phastCons File Format

phastCons data files contain the compressed conservation scores that underlie the Conservation annotation track and the phastCons table. For a detailed description of the algorithm used to produce the scores, see the Genome Browser description page associated with the Conservation track.

File Format (assemblies released Nov. 2004 and later)

When uncompressed, the file contains a declaration line and one column of data in wiggle table fixed-step format:

  fixedStep chrom=scaffold_1 start=3462 step=1

1. Declaration line: The declaration line specifies the starting point of the data in the assembly. It consists of the following fields:

  • fixedStep -- keyword indicating the wiggle track format used to write the data. In fixed step format, the data is single-column with a fixed interval between values.
  • chrom -- chromosome or scaffold on which first value is located.
  • start -- position of first value on chromosome or scaffold specified by chrom. NOTE: Unlike most Genome Browser coordinates, these are one-based.
  • step -- size of the interval (in bases) between values.
A new declaration line is inserted in the file when the chrom value changes, when a gap is encountered (requiring a new start value), or when the step interval changes.

2. Data lines: The first data value below the header shows the score corresponding to the position specified in the header. Subsequent score values step along the assembly in one-base intervals. The score shows the posterior probability that phastCons's phylogenetic hidden Markov model (HMM) is in its most-conserved state at that base position.

File Format (assemblies prior to Nov. 2004)

When uncompressed, the data file contains two columns:

  294	0.0953	
  295	0.0948	
  296	0.0943	
  297	0.0936	
  298	0.0929	
  299	0.0921
Column #1 contains a one-based position coordinate. Column #2 contains a score showing the posterior probability that phastCons's phylogenetic hidden Markov model (HMM) is in its most conserved state at that base position.

References for phastCons

Siepel A and Haussler D (2005). Phylogenetic hidden Markov models. In R. Nielsen, ed., Statistical Methods in Molecular Evolution, pp. 325-351, Springer, New York.

Siepel, A., Bejerano, G., Pedersen, J.S., Hinrichs, A., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L.W., Richards, S., Weinstock, G.M., Wilson, R. K., Gibbs, R.A., Kent, W.J., Miller, W., and Haussler, D. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15, 1034-1050 (2005).

For a discussion of the methods used to calculate the phastCons scores, see the description page for the hg17 Conservation track in the Genome Browser.