198c9b8daecc44fbda6a6494c566c723920f030a
lrnassar
Wed Mar 11 18:25:21 2026 -0700
Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html
index 33d8b77a519..f86cda14dbd 100755
--- src/hg/htdocs/goldenPath/newsarch.html
+++ src/hg/htdocs/goldenPath/newsarch.html
@@ -138,31 +138,31 @@
The JASPAR database is a joint effort among several labs (please see the latest
JASPAR paper). Binding site
predictions and UCSC tracks were computed by the
CBGR team at NCMBM using code developed at
the Wasserman Lab. We would like to thank Luis Nassar and Gerardo Perez for their efforts on this
release.
Feb. 09, 2026 Phased variants track for human (hg38 and hg19)
We are pleased to announce the release of the Phased Variants container track for
hg38/GRCh38
-and hg19/GRCh19.
+and hg19/GRCh37.
This new track brings together
phased individual-level genotype data from four projects: Human Diversity Genome Project,
Simons Genome Diversity Project, gnomad's HGDP+1000 Genomes callset, and the Mexico Biobank.
The Phased Variants track includes the following
subtracks:
-
Mexico Biobank (MXB) 6k Array
–
Phased alleles from array genotyping of 6,011 individuals sampled across all 32 states of
@@ -585,31 +585,31 @@
We would like to thank the European Variation
Archive for making these data publicly available. We would also like to thank Gerardo Perez, Luis Nassar,
and Angie Hinrichs for the creation and release of these tracks.
Dec. 15, 2025 Ancient Hominids track for hg38
We are happy to announce the release of the
Ancient Hominids track
featuring data from Archaic Sequence Hub (ArcSeqHub). This track shows variants
identified by ArcSeqHub's remapping of high-quality Altai Neanderthal and
Denisovan genomes onto the hg38/GRCh38 genome. Variants are divided into two subtracks,
-one for Denisovian variants and another for Neanderthal variants.
+one for Denisovan variants and another for Neanderthal variants.
UCSC has removed those positions from the VCF without an alternate allele to show only
variants that are present in the ancient genomes.
We would like to thank the ArcSeqHub authors for making the data available.
We would also like to thank Maximilian Haeussler and Matthew Speir for the
creation and release of this track.
Dec. 03, 2025 New gnomAD Missense Deleteriousness Prediction by Constraint (MPC) track for hg19
We are happy to announce the release of the
@@ -778,31 +778,31 @@
alt="Panmask Easy 151b Regions track for the BRCA1 exon 19" width='75%'>
The pm151 regions are used to filter spurious variant calls in centromeres, long repeats, and
other genomic regions where short-read mapping is often problematic. They cover 88.2% of hg38,
92.2% of coding regions, and 96.3% of ClinVar pathogenic variants. The track can be used to filter
variant calls for clinical or research human samples. It shows regions that are easy to sequence,
rather than those that are problematic. The data was derived from the HPRC assemblies, and this
track presents the 151b-easy panmask set.
We would like to thank
Heng Li's group
at Harvard Medical School for making this data available. We
would also like to thank Max Haeussler and Gerardo Perez for their efforts on this release.
-Sep. 24, 2025 CoLoRSdb small and structure variants for hg38 and hs1
+Sep. 24, 2025 CoLoRSdb small and structural variants for hg38 and hs1
We are excited to announce the release of the CoLoRSdb Small and Structural Variant tracks for the
human assemblies
GRCh38/hg38 and
CHM13/hs1. These tracks provide a comprehensive catalog of genetic variation
discovered through long-read whole genome sequencing, contributed by the international
Consortium of Long Read Sequencing (CoLoRS). The
small variant tracks (DeepVariant + GLnexus) contain single nucleotide polymorphisms (SNPs) and
short indels, while the structural variant tracks (pbsv + Jasmine) display larger events including
insertions, deletions, and inversions. Long-read sequencing technology improves sensitivity in
repetitive regions and provides more precise breakpoint resolution than short-read approaches,
enabling accurate visualization of complex loci in the Genome Browser.
Each track includes allele frequency and sample count annotations, with additional filtering options
@@ -971,33 +971,33 @@
Australia PanelApp for providing guidance. We would also like to thank Beagan Nguy, Lou Nassar, and
Gerardo Perez of the Genome Browser team for the development and release of this track.
Aug. 01, 2025 PubTator Variants track for human, hg38 and hg19
We are excited to announce the release of the PubTator Variants track for human assemblies,
hg38 and
hg19. These tracks were created
using PubTator3 data and are freely accessible to the research community. PubTator3 is a web-based
system that offers a comprehensive set of features and tools that allow researchers to
explore biomedical literature for knowledge discovery. It uses
text mining and AI techniques to annotate and unify bio-entities and their
corresponding relations for semantic and relation searches.
-We would like to thank the PubTator 3.0 authors for generating and making the data publically
+We would like to thank the PubTator 3.0 authors for generating and making the data publicly
available. We would also like to thank Max Haeussler and Johannes Birgmeier for creating the tracks,
-and Jairo Navarro the release of the tracks.
+and Jairo Navarro for the release of the tracks.
July 31, 2025 New bedMethyl and bigMethyl track type
We are excited to announce support for a new track format for visualizing DNA
methylation data:
bedMethyl.
This format, and its binary-indexed counterpart, bigMethyl, is designed to
represent methylation calls from bisulfite sequencing or similar methods at single-base resolution
across the genome.
The bedMethyl format extends the standard
BED 9 format to include additional fields
@@ -1071,31 +1071,31 @@
for more information and interpretation guidelines.
We would like to thank the authors of MutScore and M-CAP for creating and providing these data. We would also
like to thank Max Haeussler and Lou Nassar for the development and release of these tracks.
July 15, 2025 ENCODE4 Long-read RNA-seq Transcripts
We are pleased to announce the release of the ENCODE4 long-read RNA-seq transcripts track for
hg38 and
mm10.
-This track annotates trancripts using numerical triplets representing the
+This track annotates transcripts using numerical triplets representing the
identity of the start site, exon junction chain, and transcript end site of
each transcript. This is presented alongside sample enrichment information to
show how promoter selection, splice pattern, and 3’ processing are deployed
across human tissues.
Transcripts are labeled with triplets, e.g. [1,1,1] or [1,1,3] or [2,1,3].
If transcripts share a number in any of the positions that means they share
that feature, e.g. sharing a 8 in the second position but different numbers in
the others means those two transcripts share the same set of exons, but different
@@ -2592,56 +2592,56 @@
These variants are classified by EVA into one of the following sequence ontology terms:
- substitution —
A single nucleotide in the reference is replaced by another, alternate allele
- deletion —
One or more nucleotides are deleted. The representation in the database is to
display one additional nucleotide in both the Reference field (Ref) and the
Alternate Allele field (Alt). E.g. a variant that is a deletion of an A
- maybe be represented as Ref = GA and Alt = G.
+ may be represented as Ref = GA and Alt = G.
- insertion —
One or more nucleotides are inserted. The representation in the database is to
display one additional nucleotide in both the Reference field (Ref) and the
Alternate Allele field (Alt). E.g. a variant that is an insertion of a T may
be represented as Ref = G and Alt = GT
- delins —
Similar to a tandem repeat, in that the runs of Ref and Alt Alleles are of
different length, except that there is more than one type of nucleotide,
e.g., Ref = CCAAAAACAAAAACA, Alt = ACAAAAAC.
- multipleNucleotideVariant —
More than one nucleotide is substituted by an equal number of different
nucleotides, e.g., Ref = AA, Alt = GC.
- sequence alteration —
A parent term meant to signify a deviation from another sequence. Can be
assigned to variants that have not been characterized yet.
The variants have also been annotated with our Variant
Annotation Integrator tool with functional classes such as synonymous variant,
missense variant, stop gained, etc. For additional details on the track colors,
as well as the filters and metadata on each variant, see the track description page.
We would like to thank the European Variation
-Archive for making these data publically available. We would also like to thank Luis Nassar, Chris Lee,
+Archive for making these data publicly available. We would also like to thank Luis Nassar, Chris Lee,
and Angie Hinrichs for the creation and release of these tracks.
Jul. 12, 2024 First update to hg19's UCSC Genes track since 2013
The UCSC Genome Browser is getting ready to update hg19's UCSC Genes dataset for the first time
since 2013. In this update, the UCSC Genes track will now use GENCODE v45 gene models lifted to hg19
and replace the old UCSC transcript IDs with the official GENCODE IDs.
The anticipated release date for this update is July 31, 2024.
As an example of what to expect, here are some GENCODE IDs that will replace the UCSC IDs in the
@@ -3233,62 +3233,62 @@
target="_blank">hg38,
hg19
mm39,
mm10,
mm9
The VISTA Enhancers track contains potential enhancers whose activity was experimentally validated
in transgenic mice. Most of these non-coding elements were selected for testing based on their
extreme conservation in other vertebrates or epigenomic evidence (ChIP-Seq) of putative enhancer
marks. The goal of VISTA Enhancers project is to identify distant-acting transcriptional enhancers
-in the human and mouse genomes. More information about can be found on the
+in the human and mouse genomes. More information can be found on the
VISTA Enhancer Browser website.
We would like to thank the Lawrence Berkeley National Laboratory and the VISTA Enhancer team for
providing this data. We would also like to thank Gerardo Perez and Jairo Navarro for the creation
and release of these tracks.
Nov. 30, 2023 Support for previous RefSeq transcripts while searching on hg38
Have you ever found a variant in a paper and searched for it on the Genome Browser only
to receive an error that the sequence cannot be found? Or perhaps looked up a familiar
NM_ identifier and suddenly found no results?
We are pleased to share that we now have support for searching previous RefSeq
transcript versions on hg38. This support works for both NM_ accessions
and HGVS
searching as demonstrated below:
Searching for the latest transcript which always worked:
-Searching for a previous version that now works::
+Searching for a previous version that now works:
We thank NCBI and Terence
Murphy for creating the archive of deprecated transcripts that allows this feature
to work. We would also like to thank the users who wrote requesting the feature
allowing us to prioritize it effectively. Finally, we would like to thank Chris Lee,
Max Haeussler, Gerardo Perez, and Lou Nassar for developing and testing this feature.
@@ -3439,50 +3439,50 @@
target="_blank">(danRer11)
Variants are classified by EVA into one of the following sequence ontology terms:
- substitution —
A single nucleotide in the reference is replaced by another, alternate allele
- deletion —
One or more nucleotides is deleted. The representation in the database is to
display one additional nucleotide in both the Reference field (Ref) and the
Alternate Allele field (Alt). E.g. a variant that is a deletion of an A
- maybe be represented as Ref = GA and Alt = G.
+ may be represented as Ref = GA and Alt = G.
- insertion —
One or more nucleotides is inserted. The representation in the database is to
display one additional nucleotide in both the Reference field (Ref) and the
Alternate Allele field (Alt). E.g. a variant that is an insertion of a T maybe
be represented as Ref = G and Alt = GT
- delins —
Similar to tandemRepeat, in that the runs of Ref and Alt Alleles are of
different length, except that there is more than one type of nucleotide,
e.g., Ref = CCAAAAACAAAAACA, Alt = ACAAAAAC.
- multipleNucleotideVariant —
More than one nucleotide is substituted by an equal number of different
nucleotides, e.g., Ref = AA, Alt = GC.
- sequence alteration —
A parent term meant to signify a deviation from another sequence. Can be
assigned to variants that have not been characterized yet.
We would like to thank the European Variation
-Archive making this data publically available. We would also like to thank Luis Nassar and Jairo
+Archive making this data publicly available. We would also like to thank Luis Nassar and Jairo
Navarro for the creation and release of these tracks.
Sep. 15, 2023 New COSMIC Track for hg38
We are pleased to announce the release of the new
COSMIC track
for hg38. The
Catalogue Of Somatic Mutations In Cancer
(COSMIC) is an online database of expert manually curated somatic mutation information relating to
human cancers. This new track displays data from the
COSMIC v98 release,
which consists of 410,000 new genomic variants, 585,000 new coding mutations, 290,000 non-coding
@@ -3784,50 +3784,50 @@
target="_blank">(danRer11)
Variants are classified by EVA into one of the following sequence ontology terms:
- substitution —
A single nucleotide in the reference is replaced by another, alternate allele
- deletion —
One or more nucleotides is deleted. The representation in the database is to
display one additional nucleotide in both the Reference field (Ref) and the
Alternate Allele field (Alt). E.g. a variant that is a deletion of an A
- maybe be represented as Ref = GA and Alt = G.
+ may be represented as Ref = GA and Alt = G.
- insertion —
One or more nucleotides is inserted. The representation in the database is to
display one additional nucleotide in both the Reference field (Ref) and the
Alternate Allele field (Alt). E.g. a variant that is an insertion of a T maybe
be represented as Ref = G and Alt = GT
- delins —
Similar to tandemRepeat, in that the runs of Ref and Alt Alleles are of
different length, except that there is more than one type of nucleotide,
e.g., Ref = CCAAAAACAAAAACA, Alt = ACAAAAAC.
- multipleNucleotideVariant —
More than one nucleotide is substituted by an equal number of different
nucleotides, e.g., Ref = AA, Alt = GC.
- sequence alteration —
A parent term meant to signify a deviation from another sequence. Can be
assigned to variants that have not been characterized yet.
We would like to thank the European Variation
-Archive making this data publically available. We would also like to thank Luis Nassar and Jairo
+Archive making this data publicly available. We would also like to thank Luis Nassar and Jairo
Navarro for the creation and release of these tracks.
Apr. 24, 2023 New DGV Gold Standard track for hg38
We are pleased to announce the addition of the new
DGV Gold Standard track
for hg38. The track displays curated variants from a selected number of studies in the
Database of Genomic Variants (DGV)
with a criterion that requires a variant to be found in at least two different studies and found in
at least two different samples. More information on this track can be found on the
track description page.
@@ -5980,31 +5980,31 @@
SARS-CoV-2 browser, the updated
Variants of Concern (VOC) track. This data track
includes amino acid and nucleotide annotations for 10 different COVID variants,
including the Delta and Mu variants, mapped along the SARS-CoV-2 reference genome.
These variants are
classified by the WHO into several categories: Variants of Concern (VOC),
Variants of Interest (VOI), and Variants under Investigation (VUM). These tracks help
provide a more clear understanding of the mutations that comprise each named variant.
This track's items also include links to
Outbreak.info, providing geographic distibutions for each variant.
-The underlying data is publically accessible and compatible with many analysis tools, including
+The underlying data is publicly accessible and compatible with many analysis tools, including
our Table Browser,
Data Integrator,
and JSON API. More information on this track
can be found on the
Variants of Concern (VOC) track description page.
Oct. 18, 2021 Addition of GRCh38 patch 13 sequences to hg38
We are pleased to announce the addition of GRCh38 patch release 13 to the
hg38 assembly. hg38 has been updated with patches
since its release in 2013. The GRC patch releases do not change any previously existing
sequences; they simply add new sequences for fix patches or alternate haplotypes that correspond
to specific regions of the main chromosome sequences. For most users, the patches are unlikely
to make a difference and may complicate the analysis as they introduce more duplication.
