Supplementary Information

16 October 2008

Article

“High-resolution mapping of meiotic crossovers and noncrossovers in yeast”

Eugenio Mancera, Richard Bourgon, Alessandro Brozzi, Wolfgang Huber and Lars M. Steinmetz

Supplementary Information

Supplementary methods, discussion, figures, and tables are available here (4.4MB).

Supplementary data and images

File name Description
tetrad_plots.tar.gz

(3.3MB)

A whole-tetrad plot across all sixteen chromosomes of inferred recombination events, similar to Figure 1b. Events incorporating more than two genotype changes (e.g., the CO in Figure 1c) are indicated in orange.
genotypes.txt.gz

(1.1MB)

Marker coordinates and genotype calls for all spores. The first and last columns correspond to and v and w, as defined in Section 2.1. The type column contains S for SNPs, I for insertions, D for deletions, and M for probe sets which interrogated more than one polymorphism (i.e., consecutive SNPs, or a SNP near an insertion or deletion). A genotype call of 1 corresponds to S288c. Genotype call column headers give tetrad type (wt, msh4, or mms4), tetrad number, and spore letter.
genotype_summaries.txt.gz

(398KB)

Summaries apply to wildtype data only. For each marker, S288c and YJM789 give total genotype calls of each type, and no_call gives the number no-calls arising from call-level filtering. The non_mendelian column gives the number (out of 46 retained wildtype tetrads) in which the marker exhibited a non-Mendelian ratio, i.e., at least 3 identical called genotypes. The in_CO and in_NCO columns give the frequency with which the marker was involved in a recombination event of the corresponding type. Finally, S288c_in_CO, S288c_in_NCO, etc., give genotype calls within recombination events only.
event_intervals.txt

(256KB)

Inferred CO and NCO interval locations. The first and last columns correspond to the midpoint method described in Section 3. Note that size is not given in cases where a CO falls completely between two consecutive markers, since it would be 0 in such cases. In the type column, X denotes a CO; M denotes a CO with a complex, discontinuous conversion tract; C denotes an NCO; and CC denotes a NCO with a discontinuous conversion tract.
hot_spots.txt

(7KB)

Inferred CO, NCO, and total recombination hot spot interval locations. A p-value cutoff of .001 was used, and hot spots separated by less than 500 bp were merged. In the type column, CO, NCO, or total denote a significant excess of CO, NCO, or combined event activity, respectively. (Note that a total activity hot spot may also be a CO and/or NCO hot spot.)
imi_statistics.txt.gz

(1.6MB)

Raw and adjusted counts of recombination events overlapping each intermarker interval, as well as corresponding p-values. Adjusted counts are computed by scaling by size-dependent expectation, then adjusting globally to match original total count. The CO_high_p and NCO_high_p p-values correspond to extreme CO/NCO ratios.

Additional data

This section contains additional data files made publicly available after the original publication date. All are based on the same source material used for published analyses, but include additional information not previously released.

File name Description
SNP_conversion.tar.gz

(640KB)

For each SNP within an observed NCO or CO-associated conversion interval, we record the S96 and YJM789 bases, as well as the base found in the involved spores (a single spore for NCOs, and two spores for COs). The fact that particular SNPs can appear in multiple recombination intervals across the full set of tetrads means that computations done straight from these tables will automatically be "event weighted", in the sense of Section 9.1 of Supplementary Information.

The tables include the following columns: (1) an identifier, giving chromosome, tetrad label, event ID, and SNP index within that event; (2) an ID for the SNP; (3) the genotype found in the spore, where "1" denotes S96, "2" denotes YJM789, and "NA" means that our algorithm decided not to make a genotype call, based on the quality filtering criteria given in the paper; (4) the YJM789 base at that SNP; (5) the S96 base at that SNP; (6) the SNP position in S96 coordinates; and (7) the base found in the spore, where "NA" is as for column 3.