The Genome Tolerance Browser is an online genome browser for visualizing the predicted tolerance of the human genome. For each position across the genome, we compiled normalized functional predictions from numerous non-synonymous computational predictions algorithms, such as SIFT and PolyPhen, genome-wide computational prediction algortihms, such as FATHMM-MKL and CADD, and cancer-specific prediction algorithms, such as FATHMM-Cancer and TransFIC. The interactive browser can be used to facilitate the rapid identification of predicted intolerant regions across the genome and can also be used to visualize the concordance & subtle differences between multiple prediction algorithms.

If you have found this resource useful, please cite our publication:

Available Methods

id Method/Description Download

Non-Synonymous/Coding Prediction Algorithms

SIFT SIFT bigWig, bed
PPH2_HVAR PolyPhen-2 (HumVar) bigWig, bed
PPH2_HDIV PolyPhen-2 (HumDiv) bigWig, bed
FATHMM_MKLC FATHMM-MKL (Coding) bigWig, bed
FATHMM_U FATHMM (Unweighted) bigWig, bed
FATHMM_W FATHMM (Weighted) bigWig, bed
MA Mutation Assessor bigWig, bed
MT MutationTaster bigWig, bed
VEST VEST bigWig, bed
LRT LRT bigWig, bed
MetaLR MetaLR bigWig, bed
MetaSVM MetaSVM bigWig, bed

Genome-Wide Prediction Algorithms

FATHMM_MKLNC FATHMM-MKL (Non-Coding) bigWig, bed
CADD CADD bigWig, bed
DANN DANN bigWig, bed
PP46 PhyloP: based on the MSA of 45 vertebrate genomes to the human genome bigWig, bed
PP100 PhyloP: based on the MSA of 99 vertebrate genomes to the human genome bigWig, bed
PC46 PhastCons: based on the MSA of 45 vertebrate genomes to the human genome bigWig, bed
PC100 PhastCons: based on the MSA of 99 vertebrate genomes to the human genome bigWig, bed
GERP_RS GERP++ Rejected Substitutions (RS Scores) bigWig, bed
GERP_CE GERP++ Constrained Elements bigWig, bed

Cancer-Specific Prediction Algorithms

FATHMM_C FATHMM-Cancer bigWig, bed
TFIC_SIFT TransFIC (SIFT) bigWig, bed
TFIC_PPH2 TransFIC (PolyPhen-2) bigWig, bed
TFIC_MA TransFIC (MutationAssessor) bigWig, bed

Adding & Amending Tracks

You can add additional tracks representing a range of computational prediction algorithms (please see the above list) using the icon. You can also add custom tracks, representing your own annotation data in bigWig and bigBed format, through the same option. Once added to the browser, the appearance of tracks (e.g. color, height etc.) can be amended using the icon.

Exporting Images

Once you are happy with the tracks displayed in the browser, publication quality images in SVG or PNG format can be generated using the icon.

Exporting Data

Scores used in the GTB are made available in bed format from the above table (see Available Methods). From here, users can extract scores pertaining to specific regions using tabix (see https://github.com/samtools/tabix).

The following syntax should be used to extract data from specific databases:

tabix <database> <chrom>:<start>-<stop>

For example, to extract SIFT GTB scores falling within 27,180,538 and 27,183,448 in chromosome 7, you should run the following command:

tabix SIFT.bed.gz 7:27180538-27183448

Unresponsive Browser

The Genome Tolerance Browser is a client-side JavaScript application. This means that all rendering is performed on your web browser and not on our server. As a result, your browser may become slow or unresponsive when viewing large amounts of data. Therefore, we recommend that users remove all genome-wide prediction algorithms before zooming out too far or when searching for large genes.

Contact Us

We welcome any comments or suggestions that you may have regarding our browser - please send an email directly to:

We also encourage developers of functional prediction algorithms wishing to include their algorithm in our browser to contact us.