Windows QTL Cartographer 2.5 - FTP Directory Listing

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Windows QTL Cartographer 2.5
File's ID number; usually a 10-digit number.
Token /* and */ (Lines 2 – 5)
Insert multiple-line comments between these tokens.
Token #bychromosome (Line 6)
Indicates start of chromosome information.
Token // (Lines 6 – 10)
Insert one-line comments after the double-slash.
Token –type (Line 7)
Indicates how marker positions are numbered along the chromosome. It takes one parameter that can
be either "position" or "interval".
Position indicates that the numbers are positions from the left telomere of the current chromosome.
So numbers should be in increasing order.
Interval indicates that the numbers are the interval distance after a marker. So the last number
and only the last number in the series should be zero.
-type
position 0.0 9.3 17.2 29.9 38.7 52.8 57.8 72.4 76.6 93.2 97.0 115.5
116.5
interval 9.3 7.9 12.7 8.8 14.1 5.0 14.6 4.2 16.6 3.8 18.5 1.0 0.0
Token –function (Line 8)
Indicates which map function is used to transfer recombination frequency (r) between markers to
distance in Morgan (M). The parameter can be an integer from 1 – 8. Haldane and Kosambi are the two
most useful map functions.
Code Reference Note
1 Haldane (1919) Default
2 Kosambi (1944)
3 Morgan (1994) "Fixed"
4 Carter and Falconer (1951)
5 Rao et al. (1979) 0 £ p £ 1
6 Sturt (1976) L
7 Felsenstein (1979) -¥ < K < ¥, K ¹ 2
8 Karlin (1984) Binomial, N > 0
The following Haldane and Kosambi formula can be used to convert marker distance from r to M or vice
versa.
------------------------------
Haldane: dM = -0.5ln(1-2r) r = 0.5(1-exp(-2dM)
Kosambi: dM = 0.25ln((1+2r)/(1-2r)) r = (1-exp(-4dM))/(2(1+exp(-4dM)))
------------------------------
Token –Units (Line 9)
Indicates unit of marker positions. There are three choices:
cM (centiMorgan)
M (Morgan)
© 2010 N.C. State University, Bioinformatics Research Center