The two haplotypes of the HG002v1.1 assembly are viewable in a UCSC assembly hub hosted by NHGRI within its T2T-genomes browser. The configuration files for the T2T Browser are stored on github here. The larger data files (linked to in the "Data URL" column below) are sources for the data tracks in the HG002 browser and are stored in the human-pangenomics AWS bucket. Their locations are listed below.
| Track name | Browser URL | Data URL | Description |
|---|---|---|---|
| GC Percent in 5-Base Windows | Browser | Data | GC Content of 5-base Windows |
| CpG Islands | Browser | Data | CpG Island Annotations |
| Microsatellite Repeats | Browser | Data | Microsatellite Repeat Content |
| v1.1 Assembly Issues (v4) | Browser | Data | V4 Low-Confidence Regions in HG002v1.1 |
| v1.1 Error k-mers | Browser | Data | Location of Merqury Error K-mers |
| HG002v1.1-HiFi-Revio-nucfreq | Browser | Data A, Data B | NucFreq B-Allele Frequencies for HiFi Revio Reads |
| HG002v1.1-ONT-UL-nucfreq | Browser | Data A, Data B | NucFreq B-Allele Frequencies for ONT Reads |
| Homopolymer Runs | Browser | Data | Locations of Homopolymers at Least 10bp in Length |
| Chains to v1.0.1 | Browser | Data | Chain Files from HG002v1.1 to v1.0.1 |
| RepeatMasker Elements | Browser | Data | RepeatMasker Tracks from UConn |
| Subtelomeric Repeats | Browser | Data | Subtelomeric Repeats from Old Dominion U |
| SEDEF Segmental Duplications | Browser | Data | Segmental Duplications from UWash |
| Centromeric Satellite Annotations | Browser | Data | Human Centromere Satellite Annotations from UCSC |
| Liftoff Gene Annotations | Browser | Data | LiftOff of RefSeq v110 Genes from CHM13 |
| Kinnex Iso-seq Alignments | Browser | Data | Kinnex Iso-seq Alignments October 2024 |
| MAS-seq Alignments | Browser | Data | MAS-Seq Single Cell Alignments May 2023 |
| Methylation Calls | Browser | Data | ONT 5mC CpG (Guppy 6.3.8) Calls |
| Fiber-seq FIRE Tracks | Browser | Data | Fiber-seq Inferred Regulatory Elements |
| HG002 Heterozygous Sites | Browser | Data | Discrepancies in alignments of MAT and PAT autosomes |
| HG002 Heterozygosity | Browser | Data | Heatmap of HG002 heterozygosity in windows of 20 kb |
| Chain to Alternate HG002v1.1 Haplotype | Browser | Data | Chain File of Alignments from Mat to Pat Haplotype and Back |
| Non-synteny With Other References | Browser | Data | Non-syntenic regions wrt. other references |
| Synteny With Other References | Browser | Data | Syntenic regions wrt. other references |