PMC:4502374 / 9059-10694
Annnotations
{"target":"http://pubannotation.org/docs/sourcedb/PMC/sourceid/4502374","sourcedb":"PMC","sourceid":"4502374","source_url":"https://www.ncbi.nlm.nih.gov/pmc/4502374","text":"A linkage map for this population has been published in Shirasawa et al. (2013). This map contained 773 microsatellite and 25 miniature inverted-repeat transposable element loci. We used these 798 markers plus 26 newly genotyped microsatellite markers to construct an updated linkage map, by using Mapmaker Macintosh 2.0 and Mapmaker/EXP 3.0 (Lander et al. 1987; Lincoln et al. 1992). A χ2 test was performed to test the null hypothesis of 1:1 segregation on all scored markers. A minimum logarithm of the odds (LOD) score of 6.0 and maximum recombination fraction (θ) of 0.35 were set as thresholds for linkage groups (LGs) determination with the “group” command. The most likely marker order within each LG was estimated by the matrix correlation method using the “first order” command. Marker orders were confirmed by comparing the log-likelihood of the possible orders by permuting all adjacent triple orders (“ripple” command). After establishment of the group orders, the LOD score was set to 3.0 to include additional markers in the groups. The “try” command was then used to determine the exact position of the new markers within each group. The new marker orders were again confirmed with the “ripple” command. Recombination fractions were converted into map distances in centimorgans (cM) using the Kosambi’s mapping function and the “error detection” command available in Mapmaker/EXP 3.0 (Lander et al. 1987, Lincoln et al. 1992). Based on this map, genomic regions with no recombination or identical markers were identified and all loci but one were removed from these regions (pairs or groups of loci with 0 cM distance).","tracks":[{"project":"2_test","denotations":[{"id":"25943521-23315685-43367125","span":{"begin":74,"end":78},"obj":"23315685"},{"id":"25943521-3692487-43367126","span":{"begin":357,"end":361},"obj":"3692487"},{"id":"25943521-3692487-43367127","span":{"begin":1415,"end":1419},"obj":"3692487"}],"attributes":[{"subj":"25943521-23315685-43367125","pred":"source","obj":"2_test"},{"subj":"25943521-3692487-43367126","pred":"source","obj":"2_test"},{"subj":"25943521-3692487-43367127","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#93d3ec","default":true}]}]}}