Description

This track shows multiple alignments of 11 primate assemblies on this target/reference assembly (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	90.843	GCA_029289425.2	syntenic net	pygmy chimpanzee/2024-01-08/NHGRI/NIH
02	90.107	hg38	syntenic net	Human/hg38/Dec. 2013 (GRCh38/hg38)/GRCh38 Genome Reference Consortium Human Reference 38 (GCA_000001405.15)
03	89.910	hs1	syntenic net	Human/hs1/Jan. 2022 (T2T CHM13v2.0/hs1)/Telomere to telomere (T2T) assembly of haploid CHM13 + chrY (GCA_009914755.4)
04	88.771	GCA_029281585.2	syntenic net	western lowland gorilla/2024-01-08/NHGRI/NIH
05	87.464	GCA_028885655.2	syntenic net	Sumatran orangutan/2024-01-05/NHGRI/NIH
06	87.442	GCA_028885625.2	syntenic net	Bornean orangutan/2024-01-08/NHGRI/NIH
07	83.429	GCA_028878055.2	syntenic net	siamang/2024-01-05/NHGRI/NIH
08	66.270	GCF_011100555.1	maf net	white-tufted-ear marmoset/2021-04-28/VGP
09	31.443	GCF_020740605.2	maf net	Ring-tailed lemur/2021-11-04/VGP
10	14.787	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
90.843	90.646	89.718	90.827	pygmy chimpanzee	GCA_029289425.2
90.107	89.384	87.125	90.029	Human	hg38
89.910	89.391	87.374	89.866	Human	hs1
88.771	88.237	86.612	88.741	western lowland gorilla	GCA_029281585.2
87.464	86.542	83.975	87.401	Sumatran orangutan	GCA_028885655.2
87.442	86.573	83.967	87.380	Bornean orangutan	GCA_028885625.2
83.429	82.409	79.458	83.368	siamang	GCA_028878055.2
66.270	65.024	63.067	66.189	white-tufted-ear marmoset	GCF_011100555.1
31.443	30.652	30.083	31.409	Ring-tailed lemur	GCF_020740605.2
14.787	13.874	14.137	14.761	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 chimpanzee//hive/data/genomes/asmHubs/genbankBuild/GCA/028/858/775/GCA_028858775.2_NHGRI_mPanTro3-v2.0_pri/html/GCA_028858775.2_NHGRI_mPanTro3-v2.0_pri.names.tab/GCA_028858775.2/2024-01-08 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