These tracks show regions of this target genome (Human - Dec. 2013 (GRCh38/hg38) - GRCh38 Genome Reference Consortium Human Reference 38 (GCA_000001405.15)) that have alignments to other query genome assemblies, aligned with lastz or minimap2. The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns.
Query genome assemblies aligned to this target genome assembly:
The minimap2 alignments are intended for pairs of very similar same-species/same-individual assemblies, for example the haplotypes of a diploid assembly, or closely related strain assemblies, where minimap2's splice-free asm5/asm10/asm20 presets do a better job with the larger indels and structural differences seen between such assemblies than lastz's general-purpose scoring does.
| common name | assembly | method | chains | syntenic | reciprocal best | lift over | quickLift (% of query) |
|---|---|---|---|---|---|---|---|
| Human | hs1 | lastz | 92.821 | 92.734 | 87.633 | 92.035 | |
| Human | hs1 | lastz (swap) | 92.857 | 92.063 | |||
| Human | hs1 | minimap2 (swap) | 94.375 | 94.372 | 92.895 | ||
| Human | hs1 | minimap2 | 92.241 | 92.239 | 93.016 |
The chain tracks show alignments of the query genome assemblies to the target genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both query and target genomes simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species.
The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the query assembly or an insertion in the target assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the target genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes.
In the "pack" and "full" display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment.
The types of chains measured in the table above:
A (swap) alignment was made with the query as the target genome, and then swapped to this target genome coordinates.
The lastz alignments also have a net track, which shows the best query chain for every part of the target genome.
By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the "off" button next to: Color track based on chromosome.
To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome.
In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth.
Individual items in the display are categorized as one of four types (other than gap):
The query genome was aligned to the target genome with lastz. The resulting alignments were converted into PSL format and fed into axtChain, which organizes all alignments between a single query chromosome and a single target chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks.
The chains were sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. The syntenic and lift over chains were extracted from the net with netChainSubset.
| assembly | method | lastz version | lastz settings | axtChain minScore | axtChain linearGap |
|---|---|---|---|---|---|
| hs1 | lastz | 1.04.03 | T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q | 5000 | medium |
The query genome was aligned to the target genome with minimap2, one job per target sequence against the whole query genome. The minimap2 alignment preset was selected from the mash distance between the two assemblies. The resulting PAF alignments were converted into PSL format using the pafToPsl program, and fed into axtChain to construct the chains in the same way as for the lastz alignments. The chain was placed with chainNet, and the program netChainSubset was used to extract the best/longest syntenic part of that net back out of the chain, giving the lift over chain.
| assembly | method | minimap2 version | mash distance | preset | command |
|---|---|---|---|---|---|
| hs1 | minimap2 | 2.31-r1302 | 0.000984402 | asm5 | minimap2 -cx asm5 -N 5 -p 0.8 -t 8 target.fa query.fa > out.paf |
The lift over chain files are available in the liftOver directory of our download server, for use with the liftOver command line tool, available from the utilities download directory. The complete lastz chain and net files are in the vsHs1 download directory.
lastz was developed by Robert Harris, Pennsylvania State University.
minimap2 was developed by Heng Li.
The mash program, used to estimate the divergence between the target and query assemblies and automatically select the minimap2 alignment preset, was developed by Brian Ondov, Todd Treangen, and colleagues at the National Biodefense Analysis and Countermeasures Center and the University of Maryland.
The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.
The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent.
The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent.
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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
Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018 Sep 15;34(18):3094-3100. PMID: 29750242; PMC: PMC6137996
Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol. 2016 Jun 20;17(1):132. PMID: 27323842; PMC: PMC4915045
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