation": ["ACACCAGGCCGGCCCCGGGCTCCACCGCCCCCCCCAGCCCACGGTGTCACCTCGGCCCCGG"],
-  "benign_motif_reference_orientation": ["ACACCAGGCCGGCCCCGGGCTCCACCGCCCCCCCAGCCCACGGTGTCACCTCGGCCCCGG"],
+  "pathogenic_motif_reference_orientation": ["CCGGGGCCGAGGTGACACCGTGGGCTGGGGGGGGCGGTGGAGCCCGGGGCCGGCCTGGTGT"],
+  "benign_motif_reference_orientation": ["CCGGGGCCGAGGTGACACCGTGGGCTGGGGGGGCGGTGGAGCCCGGGGCCGGCCTGGTGT"],
   "unknown_motif_reference_orientation": [],
   "interruption_reference_orientation": [],
   "pathogenic_motif_gene_orientation": ["ACACCAGGCCGGCCCCGGGCTCCACCGCCCCCCCCAGCCCACGGTGTCACCTCGGCCCCGG"],
@@ -3099,7 +3099,7 @@
   "intermediate_max": null,
   "pathogenic_min": null,
   "pathogenic_max": null,
-  "motif_len": 1,
+  "motif_len": 61,
   "ref_copies": null,
   "novel": "ref",
   "gard": ["7002"],
@@ -3985,7 +3985,7 @@
   "details": "TTTTA repeat expansions and TTTCA repeat insertions in intron 4 of the RAI1 gene that co-segregated with disease status in a single large family from Mali [@pmid:37994247]. Ten affected individuals were studied. Both TTTTA and TTTCA motifs were observed in all eight of the affected individuals with spanning reads, with allele sizes in the range: (TTTTA)278-773(TTTCA)9-334. A single individual was observed with additional motifs and interruptions in one allele with the structure: (TTTTA)exp(GGGGT)ins(GGGAT)ins(TTTCA)ins. TTTCA repeats were absent in 200 Malian controls, who had alleles in the range: (TTTCA)16-20. Reviewed in [@pmid:38876750]. It is uncertain if expansions at both the TTTTA and TTTCA motifs, or only the TTTCA motif are required for pathogenicity. The pathogenic range in STRchive is for the TTTCA motif only. Note: locus is partially deleted in T2T reference genome.",
   "detection": null,
   "mechanism": "Unknown",
-  "mechanism_detail": "Expression isn't changed [@pmid:7994247].",
+  "mechanism_detail": "Expression isn't changed [@pmid:37994247].",
   "year": "2024 [@pmid:37994247]",
   "location_in_gene": "Intron 4",
   "gene_strand": "+",
@@ -4032,7 +4032,7 @@
   "webstr_hg19": [],
   "locus_tags": ["motif_affects_onset"],
   "disease_tags": ["familial_adult_myoclonic_epilepsy"],
-  "references": ["pmid:7994247", "pmid:37994247", "pmid:38876750"],
+  "references": ["pmid:37994247", "pmid:38876750"],
   "additional_literature": ["pmid:41874439", "pmid:41219789", "pmid:40541176", "pmid:38871700", "pmid:37339841", "pmid:34565721", "pmid:33186760", "pmid:32283749", "pmid:32281848", "pmid:30891880", "pmid:30622881", "pmid:25663198", "pmid:23897707", "pmid:17457615", "pmid:15148657", "pmid:11594924", "pmid:10915763", "pmid:8817239"]
 },
 {
@@ -4280,7 +4280,7 @@
   "age_onset_max": 0.0,
   "typ_age_onset_min": null,
   "typ_age_onset_max": null,
-  "details": "Benign range (4-17 repeats) established from gnomAD and primary literature; pathogenic ranges (20-27) reflect two clinical cases to date [@gnomad:RUNX2; @pmid:26220009]. Intermediate alleles (i.e, 18 repeats; 19 not reported) appear to not be associated with disease [@pmid:20560987; @pmid:26220009]. The gene RUNX2 was previously called CBFA1, as reflected in some of the literature [@pmid:9182765].",
+  "details": "Benign range (4-17 repeats) established from gnomAD and primary literature; pathogenic ranges (20-27) reflect two clinical cases to date [@gnomad:RUNX2; @pmid:26220009]. Intermediate alleles (i.e, 18 repeats; 19 not reported) appear to not be associated with disease [@pmid:20560987; @pmid:26220009]. The gene RUNX2 was previously called CBFA1, as reflected in some of the literature [@pmid:9182765]. Pathogenic range alleles up to 23 repeats have been detected in asymptomatic individuals, indicating potential incomplete penetrance [@pmid:40585427]. A polyglutamine expansion has also been noted in this locus. A 4 CAG motif expansion in the polyQ region has been found in one proband with CCD, while a 7 CAG expansion has been found in unaffected individuals. [@pmid:25852448].",
   "detection": null,
   "mechanism": "LoF",
   "mechanism_detail": "Polyalanine expansion leading to haploinsufficiency [@pmid:26220009].",
@@ -4742,7 +4742,7 @@
   "webstr_hg19": [],
   "locus_tags": ["somatic_instability", "anticipation", "paternal_expansion", "length_affects_onset", "length_affects_penetrance", "length_affects_phenotype", "motif_affects_instability"],
   "disease_tags": ["spinocerebellar_ataxia"],
-  "references": ["omim:607136,@pmid:35053321,@genereviews:NBK1438,@pmid:12805114,@genereviews:NBK1438", "pmid:35245110,@genereviews:NBK1438,@pmid:29100084,@pmid:10484774,@mondo:0011781"],
+  "references": ["omim:607136", "pmid:35053321", "genereviews:NBK1438", "pmid:12805114", "pmid:35245110", "pmid:29100084", "pmid:10484774", "mondo:0011781"],
   "additional_literature": ["pmid:42196324", "pmid:42038259", "pmid:41843312", "pmid:41762523", "pmid:41612618", "pmid:41009775", "pmid:40488180", "pmid:40478462", "pmid:39950762", "pmid:39820777", "pmid:39680235", "pmid:39456985", "pmid:39125760", "pmid:38973070", "pmid:38961870", "pmid:38494459", "pmid:37855597", "pmid:37632648", "pmid:37146135", "pmid:36599645", "pmid:36476347", "pmid:36422518", "pmid:35926480", "pmid:35868859", "pmid:35493319", "pmid:35482253", "pmid:35275350", "pmid:35182509", "pmid:34906452", "pmid:34600502", "pmid:34565721", "pmid:34256333", "pmid:34235484", "pmid:33502644", "pmid:33377399", "pmid:32675418", "pmid:32533168", "pmid:32386547", "pmid:31940111", "pmid:31919387", "pmid:31522753", "pmid:30920184", "pmid:30891880", "pmid:30617627", "pmid:30615214", "pmid:30532692", "pmid:30314815", "pmid:30120431", "pmid:29801887", "pmid:29564144", "pmid:29249939", "pmid:29057148", "pmid:28821675", "pmid:28585930", "pmid:28444220", "pmid:28153533", "pmid:27865706", "pmid:27400454", "pmid:27172828", "pmid:26476771", "pmid:26387956", "pmid:26374734", "pmid:26267067", "pmid:26077168", "pmid:25672822", "pmid:24972706", "pmid:24677642", "pmid:24534762", "pmid:23665119", "pmid:23475385", "pmid:21710129", "pmid:21562248", "pmid:21437269", "pmid:20587494", "pmid:20199210", "pmid:20004653", "pmid:19595623", "pmid:19566714", "pmid:18218637", "pmid:18043721", "pmid:17961920", "pmid:17420317", "pmid:17273961", "pmid:17033685", "pmid:16858508", "pmid:16626296", "pmid:16223509", "pmid:16054804", "pmid:15850778", "pmid:15533937", "pmid:15503103", "pmid:15381080", "pmid:15365789", "pmid:15225551", "pmid:15193429", "pmid:14985389", "pmid:14967767", "pmid:12953269", "pmid:12891385", "pmid:12853230", "pmid:12758065", "pmid:11939898", "pmid:11571212", "pmid:11313753", "pmid:9399691", "pmid:8886170", "pmid:7892196", "pmid:8503450"]
 },
 {
@@ -4837,7 +4837,7 @@
   "typ_age_onset_min": 40.0,
   "typ_age_onset_max": 59.0,
   "details": "Most controls have <40 repeats while majority of patients have >50 repeats; penetrance is <100%, as unaffected individuals have been documented with >80 repeats and alleles of affected individuals range from 12-2600 [@genereviews:NBK535148; @pmid:25168903]. Expansions are causative in approximately 70% of disease cases [@genereviews:NBK535148].",
-  "detection": null,
+  "detection": "Short-read sequencing methods are reportedly unable to detect these expansions due to repeat size and GC richness [@pmid:32735996]. While RP-PCR and Small pool PCR can detect expansions, sequence level resolution generally required long-read sequencing [@pmid:32735996].",
   "mechanism": "GoF",
   "mechanism_detail": "Sequestration of MBNL1 in RNA foci, similar to the mechanism underlying myotonic dystrophy-1 [@pmid:25593321]. Variation in RAN translation [@pmid:38467784].",
   "year": "2012 [@pmid:23185296]",
@@ -5003,7 +5003,7 @@
   "intermediate_max": null,
   "pathogenic_min": 1100,
   "pathogenic_max": 1100,
-  "motif_len": 3,
+  "motif_len": 5,
   "ref_copies": 18.8,
   "novel": "novel",
   "gard": ["16758"],

data/catalogs/STRchive-disease-loci.T2T-chm13.TRGT.bed

@@ -2,7 +2,7 @@ chr1	870158	870178	ID=HMNR7_VWA1;MOTIFS=AGCGGCGCGG,GGCGCGGAGC;STRUC=<TR>
 chr1	57245935	57245973	ID=SCA37_DAB1;MOTIFS=AAAAT,GAAAT,TGAAA;STRUC=<TR>
 chr1	94266544	94266567	ID=OPDM5_ABCD3;MOTIFS=CCG;STRUC=<TR>
 chr1	148519695	148519738	ID=NIID_NOTCH2NLC;MOTIFS=CGG;STRUC=<TR>
-chr1	154328121	154330802	ID=ADTKD_MUC1;MOTIFS=ACACCAGGCCGGCCCCGGGCTCCACCGCCCCCCCCAGCCCACGGTGTCACCTCGGCCCCGG,GGCTNNGGGNGCGGTGGAGCCCGGGGCNGGNCTGNTNTCCGGGGCCGAGGTGACANCNTG,ACACCAGGCCGGCCCCGGGCTCCACCGCCCCCCCAGCCCACGGTGTCACCTCGGCCCCGG;STRUC=<TR>
+chr1	154328121	154330802	ID=ADTKD_MUC1;MOTIFS=CCGGGGCCGAGGTGACACCGTGGGCTGGGGGGGGCGGTGGAGCCCGGGGCCGGCCTGGTGT,GGCTNNGGGNGCGGTGGAGCCCGGGGCNGGNCTGNTNTCCGGGGCCGAGGTGACANCNTG,CCGGGGCCGAGGTGACACCGTGGGCTGGGGGGGCGGTGGAGCCCGGGGCCGGCCTGGTGT;STRUC=<TR>
 chr1	155728131	155728159	ID=NME_NAXE;MOTIFS=CCGGG,GGGCC;STRUC=<TR>
 chr2	96703674	96703732	ID=FAME2_STARD7;MOTIFS=AAATG,AAAAT,TGAAA;STRUC=<TR>
 chr2	100563685	100563738	ID=FRA2A_AFF3;MOTIFS=CCG;STRUC=<TR>

data/catalogs/STRchive-disease-loci.T2T-chm13.atarva.bed

@@ -3,7 +3,7 @@ chr1	870158	870178	AGCGGCGCGG	10	HMNR7_VWA1
 chr1	57245970	57245973	GAAAT	5	SCA37_DAB1
 chr1	94266544	94266567	CCG	3	OPDM5_ABCD3
 chr1	148519695	148519738	CGG	3	NIID_NOTCH2NLC
-chr1	154328121	154330802	ACACCAGGCCGGCCCCGGGCTCCACCGCCCCCCCCAGCCCACGGTGTCACCTCGGCCCCGG	61	ADTKD_MUC1
+chr1	154328121	154330802	CCGGGGCCGAGGTGACACCGTGGGCTGGGGGGGGCGGTGGAGCCCGGGGCCGGCCTGGTGT	61	ADTKD_MUC1
 chr1	155728131	155728159	CCGGG	5	NME_NAXE
 chr2	96703674	96703677	AAATG	5	FAME2_STARD7
 chr2	100563685	100563738	CCG	3	FRA2A_AFF3

data/catalogs/STRchive-disease-loci.T2T-chm13.general.bed

@@ -3,7 +3,7 @@ chr1	870158	870178	HMNR7_VWA1	VWA1	GGCGCGGAGC	AGCGGCGCGG	1	AR	Neuronopathy, dist
 chr1	57245935	57245973	SCA37_DAB1	DAB1	AAAAT	TGAAA	31	AD	Spinocerebellar ataxia type 37
 chr1	94266544	94266567	OPDM5_ABCD3	ABCD3	CCG	CCG	118	AD	Oculopharyngodistal myopathy type 5
 chr1	148519695	148519738	NIID_NOTCH2NLC	NOTCH2NLC	CGG	CGG	66	AD	Neuronal intranuclear inclusion disease, Alzheimer disease and parkinsonism phenotype, Oculopharyngodistal myopathy (OPDM) type 3, hereditary essential tremor type 6
-chr1	154328121	154330802	ADTKD_MUC1	MUC1	GGCTNNGGGNGCGGTGGAGCCCGGGGCNGGNCTGNTNTCCGGGGCCGAGGTGACANCNTG	ACACCAGGCCGGCCCCGGGCTCCACCGCCCCCCCCAGCCCACGGTGTCACCTCGGCCCCGG	None	AD	Autosomal dominant tubulointerstitial kidney disease
+chr1	154328121	154330802	ADTKD_MUC1	MUC1	GGCTNNGGGNGCGGTGGAGCCCGGGGCNGGNCTGNTNTCCGGGGCCGAGGTGACANCNTG	CCGGGGCCGAGGTGACACCGTGGGCTGGGGGGGGCGGTGGAGCCCGGGGCCGGCCTGGTGT	None	AD	Autosomal dominant tubulointerstitial kidney disease
 chr1	155728131	155728159	NME_NAXE	NAXE	GGGCC	CCGGG	200	AR	NAXE-related mitochondrial encephalopathy
 chr2	96703674	96703732	FAME2_STARD7	STARD7	AAAAT	TGAAA	274	AD	Familial adult myoclonic epilepsy 2
 chr2	100563685	100563738	FRA2A_AFF3	AFF3	CCG	CCG	300	AD	Intellectual disability associated with fragile site FRA2A

data/catalogs/STRchive-disease-loci.T2T-chm13.longTR.bed

@@ -2,7 +2,7 @@ chr1	870159	870178	AGCGGCGCGG,GGCGCGGAGC	HMNR7_VWA1
 chr1	57245936	57245973	TGAAA,AAAAT	SCA37_DAB1
 chr1	94266545	94266567	CCG	OPDM5_ABCD3
 chr1	148519696	148519738	CGG	NIID_NOTCH2NLC
-chr1	154328122	154330802	ACACCAGGCCGGCCCCGGGCTCCACCGCCCCCCCCAGCCCACGGTGTCACCTCGGCCCCGG,ACACCAGGCCGGCCCCGGGCTCCACCGCCCCCCCAGCCCACGGTGTCACCTCGGCCCCGG,GGCTNNGGGNGCGGTGGAGCCCGGGGCNGGNCTGNTNTCCGGGGCCGAGGTGACANCNTG	ADTKD_MUC1
+chr1	154328122	154330802	CCGGGGCCGAGGTGACACCGTGGGCTGGGGGGGGCGGTGGAGCCCGGGGCCGGCCTGGTGT,CCGGGGCCGAGGTGACACCGTGGGCTGGGGGGGCGGTGGAGCCCGGGGCCGGCCTGGTGT,GGCTNNGGGNGCGGTGGAGCCCGGGGCNGGNCTGNTNTCCGGGGCCGAGGTGACANCNTG	ADTKD_MUC1
 chr1	155728132	155728159	CCGGG,GGGCC	NME_NAXE
 chr2	96703675	96703732	TGAAA,AAAAT	FAME2_STARD7
 chr2	100563686	100563738	CCG	FRA2A_AFF3

data/catalogs/STRchive-disease-loci.hg19.TRGT.bed

@@ -2,7 +2,7 @@ chr1	1371178	1371198	ID=HMNR7_VWA1;MOTIFS=AGCGGCGCGG,GGCGCGGAGC;STRUC=<TR>
 chr1	57832715	57832793	ID=SCA37_DAB1;MOTIFS=AAAAT,GAAAT,TGAAA;STRUC=<TR>
 chr1	94883977	94884000	ID=OPDM5_ABCD3;MOTIFS=CCG;STRUC=<TR>
 chr1	145209323	145209354	ID=NIID_NOTCH2NLC;MOTIFS=CGG;STRUC=<TR>
-chr1	155160981	155162030	ID=ADTKD_MUC1;MOTIFS=ACACCAGGCCGGCCCCGGGCTCCACCGCCCCCCCCAGCCCACGGTGTCACCTCGGCCCCGG,GGCTNNGGGNGCGGTGGAGCCCGGGGCNGGNCTGNTNTCCGGGGCCGAGGTGACANCNTG,ACACCAGGCCGGCCCCGGGCTCCACCGCCCCCCCAGCCCACGGTGTCACCTCGGCCCCGG;STRUC=<TR>
+chr1	155160981	155162030	ID=ADTKD_MUC1;MOTIFS=CCGGGGCCGAGGTGACACCGTGGGCTGGGGGGGGCGGTGGAGCCCGGGGCCGGCCTGGTGT,GGCTNNGGGNGCGGTGGAGCCCGGGGCNGGNCTGNTNTCCGGGGCCGAGGTGACANCNTG,CCGGGGCCGAGGTGACACCGTGGGCTGGGGGGGCGGTGGAGCCCGGGGCCGGCCTGGTGT;STRUC=<TR>
 chr1	156561557	156561575	ID=NME_NAXE;MOTIFS=CCGGG,GGGCC;STRUC=<TR>
 chr2	96862804	96862862	ID=FAME2_STARD7;MOTIFS=AAATG,AAAAT,TGAAA;STRUC=<TR>
 chr2	100721260	100721286	ID=FRA2A_AFF3;MOTIFS=CCG;STRUC=<TR>

data/catalogs/STRchive-disease-loci.hg19.atarva.bed

@@ -3,7 +3,7 @@ chr1	1371178	1371198	AGCGGCGCGG	10	HMNR7_VWA1
 chr1	57832750	57832793	GAAAT	5	SCA37_DAB1
 chr1	94883977	94884000	CCG	3	OPDM5_ABCD3
 chr1	145209323	145209354	CGG	3	NIID_NOTCH2NLC
-chr1	155160981	155162030	ACACCAGGCCGGCCCCGGGCTCCACCGCCCCCCCCAGCCCACGGTGTCACCTCGGCCCCGG	61	ADTKD_MUC1
+chr1	155160981	155162030	CCGGGGCCGAGGTGACACCGTGGGCTGGGGGGGGCGGTGGAGCCCGGGGCCGGCCTGGTGT	61	ADTKD_MUC1
 chr1	156561557	156561575	CCGGG	5	NME_NAXE
 chr2	96862804	96862807	AAATG	5	FAME2_STARD7
 chr2	100721260	100721286	CCG	3	FRA2A_AFF3

data/catalogs/STRchive-disease-loci.hg19.general.bed

@@ -3,7 +3,7 @@ chr1	1371178	1371198	HMNR7_VWA1	VWA1	GGCGCGGAGC	AGCGGCGCGG	1	AR	Neuronopathy, di
 chr1	57832715	57832793	SCA37_DAB1	DAB1	AAAAT	TGAAA	31	AD	Spinocerebellar ataxia type 37
 chr1	94883977	94884000	OPDM5_ABCD3	ABCD3	CCG	CCG	118	AD	Oculopharyngodistal myopathy type 5
 chr1	145209323	145209354	NIID_NOTCH2NLC	NOTCH2NLC	CGG	CGG	66	AD	Neuronal intranuclear inclusion disease, Alzheimer disease and parkinsonism phenotype, Oculopharyngodistal myopathy (OPDM) type 3, hereditary essential tremor type 6
-chr1	155160981	155162030	ADTKD_MUC1	MUC1	GGCTNNGGGNGCGGTGGAGCCCGGGGCNGGNCTGNTNTCCGGGGCCGAGGTGACANCNTG	ACACCAGGCCGGCCCCGGGCTCCACCGCCCCCCCCAGCCCACGGTGTCACCTCGGCCCCGG	None	AD	Autosomal dominant tubulointerstitial kidney disease
+chr1	155160981	155162030	ADTKD_MUC1	MUC1	GGCTNNGGGNGCGGTGGAGCCCGGGGCNGGNCTGNTNTCCGGGGCCGAGGTGACANCNTG	CCGGGGCCGAGGTGACACCGTGGGCTGGGGGGGGCGGTGGAGCCCGGGGCCGGCCTGGTGT	None	AD	Autosomal dominant tubulointerstitial kidney disease
 chr1	156561557	156561575	NME_NAXE	NAXE	GGGCC	CCGGG	200	AR	NAXE-related mitochondrial encephalopathy
 chr2	96862804	96862862	FAME2_STARD7	STARD7	AAAAT	TGAAA	274	AD	Familial adult myoclonic epilepsy 2
 chr2	100721260	100721286	FRA2A_AFF3	AFF3	CCG	CCG	300	AD	Intellectual disability associated with fragile site FRA2A

data/catalogs/STRchive-disease-loci.hg19.longTR.bed

@@ -2,7 +2,7 @@ chr1	1371179	1371198	AGCGGCGCGG,GGCGCGGAGC	HMNR7_VWA1
 chr1	57832716	57832793	TGAAA,AAAAT	SCA37_DAB1
 chr1	94883978	94884000	CCG	OPDM5_ABCD3
 chr1	145209324	145209354	CGG	NIID_NOTCH2NLC
-chr1	155160982	155162030	ACACCAGGCCGGCCCCGGGCTCCACCGCCCCCCCCAGCCCACGGTGTCACCTCGGCCCCGG,ACACCAGGCCGGCCCCGGGCTCCACCGCCCCCCCAGCCCACGGTGTCACCTCGGCCCCGG,GGCTNNGGGNGCGGTGGAGCCCGGGGCNGGNCTGNTNTCCGGGGCCGAGGTGACANCNTG	ADTKD_MUC1
+chr1	155160982	155162030	CCGGGGCCGAGGTGACACCGTGGGCTGGGGGGGGCGGTGGAGCCCGGGGCCGGCCTGGTGT,CCGGGGCCGAGGTGACACCGTGGGCTGGGGGGGCGGTGGAGCCCGGGGCCGGCCTGGTGT,GGCTNNGGGNGCGGTGGAGCCCGGGGCNGGNCTGNTNTCCGGGGCCGAGGTGACANCNTG	ADTKD_MUC1
 chr1	156561558	156561575	CCGGG,GGGCC	NME_NAXE
 chr2	96862805	96862862	TGAAA,AAAAT	FAME2_STARD7
 chr2	100721261	100721286	CCG	FRA2A_AFF3

data/catalogs/STRchive-disease-loci.hg38.TRGT.bed

@@ -2,7 +2,7 @@ chr1	1435798	1435818	ID=HMNR7_VWA1;MOTIFS=AGCGGCGCGG,GGCGCGGAGC;STRUC=<TR>
 chr1	57367043	57367121	ID=SCA37_DAB1;MOTIFS=AAAAT,GAAAT,TGAAA;STRUC=<TR>
 chr1	94418421	94418444	ID=OPDM5_ABCD3;MOTIFS=CCG;STRUC=<TR>
 chr1	149390802	149390842	ID=NIID_NOTCH2NLC;MOTIFS=CGG;STRUC=<TR>
-chr1	155188505	155192239	ID=ADTKD_MUC1;MOTIFS=ACACCAGGCCGGCCCCGGGCTCCACCGCCCCCCCCAGCCCACGGTGTCACCTCGGCCCCGG,GGCTNNGGGNGCGGTGGAGCCCGGGGCNGGNCTGNTNTCCGGGGCCGAGGTGACANCNTG,ACACCAGGCCGGCCCCGGGCTCCACCGCCCCCCCAGCCCACGGTGTCACCTCGGCCCCGG;STRUC=<TR>
+chr1	155188505	155192239	ID=ADTKD_MUC1;MOTIFS=CCGGGGCCGAGGTGACACCGTGGGCTGGGGGGGGCGGTGGAGCCCGGGGCCGGCCTGGTGT,GGCTNNGGGNGCGGTGGAGCCCGGGGCNGGNCTGNTNTCCGGGGCCGAGGTGACANCNTG,CCGGGGCCGAGGTGACACCGTGGGCTGGGGGGGCGGTGGAGCCCGGGGCCGGCCTGGTGT;STRUC=<TR>
 chr1	156591765	156591783	ID=NME_NAXE;MOTIFS=CCGGG,GGGCC;STRUC=<TR>
 chr2	96197066	96197124	ID=FAME2_STARD7;MOTIFS=AAATG,AAAAT,TGAAA;STRUC=<TR>
 chr2	100104798	100104824	ID=FRA2A_AFF3;MOTIFS=CCG;STRUC=<TR>

data/catalogs/STRchive-disease-loci.hg38.atarva.bed

@@ -3,7 +3,7 @@ chr1	1435798	1435818	AGCGGCGCGG	10	HMNR7_VWA1
 chr1	57367078	57367121	GAAAT	5	SCA37_DAB1
 chr1	94418421	94418444	CCG	3	OPDM5_ABCD3
 chr1	149390802	149390842	CGG	3	NIID_NOTCH2NLC
-chr1	155188505	155192239	ACACCAGGCCGGCCCCGGGCTCCACCGCCCCCCCCAGCCCACGGTGTCACCTCGGCCCCGG	61	ADTKD_MUC1
+chr1	155188505	155192239	CCGGGGCCGAGGTGACACCGTGGGCTGGGGGGGGCGGTGGAGCCCGGGGCCGGCCTGGTGT	61	ADTKD_MUC1
 chr1	156591765	156591783	CCGGG	5	NME_NAXE
 chr2	96197066	96197069	AAATG	5	FAME2_STARD7
 chr2	100104798	100104824	CCG	3	FRA2A_AFF3