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This page supplements the demonstrations of the use of DracoBase. It is intended for developers.

Please contact Paul Szauter with comments and questions.

This is a supplement to the discussions of mapping X-linked traits in drakes. We need a set of recombinant X chromosomes to demonstrate mapping. This set of recombinant X chromosomes will be defined by the positions of the crossovers, and will be used for several different mapping demonstrations by adding markers to the set of chromosomes.

The X chromosome of drakes is 70 cM long. It is 70 Mbp in length. The frequency of recombination per unit of physical distance is uniform.

We would like to generate 200 recombinant X chromosomes to simulate the amount of data that a classroom group might collect. For the purpose of this demonstration, we will not use the meiosis engine in Geniverse, but simply generate random numbers as described below.

Picture the X chromosome as divided into seven intervals, corresponding to 0-10 cM, 10-20 cM, etc. In strand data, there will be a 10% chance of a crossover in each of these intervals in the absence of chiasma interference (which we will ignore for this demonstration). We will generate 200 seven-digit random numbers (http://www.random.org/). A "9" in a particular interval will indicate a crossover.

In the table below, each of 200 X chromosomes is given an ID number. Each chromosome is given a random seven-digit integer (the table is sorted by this number). For each chromosome, the strand recovered is given. Strand "a" is the strand with the first bp (at 1 bp on the X) from the "a" chromosome; strand "b" is the strand with the first bp from the "b" chromosome. The crossover rank is given: noncrossover (NCO), single crossover (SCO1 - SCO7), double crossover (DCO1,2 etc.), and triple crossover (TCO1,2,3 etc.). The exact position in base pairs of each crossover is given.

We should now check to see that the map produced by these chromosomes is reasonable.

Out of 200 chromosomes, there are 92 noncrossover (NCO) chromosomes.

There are 73 single crossover chromosomes (SCO), with the single crossovers distributed as summarized below.

SCO1 = 8
SCO2 = 10
SCO3 = 11
SCO4 = 9
SCO5 = 10
SCO6 = 14
SCO7 = 11
Total SCO = 73

There are 28 double crossover chromosomes (DCO), with the crossovers distributed as summarized below.

DCO1,2 = 2
DCO1,3 = 3
DCO1,4 = 2
DCO1,5 = 1
DCO1,6 = 1
DCO1,7 = 1
DCO2,4 = 1
DCO2,7 = 3
DCO3,4 = 2
DCO3,5 = 1
DCO3,6 = 1
DCO3,7 = 2
DCO4,6 = 2
DCO4,7 = 1
DCO5,6 = 2
DCO5,7 = 1
DCO6,7 = 2
Total DCO = 28

There are 7 triple crossover chromosomes (TCO), with the crossovers distributed as summarized below.

TCO1,4,6 = 1
TCO1,5,7 = 1
TCO2,3,4 = 1
TCO2,4,5 = 1
TCO3,4,6 = 1
TCO3,5,6 = 2
Total TCO = 7

So we get:

Here are the observed map lengths of the intervals.

Region 1

SCO1 = 8
DCO1,2 + DCO1,3 + DCO1,4 + DCO1,5 + DCO1,6 + DCO1,7 = 10
TCO1,4,6 + TCO1,5,7 = 2
Total crossovers in region 1 = 20; 20/200 = 10 cM

Region 2

SCO2 = 10
DCO1,2 + DCO2,3 + DCO2,4 + DCO2,5 + DCO2,6 + DCO2,7 = 6
TCO2,3,4 + TCO2,4,5 = 2
Total crossovers in region 2 = 18; 18/200 = 9 cM

Region 3

SCO3 = 11
DCO1,3 + DCO2,3 + DCO3,4 + DCO3,5 + DCO3,6 + DCO3,7 = 9
TCO2,3,4 + TCO3,4,6 + TCO3,5,6 = 4
Total crossovers in region 3 = 24; 24/200 = 12 cM

Region 4

SCO4 = 9
DCO1,4 + DCO2,4 + DCO3,4 + DCO4,5 + DCO4,6 + DCO4,7 = 2+1+2+0+2+1 = 8
TCO1,4,6 + TCO2,3,4 + TCO2,4,5 + TCO3,4,6 = 4
Total crossovers in region 4 = 21; 21/200 = 10.5 cM

Region 5

SCO5 = 10
DCO1,5 + DCO2,5 + DCO3,5 + DCO4,5 + DCO5,6 + DCO5,7 = 1+0+1+0+2+1 = 5
TCO1,5,7 + TCO2,3,5 + TCO3,5,6 = 4
Total crossovers in region 5 = 19; 19/200 = 9.5 cM

Region 6

SCO6 = 14
DCO1,6 + DCO2,6 + DCO3,6 + DCO4,6 + DCO5,6 + DCO6,7 = 1+0+1+2+2+2 = 8
TCO1,4,6 + TCO3,4,6 + TCO3,5,6 = 4
Total crossovers in region 6 = 26; 26/200 = 13 cM

Region 7

SCO7 = 11
DCO1,7 + DCO2,7 + DCO3,7 + DCO4,7 + DCO5,7 + DCO6,7 = 1+3+2+1+1+2 = 10
TCO1,5,7 = 1
Total crossovers in region 7 = 22 ; 22/200 = 11 cM

Total map length = 10 + 9 + 12 + 10.5 + 9.5 + 13 + 11 = 75 cM