bac95a147f49cd331052e597006e04b3deee40fc max Wed Apr 22 10:43:20 2026 -0700 lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258 diff --git src/hg/makeDb/trackDb/human/tommoJpSv.html src/hg/makeDb/trackDb/human/tommoJpSv.html index 10c3117337e..91d181cf572 100644 --- src/hg/makeDb/trackDb/human/tommoJpSv.html +++ src/hg/makeDb/trackDb/human/tommoJpSv.html @@ -1,103 +1,132 @@

Description

This track shows structural variants (SVs) identified by Oxford Nanopore long-read sequencing of 333 Japanese individuals from the Tohoku Medical Megabank (ToMMo) project. The 333 individuals form 111 parent-offspring trios, enabling Mendelian consistency checks on the SV calls. Activated T lymphocytes were used as a source of high-molecular-weight DNA for nanopore sequencing at a median coverage of 22.2x with an N50 read length of 25.8 kb.

The dataset contains 74,201 SVs (37,981 deletions and 36,220 insertions), merged across individuals using SURVIVOR v1.0.6. Over 95% of the SVs are concordant with Mendelian inheritance in the trio families.

Display Conventions and Configuration

Items are colored by SV type:

Deletions (DEL) - red
Insertions (INS) - blue

Filters are available for SV type, SV length, and allele frequency. For insertions, the item is placed at the insertion site with a width of 1 bp; for deletions, the item spans the deleted region.

The detail page for each item shows:

Allele Frequency: fraction of alleles carrying this variant (based on 444 alleles from 222 unrelated parents)
Allele Count / Allele Number: number of variant alleles and total alleles genotyped
Mendelian Error Rate: fraction of trio families showing inheritance errors for this variant
Families with Errors / Families Genotyped: number of families with Mendelian errors and total families with complete genotype calls

Methods

Otsuki et al. 2022 extracted high-molecular-weight genomic DNA from activated T lymphocytes of 333 individuals (111 parent-offspring trios) from the Tohoku Medical Megabank (ToMMo) BirThree cohort and performed Oxford Nanopore whole-genome sequencing on PromethION instruments with R9.4.1 flow cells (SQK-LSK109 libraries, Guppy v4.2.2 high-accuracy base-calling). After QC, median per-sample sequencing coverage was 22.2x with a read N50 of 25.8 kb. Reads were aligned to GRCh38 with LRA, SVs were called per sample with CuteSV v1.0.9 (-min_sv_length 50), and per-sample calls were merged with SURVIVOR v1.0.6 (1000 bp distance, type-match, no length-match) into a nonredundant panel of 74,201 autosomal SVs (37,981 deletions and 36,220 insertions). Over 95% of the SVs were concordant with Mendelian inheritance in the 111 trio families; allele frequencies in this track are computed from the 222 unrelated parents to avoid double-counting.

The site-only VCF tommo-JSV1-20211208-GRCh38-without-genotype-count.vcf.gz -was downloaded from the jMorp JSV1 dataset page, - +was downloaded from the jMorp JSV1 download page, + tommo-jsv1-20211208-af.

The step-by-step build commands (download, format conversion, bigBed build) are recorded in the UCSC makeDoc for this track container: doc/hg38/lrSv.txt. The conversion scripts and autoSql schemas live in makeDb/scripts/lrSv.

Data Access

Source data is available from the -jMorp downloads page (ToMMo Japanese Multi Omics Reference Panel). +tommo-jsv1-20211208-af download page on the jMorp +portal (ToMMo Japanese Multi Omics Reference Panel). +

+ +

Conditions of Use

+The information in the ToMMo jMorp database is provided only to persons +who agree to jMorp's + +Conditions of Use. By using these data, you are deemed to have read +and understood those conditions and to agree to the following obligations: +

Do not attempt to identify or contact any person who provided specimens +used to construct the information.
Request permission from dist [AT] megabank [DOT] tohoku [DOT] ac [DOT] jp +prior to using the data for commercial purposes.
Notify dist [AT] megabank [DOT] tohoku [DOT] ac [DOT] jp when providing +re-edited data to any third party.
Cite the jMorp paper in publications that report analyses based on +these data: Tadaka S, Kawashima J, Hishinuma E, et al., +“jMorp: Japanese Multi-Omics Reference Panel update report 2023”, +Nucleic Acids Research, 2023 Nov 1, +doi:10.1093/nar/gkad978; +please also refer to the per-dataset citation notes linked from that page.

+The copyright in the information and the database is owned by ToMMo. If a +dataset-specific contact or Data Transfer Agreement is attached to a given +dataset, those should be followed in preference to this generic page. +Questions should be directed to +tommo-jmorp [AT] grp [DOT] tohoku [DOT] ac [DOT] jp.

Credits

Thanks to the Tohoku Medical Megabank Organization for making their structural variant calls publicly available through the jMorp data portal.

References

Otsuki A, Okamura Y, Ishida N, Tadaka S, Takayama J, Kumada K, Kawashima J, Taguchi K, Minegishi N, Kuriyama S et al. Construction of a trio-based structural variation panel utilizing activated T lymphocytes and long- read sequencing technology. Commun Biol. 2022 Sep 20;5(1):991. PMID: 36127505; PMC: PMC9489684