Description

This track shows multiple alignments of 11 primate assemblies on this target/reference assembly (pygmy chimpanzee - 2024-01-08 - National Human Genome Research Institute, National Institutes of Health).

The multiple alignments were generated using multiz and other tools in the UCSC/Penn State Bioinformatics comparative genomics alignment pipeline.

count	alignment percent	assembly and browser link	maf file type	common name/assembly date assembly submitter
01	89.082	GCA_028858775.2	syntenic net	chimpanzee/2024-01-08/NHGRI/NIH
02	88.572	hg38	syntenic net	Human/hg38/Dec. 2013 (GRCh38/hg38)/GRCh38 Genome Reference Consortium Human Reference 38 (GCA_000001405.15)
03	88.326	hs1	syntenic net	Human/hs1/Jan. 2022 (T2T CHM13v2.0/hs1)/Telomere to telomere (T2T) assembly of haploid CHM13 + chrY (GCA_009914755.4)
04	87.136	GCA_029281585.2	syntenic net	western lowland gorilla/2024-01-08/NHGRI/NIH
05	85.986	GCA_028885655.2	syntenic net	Sumatran orangutan/2024-01-05/NHGRI/NIH
06	85.961	GCA_028885625.2	syntenic net	Bornean orangutan/2024-01-08/NHGRI/NIH
07	81.986	GCA_028878055.2	syntenic net	siamang/2024-01-05/NHGRI/NIH
08	65.027	GCF_011100555.1	maf net	white-tufted-ear marmoset/2021-04-28/VGP
09	30.829	GCF_020740605.2	maf net	Ring-tailed lemur/2021-11-04/VGP
10	14.512	GCF_027406575.1	maf net	slow loris/2022-12-28/VGP

Alignments identity

showing percent identity, how much of the target is matched by the query

chains	syntenic	reciprocal best	lift over	common name	assembly
89.082	88.890	87.894	89.067	chimpanzee	GCA_028858775.2
88.572	87.825	85.338	88.499	Human	hg38
88.326	87.723	85.551	88.283	Human	hs1
87.136	86.589	84.821	87.108	western lowland gorilla	GCA_029281585.2
85.986	85.070	82.236	85.926	Sumatran orangutan	GCA_028885655.2
85.961	85.004	82.225	85.902	Bornean orangutan	GCA_028885625.2
81.986	80.853	77.796	81.914	siamang	GCA_028878055.2
65.027	63.749	61.765	64.946	white-tufted-ear marmoset	GCF_011100555.1
30.829	30.020	29.460	30.795	Ring-tailed lemur	GCF_020740605.2
14.512	13.587	13.843	14.488	slow loris	GCF_027406575.1

Display Conventions and Configuration

In full and pack display modes, conservation scores are displayed as a wiggle track (histogram) in which the height reflects the size of the score. The conservation wiggles can be configured in a variety of ways to highlight different aspects of the displayed information. Click the Graph configuration help link for an explanation of the configuration options.

Methods

Pairwise alignments of each species to the pygmy chimpanzee//hive/data/genomes/asmHubs/genbankBuild/GCA/029/289/425/GCA_029289425.2_NHGRI_mPanPan1-v2.0_pri/html/GCA_029289425.2_NHGRI_mPanPan1-v2.0_pri.names.tab/GCA_029289425.2/2024-01-08 genome are displayed below the conservation histogram as a grayscale density plot (in pack mode) or as a wiggle (in full mode) that indicates alignment quality. In dense display mode, conservation is shown in grayscale using darker values to indicate higher levels of overall conservation as scored by phastCons.

Checkboxes on the track configuration page allow selection of the species to include in the pairwise display. Note that excluding species from the pairwise display does not alter the the conservation score display.

To view detailed information about the alignments at a specific position, zoom the display in to 30,000 or fewer bases, then click on the alignment.

Credits

This track was created using the following programs:

• Alignment tools: lastz (formerly blastz) and multiz by Minmei Hou, Scott Schwartz and Webb Miller of the Penn State Bioinformatics Group
• Chaining and Netting: axtChain, chainNet by Jim Kent at UCSC
• Conservation scoring: phastCons, phyloP, phyloFit, tree_doctor, msa_view and other programs in PHAST by Adam Siepel at Cold Spring Harbor Laboratory (original development done at the Haussler lab at UCSC).
• MAF Annotation tools: mafAddIRows by Brian Raney, UCSC; mafAddQRows by Richard Burhans, Penn State; genePredToMafFrames by Mark Diekhans, UCSC
• Tree image generator: phyloPng by Galt Barber, UCSC
• Conservation track display: Kate Rosenbloom, Hiram Clawson (wiggle display), and Brian Raney (gap annotation and codon framing) at UCSC

References

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

PhyloP:

Cooper GM, Stone EA, Asimenos G, NISC Comparative Sequencing Program., Green ED, Batzoglou S, Sidow A. Distribution and intensity of constraint in mammalian genomic sequence. Genome Res. 2005 Jul;15(7):901-13. PMID: 15965027; PMC: PMC1172034; DOI: 10.1101/gr.3577405

Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 2010 Jan;20(1):110-21. PMID: 19858363; PMC: PMC2798823

Siepel A, Haussler D. Phylogenetic Hidden Markov Models. In: Nielsen R, editor. Statistical Methods in Molecular Evolution. New York: Springer; 2005. pp. 325-351. DOI: 10.1007/0-387-27733-1_12

Siepel A, Pollard KS, and Haussler D. New methods for detecting lineage-specific selection. In Proceedings of the 10th International Conference on Research in Computational Molecular Biology (RECOMB 2006), pp. 190-205. DOI: 10.1007/11732990_17