chromosome 2
100800 bytes allocated in orders_morecore
3024000 bytes allocated in morecore
Option chosen: instant
Current values for parameters:
par_file = chr2.par
dat_file = chr2.dat
gen_file = chr2.gen
ord_file = chr2.ord
nb_our_alloc = 3000000 [# bytes reserved for our_alloc]
SEX_EQ = 1 [0 = sex specific analysis, 1 = sex equal]
TOL = 0.010000
PUK_NUM_ORDERS_TOL = 6
PK_NUM_ORDERS_TOL = 8
PUK_LIKE_TOL = 2.000
PK_LIKE_TOL = 2.000
use_ord_file = 1
write_ord_file = 0
use_haps = 1
Haplotyped system (distances forced to 0.0):
0 CRYG1-5 2 CRYG1-5_2 4 CRYG1-5_3
Haplotyped system (distances forced to 0.0):
1 D2S54 3 D2S54_2
Haplotyped system (distances forced to 0.0):
24 D2S38_2 23 D2S38
Haplotyped system (distances forced to 0.0):
40 D2S5_2 39 D2S5
Haplotyped system (distances forced to 0.0):
42 D2S1_2 41 D2S1
Haplotyped system (distances forced to 0.0):
44 TPO 45 TPO_2
Haplotyped system (distances forced to 0.0):
54 APOB_2 53 APOB
Haplotyped system (distances forced to 0.0):
64 D2S61_2 63 D2S61
Haplotyped system (distances forced to 0.0):
75 TGFA_3 73 TGFA_2 72 TGFA
76 TGFA_4
N.B. Only the first locus in each set is retained in the orders
objects, but the remaining loci are used in all likelihood calculations.
1 D2S54
5 ACP1
6 CALMOD
10 D2S25
13 D2S36
15 D2S34
16 D2S21
17 D2S19
18 D2S20
20 D2S41
21 D2S40
22 D2S39
24 D2S38_2
26 D2S30
28 D2S31
29 D2S27
31 D2S28
33 D2S62
34 D2S16
35 D2S17
36 IL1-RN/pcr
37 IL1A/pcr
38 IMR-6
40 D2S5_2
42 D2S1_2
44 TPO
49 LCO
50 D2S70
54 APOB_2
55 D2S51
56 D2S48
58 GYPC
59 D2S45
61 LCT
62 POMC
65 D2S47
66 D2S6
67 D2S49
68 D2S44
69 D2S43
70 D2S46
71 CD8A
75 TGFA_3
77 Prot_C/pcr
ordered loci:
55 68 1 69 33 59 40 66 56 54 50 65
inserted loci:
10 61 77 49 75 71 13 16 18 20 21 22 24 58 36 37 26 28 15 31 38 35 62 70 6 17 29 34 44 5 67 42
1 D2S54
5 ACP1
6 CALMOD
10 D2S25
13 D2S36
15 D2S34
16 D2S21
17 D2S19
18 D2S20
20 D2S41
21 D2S40
22 D2S39
24 D2S38_2
26 D2S30
28 D2S31
29 D2S27
31 D2S28
33 D2S62
34 D2S16
35 D2S17
36 IL1-RN/pcr
37 IL1A/pcr
38 IMR-6
40 D2S5_2
42 D2S1_2
44 TPO
49 LCO
50 D2S70
54 APOB_2
55 D2S51
56 D2S48
58 GYPC
59 D2S45
61 LCT
62 POMC
65 D2S47
66 D2S6
67 D2S49
68 D2S44
69 D2S43
70 D2S46
71 CD8A
75 TGFA_3
77 Prot_C/pcr
Sex_averaged map (recomb. frac., Kosambi cM):
55 D2S51 0.0
0.15 15.3
68 D2S44 15.3
0.05 4.8
1 D2S54 20.2
0.00* 0.0
3 D2S54_2 20.2
0.13 12.8
69 D2S43 33.0
0.12 12.7
33 D2S62 45.7
0.11 11.2
59 D2S45 56.9
0.26 28.6
40 D2S5_2 85.5
0.00* 0.0
39 D2S5 85.5
0.24 26.4
66 D2S6 111.9
0.15 15.8
56 D2S48 127.7
0.14 14.0
54 APOB_2 141.7
0.00* 0.0
53 APOB 141.7
0.06 5.8
50 D2S70 147.4
0.33 39.7
65 D2S47 187.2
* denotes recomb. frac. held fixed in this analysis
log10_like = -578.59
Sex-specific map (recomb. frac., Kosambi cM -- female, male ):
55 D2S51 0.0 0.0
0.18 19.0 0.00 0.0
68 D2S44 19.0 0.0
0.04 3.9 0.06 6.0
1 D2S54 22.9 6.0
0.00* 0.0 0.00* 0.0
3 D2S54_2 22.9 6.0
0.14 14.8 0.12 12.3
69 D2S43 37.6 18.2
0.21 21.9 0.00 0.2
33 D2S62 59.5 18.5
0.17 17.3 0.12 12.0
59 D2S45 76.8 30.5
0.32 37.9 0.19 20.5
40 D2S5_2 114.7 51.0
0.00* 0.0 0.00* 0.0
39 D2S5 114.7 51.0
0.30 34.7 0.13 13.8
66 D2S6 149.4 64.8
0.21 22.6 0.09 9.1
56 D2S48 172.0 73.9
0.17 17.9 0.09 9.2
54 APOB_2 189.9 83.1
0.00* 0.0 0.00* 0.0
53 APOB 189.9 83.1
0.03 2.6 0.09 8.6
50 D2S70 192.6 91.7
0.36 45.4 0.30 34.6
65 D2S47 238.0 126.3
* denotes recomb. frac. held fixed in this analysis
log10_like = -569.50
D2S25
55 68 1 69 33 59 40 66 56 54 50 65
X X X X X X X X X X X X X
-623.52
-625.09
-638.04
-618.69
-601.15
-602.47
-612.02
-627.78
-641.35
-640.53
-645.84
-634.83
-632.84
LCT
55 68 1 69 33 59 40 66 56 54 50 65
X X X X X X X X X X X X X
-599.02
-595.36
-601.83
-601.17
-607.86
-610.59
-609.78
-614.06
-620.83
-622.46
-623.16
-615.78
-612.00
Prot_C/pcr
55 68 1 69 33 59 40 66 56 54 50 65
X X X X X X X X X X X X X
-633.80
-626.70
-624.04
-624.10
-643.02
-652.19
-655.73
-665.35
-680.93
-678.86
-681.25
-668.73
-664.68
LCO
55 68 1 69 33 59 40 66 56 54 50 65
X X X X X X X X X X X X X
-623.80
-619.96
-617.64
-610.92
-622.24
-631.80
-639.12
-646.89
-662.42
-658.89
-664.40
-654.29
-651.43
TGFA_3
55 68 1 69 33 59 40 66 56 54 50 65
X X
-620.34
-620.34
CD8A
55 68 1 69 33 59 40 66 56 54 50 65
X X
-598.05
-598.07
D2S36
55 68 1 69 33 59 40 66 56 54 50 65
X X X X X X X X X X X X X
-593.08
-588.17
-589.61
-592.15
-597.26
-598.69
-597.30
-600.79
-607.22
-608.01
-611.26
-600.38
-597.55
D2S21
55 68 1 69 33 59 40 66 56 54 50 65
X X X X X X X X X X X X X
-613.90
-604.44
-595.72
-595.72
-616.77
-628.81
-630.72
-639.07
-649.54
-648.68
-650.58
-638.05
-634.26
D2S20
55 68 1 69 33 59 40 66 56 54 50 65
X X X X X X X X X X X X X
-605.07
-604.66
-607.95
-608.70
-615.99
-618.70
-615.59
-618.90
-630.26
-627.32
-627.77
-618.14
-614.30
D2S41
55 68 1 69 33 59 40 66 56 54 50 65
X X X X X X X X X X X X X
-615.28
-615.32
-613.36
-599.62
-603.09
-614.54
-618.69
-627.16
-636.38
-635.69
-639.79
-626.47
-623.99
D2S40
55 68 1 69 33 59 40 66 56 54 50 65
X X X X X X X X X X X X X
-606.68
-610.59
-631.27
-625.49
-622.90
-619.08
-612.57
-613.93
-625.57
-624.57
-625.37
-613.22
-608.69
D2S39
55 68 1 69 33 59 40 66 56 54 50 65
X X X X X X X X X X X X X
-610.17
-612.78
-627.17
-626.31
-627.94
-623.93
-617.32
-618.28
-632.24
-630.37
-632.27
-617.73
-613.20
D2S38_2
55 68 1 69 33 59 40 66 56 54 50 65
X X X X X X X X X X X X X
-631.60
-634.99
-650.25
-624.60
-606.62
-605.33
-609.49
-630.44
-647.73
-647.06
-652.64
-639.34
-636.82
GYPC
55 68 1 69 33 59 40 66 56 54 50 65
X X X X X X X X X X X X X
-606.45
-604.98
-593.39
-593.08
-608.57
-611.76
-613.57
-621.19
-637.68
-636.43
-644.59
-631.28
-627.26
IL1-RN/pcr
55 68 1 69 33 59 40 66 56 54 50 65
X X X X X X X X X X X X X
-589.44
-591.80
-597.47
-583.99
-584.02
-585.47
-585.58
-588.15
-595.03
-595.39
-602.17
-594.76
-590.93
IL1A/pcr
55 68 1 69 33 59 40 66 56 54 50 65
X X X X X X X X X X X X X
-588.67
-590.36
-595.87
-585.16
-585.16
-587.48
-587.54
-589.33
-593.18
-594.00
-602.37
-593.34
-590.02
D2S30
55 68 1 69 33 59 40 66 56 54 50 65
X X X X X X X X X X X X X
-634.80
-641.52
-664.89
-643.15
-629.56
-617.27
-612.36
-620.35
-639.90
-640.72
-647.26
-635.88
-637.21
D2S31
55 68 1 69 33 59 40 66 56 54 50 65
X X X X X X X X X X X X X
-616.29
-623.50
-651.31
-633.29
-620.31
-609.16
-599.37
-600.01
-609.46
-615.41
-625.49
-617.41
-616.80
D2S34
55 68 1 69 33 59 40 66 56 54 50 65
X X X X X X X X X X X X X
-617.83
-626.51
-652.42
-637.35
-624.79
-609.59
-601.03
-601.03
-617.44
-619.11
-621.17
-617.20
-618.61
D2S28
55 68 1 69 33 59 40 66 56 54 50 65
X X X X X X X X X X X X X
-612.77
-621.92
-647.17
-632.78
-624.76
-614.40
-599.92
-598.19
-607.23
-613.24
-617.63
-610.70
-612.38
IMR-6
55 68 1 69 33 59 40 66 56 54 50 65
X X X X X X X X X X X X X
-609.42
-612.41
-641.63
-623.24
-614.40
-609.01
-596.31
-596.44
-603.40
-612.52
-617.52
-611.00
-609.59
D2S17
55 68 1 69 33 59 40 66 56 54 50 65
X X X X X X X X X X X X X
-633.93
-641.85
-673.52
-655.72
-638.26
-630.77
-622.42
-622.22
-631.39
-634.51
-636.24
-630.89
-634.12
POMC
55 68 1 69 33 59 40 66 56 54 50 65
X X X X
-610.70
-610.12
-610.73
-610.82
D2S46
55 68 1 69 33 59 40 66 56 54 50 65
X X
-649.50
-648.71
CALMOD
55 68 1 69 33 59 40 66 56 54 50 65
X X X X X X X X X X X X X
-621.41
-625.71
-656.81
-634.50
-625.15
-620.01
-610.85
-608.62
-611.73
-622.48
-623.76
-621.01
-622.33
D2S19
55 68 1 69 33 59 40 66 56 54 50 65
X X X X X X X X X X X X X
-616.85
-623.67
-647.94
-634.58
-629.50
-623.60
-614.26
-596.62
-595.05
-605.88
-614.41
-612.19
-617.26
D2S27
55 68 1 69 33 59 40 66 56 54 50 65
X X X X X X X X X X X X X
-619.47
-628.70
-657.21
-642.88
-631.86
-620.49
-611.74
-597.21
-596.76
-602.63
-606.70
-606.10
-618.92
D2S16
55 68 1 69 33 59 40 66 56 54 50 65
X X X X X X X X X X X X X
-618.19
-626.85
-666.14
-642.07
-631.65
-623.37
-610.99
-605.43
-603.42
-596.28
-594.83
-595.51
-613.96
TPO
55 68 1 69 33 59 40 66 56 54 50 65
X X
-645.62
-645.82
ACP1
55 68 1 69 33 59 40 66 56 54 50 65
X X
-627.11
-626.89
D2S49
55 68 1 69 33 59 40 66 56 54 50 65
X X
-621.44
-621.41
D2S1_2
55 68 1 69 33 59 40 66 56 54 50 65
X X
-614.28
-614.06