Raw Data

Current RH Data

The map is currently calculated with RH TSP Map 1.3 (NCBI/Concorde) by Richa Agarwala, using a genetic framework map and "extended MLE" criteria only. Since no prior linkage group assignments are available, we calculate the entire map as one "chromosome". The software is modified to show Haldane centirays. Files are in Unix text format.

	chr1.t51.data (scoring data)
	frame.1 (genetic framework map)
	scratch_MapMarker.table (placement map)
	T51_1-2-04.tar.gz (map with linkage group assignments as submitted to ZFIN)

Published RH Data

The published map (Geisler et al. (1999) was calculated with SAMapper 1.0, from the Stanford Human Genome Center.

	zf.raw (scoring data)
	zf.anchors (genetic framework map)
	RunReport.zf (includes the unedited map)
	zf.xslip.Gcompr (edited map)
	zf.pseudo (key to marker numbers)

Mutant Data

We attempt to place mutations in an interval between two SSLP markers. If this is not possible, two markers on the same side are used to calculate the map position.

The "genotypes" file contains: template plate row (identifies the embryos scored, one line corresponds to two rows on a microtiter plate), mutant name, marker name, and 24 genotypes. Genotype format: "1", homozygous for the upper band (which may be either Tü or WIK), "2", homozygous for the lower band, "3", heterozygous, "0" or "-", not determined (bad lane or well).

The "linkages" file contains: mutant allele, abbreviation (gene symbol, "xxx" if unnamed), linkage group, genetic distance from the top of the linkage group (in cM); for each of of the two linked markers, marker name, genetic distance from the top (as published by the MGH), map distance between mutation and marker, LOD score, and number of embryos scored. Map positions calculated from two markers on the same side are marked with an asterisk ("*"), and should be used with caution.

	mutants.pcr (genotypes)
	mutants.lnk (linkages)