Description

These track shows putative unique regions of T2T CHM13 relative to GRCh38 based on various methods. Also include is alignments of unplaced sequence in GRCh38.

Methods

Base-wise negation of alignment chains using featureBits:

• GRCh38 LASTZ Liftover Unaligned Regions - using only LASTZ liftover changes
• GRCh38 Primary LASTZ Liftover Unaligned Regions - using only GRCh38 primary chromosomes, excluding chrY.
• GRCh38 Cactus Unaligned Regions - using Cactus alignments
• GRCh38 Primary Cactus Unaligned Regions - using only GRCh38 primary chromosomes, excluding chrY.
• GRCh38 unplaced aligned with Cactus - unplaced/random sequences in T2T assembly aligned with Cactus
• GRCh38 unplaced aligned with minimap - unplaced/random sequences in T2T assembly aligned with minimap2

Display Conventions and Configuration

Data access

Release history

1. 2020-09-06 - t2tChm13_20200727

Contacts

• Mark Diekhans <markd@ucsc.edu>

Credits

Chain/Net:

Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784

Lastz:

Harris RS. Improved pairwise alignment of genomic DNA. Ph.D. Thesis. Pennsylvania State University, USA. 2007.

Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961