Step 1: Input Genotype File

Upload the input genotype file (in tab delimited text format, up to 10 MB). Refer to example_input.txt for an example, or click here to load this file as input below. Click here to download or here to load a larger example with multiple LGs.

Step 2: Specify Parameters

Population type

Using DH for a RIL population will result in about a 2x inflation of map distances.

DH, BC1, Hap RIL at generation 2 RIL at generation 3 RIL at generation 4 RIL at generation 5 RIL at generation 6 RIL at generation 7 RIL at generation 8 RIL at generation 9 RIL at generation 10+

Grouping LOD Criteria

If the number of chromosomes is known beforehand, it is advisable to iterate through LOD scores until the highest LOD score yielding the expected number of chromosomes is identified.

Single LG LOD = 3 LOD = 4 LOD = 5 LOD = 6 LOD = 7 LOD = 8 LOD = 9 LOD = 10

Genetic mapping function

Specifies the distance function to be used. Possible choices are "Kosambi" and "Haldane," which refer to the commonly used Kosambi's and Haldane's distance functions respectively.

Kosambi Haldane

Try to detect genotyping errors

We recommend leaving this option as "No" unless your data is low quality.

No Yes

No. mapping size threshold

2

No. mapping missing threshold (%)

25

No. mapping distance threshold (cM)

15

Step 3: Receive Output

You will be redirected to a new page to wait for your results shortly. If input, an alert email will be sent.