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Configure Tracks on UCSC Genome Browser: CHM13 Homo sapiens T2T CHM13 (v1.1) (t2t-chm13-v1.1)
  Tracks:    Groups:
Control track and group visibility more selectively below.
-   WSSD CN (HPRC)    
WSSD CN WSSD copy number estimates
-   Mapping and Assembly    
Base Position Chromosome position in bases. (Clicks here zoom in 3x)
Validation Validation of T2T assembly
     Issues     Issues from read low-coverage
     HiFi 21-mers     HiFi 21-mers generated with Merfin
     Illumina 21-mers     Illumina 21-mers generated with Merfin
     HiFi coverage     HiFi read coverage
     ONT coverage     ONT read coverage
GC Percent GC Percent in 5-Base Windows
Restr Enzymes Restriction Enzymes from REBASE
Short Match Perfect Matches to Short Sequence ()
-   Centromeres and Telomeres    
CenSat Annotation Centromeric Satellite Annotation
New Satellites New Satellites Monomers Arrays
ASat HOR Annotation of ASat HOR monomers (T2T CHM13 v1.1, HMMs 170921)
ASat SF Annotation of ASat monomers into SF-classes (T2T CHM13 v1.1, HMMs 170921)
ASat strand Annotation of ASat strand orientation (T2T CHM13 v1.1, HMMs 170921)
ASat StV Structural variants in active HORs (T2T CHM13 v1.1, 231021)
ASat shared HORs Annotation of ASat double (13/21 and 14/22) and triple (1/5/19) HORs into chromosome-specific subtypes (T2T CHM13 v1.1, 231021)
-   Genes    
CAT Genes + LiftOff V4 CAT Gene + LiftOff Annotations V4
GENCODE BLAT BLAT of GENCODE RNAs
LiftOff Genes LiftOff Genes Annotations based on GENCODE (from UW)
-   Transcription    
PROseq_bt2-default_kmerFilt CHM13 PROseq Bowtie2 default mapped (chm13v1.1) and unique genome-wide kmer filtering Stranded and notStranded
PROseq_bt2-k100_kmerFilt CHM13 PROseq Bowtie2 k100 mapped (chm13v1.1) and unique genome-wide kmer filtering Stranded and notStranded
RNAseq default CHM13 RNAseq Bowtie2 default mapped (chm13v1.1) and unique genome-wide kmer filtering
-   Regulation    
CpG Islands CpG Islands (Islands < 300 Bases are Light Green)
-   Comparative Genomics    
Cactus Cactus Alignment Tracks
Cactus (simplified) Cactus Alignment Tracks (simplified)
     hg38 Cactus Chained     hg38 Cactus Chained Alignments
     hg38 Cactus     hg38 Cactus Alignments not chained
     hg38 Cactus Lifted     hg38 Cactus Alignments Lifted from V1.0
GRCh38 LASTZ GRCh38 Primary Assembly LASTZ Alignments
GRCh38 Synteny GRCh38 Cactus Synteny
GRCH38 non-syntenic GRCh38 non-syntenic
-   Variation    
RepeatMasker Repeating Elements by RepeatMasker
Simple Repeats Simple Tandem Repeats by TRF
Composite Repeats Composite Repeats
SEDEF Segmental Dups Segmental Duplications