1. Update the map of data set with Build37 Cox genetic map (B37) and save the new file as "Sugiyama2001_B6xA_BC_B37_Data.csv". This file is ready to be read into Rqtl; 


2. Generate a description file of the project, it includes the general information, definitions of the phenotypes, description of the genotypes and information of the missing markers;


3. For the genotypes of this cross: (cM=centimorgan, bp=basepair)
(1) Correct a genotype spelling error on marker "D1Mit156" of a mouse (mouse ID=342) from "0  9" to "0"; 

(2) Change the symbol of B6 allele from "0" to "B", heterozygous allele from "1" to "H", missing genotypes from "=" (original data) to "-" (standard format in data sets of QTL archive) in B37 data file; 

(3) Unable to find cM position of marker "D2Mit266" and "D7Nds4" from Cox map directly, bp positions assigned based on MGI, then convert them into cM through Map Converter tool (this type of markers are highlighted with light color in description file); 

(4) Six Markers miss bp positions in both Cox map and MGI database. Primer sequences found in MGI, and their locations identified using primer-BLAST in NCBI followed by UCSC In-Silico PCR (they are highlighted with green color in description file and please see description file for details); 

(5) Five markers miss bp positions in both Cox map and MGI database. Primer sequences found in MGI, but their locations don't match the result from primer-BLAST in NCBI. We could not identify the B37 bp positions of these markers currently (this type of markers are highlighted with pink color in description file and please see description file for details); 

(6) Ten markers miss their bp positions in Cox genetic map, assign the position from current MGI database. This type of markers are highlighted with orange color and please see description file for details.

(7) Potential genotype errors have been detected by Rqtl program after data input -- 173 male heterozygote genotypes are found on the X chromosome; 

(8) Some markers are at the same position (cM) after map update; 


4. For the phenotypes of the cross:
This a reciprocal backcross between C57BL/6J (B6) and A/J, only the male mice (n=250) were selected to do the test, no more problems are detected in phenotypes;


5. Except the "csv" file mentioned above, I also saved the description file, original data, data with B37 map, data process and list of missing markers together as a big excel file ("Data_Description_B6xA_BC_Sugiyama2001.xlsx") (1st curating work is finished in 2009, files are updated on 2/9/2011).


6. Information were updated on 5/25/2012:
Change the name of the map (from "Shifman" to "Cox" map) in description and readme file, add a map reference in description file.