rc2 {poolABC}

Data frame with an example of observed data

Description

Data frame with data in the ⁠_rc⁠ format for 25 populations Each row of the data frame is a different site. The first 9 columns contain general information about the site, while the remaining contain the number of reads observed at that site for each of the 25 populations.

Usage

rc2

Format

a data frame with 5000 rows and 59 columns. Each of the columns corresponds to :

col1

reference chromosome (contig).

col2

reference position.

col3

reference character.

col4

number of alleles found in all populations.

col5

allele characters in all populations (sorted by counts in all populations).

col6

sum of deletions in all populations (should be zero, if not the position may not be reliable).

col7

SNP type: [pop, rc, rc|pop]; pop: a SNP within or between the populations; rc: a SNP between the reference sequence character and the consensus of at least one populaton; rc|pop: both.

col8

most frequent allele in all populations [12345..].

col9

second most frequent allele in all populations [12345..].

col10 - col34

frequencies of the most frequent allele (major) in the form "allele-count/coverage.

col35 - col59

frequencies of the second most frequent allele (minor) in the form "allele-count/coverage".

Source

Hernán E. Morales et al., Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast. Sci. Adv.5, eaav9963(2019). DOI:10.1126/sciadv.aav9963