chromosome 2
50400 bytes allocated in orders_morecore
3024000 bytes allocated in morecore
Option chosen: twopoint
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 = 0
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.
D2S51 D2S44 D2S54 D2S43 D2S62
D2S45 D2S5_2 D2S6 D2S48 APOB_2
D2S70 D2S47
AGAINST:
TPO D2S61_2 ACP1 D2S49 POMC
D2S46 TGFA_3 CPSI D2S1_2 CD8A
D2S12 CALMOD CEB1/HINF CEB11/HINF D2S25
D2S24 D2S22 D2S36 D2S35 D2S34
D2S21 D2S19 D2S20 D2S42 D2S41
D2S40 D2S39 D2S38_2 D2S37 D2S30
D2S32 D2S31 D2S27 D2S29 D2S28
IL1-RN/pcr IL1A/pcr IMR-6 D2S72 D2S65
LCT Prot_C/pcr CRYG1-5 COL5A2 D2S16
D2S17 D2S53 D2S50 LCO D2S3
CRYGP1 D2S55 GYPC D2S90
D2S51 D2S25 rec. fracs.= 0.10, lods = 4.83
-1.48 2.37 4.49 4.83 4.64 4.22 3.66 3.00 2.28 1.51 0.73 0.00
D2S51 LCT rec. fracs.= 0.14, lods = 2.53
-2.69 0.24 2.00 2.46 2.52 2.41 2.19 1.88 1.51 1.07 0.57 0.00
D2S51 Prot_C/pcr rec. fracs.= 0.13, lods = 2.93
-3.88 0.01 2.30 2.87 2.91 2.73 2.41 2.01 1.54 1.04 0.52 0.00
D2S51 LCO rec. fracs.= 0.12, lods = 3.74
-2.98 0.90 3.18 3.71 3.69 3.44 3.03 2.51 1.91 1.26 0.59 0.00
D2S44 TGFA_3 rec. fracs.= 0.35, lods = 2.77
-125.40 -66.88 -27.84 -12.93 -5.52 -1.28 1.17 2.41 2.77 2.42 1.48 0.00
D2S44 CD8A rec. fracs.= 0.27, lods = 2.49
-42.25 -20.51 -6.33 -1.25 1.01 2.08 2.47 2.42 2.05 1.45 0.73 0.00
D2S44 D2S25 rec. fracs.= 0.28, lods = 4.90
-71.61 -35.00 -10.93 -2.13 1.92 3.95 4.80 4.83 4.24 3.16 1.67 0.00
D2S44 D2S36 rec. fracs.= 0.02, lods = 9.37
8.42 9.25 9.19 8.50 7.65 6.70 5.69 4.62 3.50 2.32 1.14 0.00
D2S44 D2S21 rec. fracs.= 0.06, lods = 25.97
15.08 22.58 25.92 25.37 23.65 21.34 18.59 15.47 12.00 8.21 4.15 0.00
D2S44 D2S20 rec. fracs.= 0.13, lods = 10.79
-13.14 0.48 8.56 10.56 10.72 10.08 8.96 7.51 5.83 3.96 1.97 0.00
D2S44 D2S41 rec. fracs.= 0.18, lods = 8.63
-32.03 -10.45 3.04 7.19 8.49 8.54 7.87 6.72 5.23 3.51 1.68 0.00
D2S44 D2S40 rec. fracs.= 0.25, lods = 3.80
-38.64 -17.89 -4.34 0.49 2.60 3.54 3.80 3.60 3.04 2.22 1.19 0.00
D2S44 D2S39 rec. fracs.= 0.19, lods = 4.76
-21.56 -7.81 0.84 3.60 4.56 4.76 4.50 3.95 3.16 2.18 1.09 0.00
D2S44 D2S38_2 rec. fracs.= 0.32, lods = 2.90
-80.61 -41.95 -16.23 -6.50 -1.76 0.87 2.28 2.85 2.80 2.24 1.27 0.00
D2S44 LCT rec. fracs.= 0.06, lods = 13.01
6.34 11.00 12.99 12.56 11.45 10.05 8.49 6.85 5.18 3.49 1.76 0.00
D2S44 Prot_C/pcr rec. fracs.= 0.05, lods = 31.90
20.78 29.02 31.88 30.19 27.27 23.80 20.02 16.07 12.02 7.93 3.89 0.00
D2S44 LCO rec. fracs.= 0.09, lods = 26.21
3.40 17.76 25.36 26.13 24.86 22.66 19.87 16.63 13.02 9.05 4.73 0.00
D2S44 GYPC rec. fracs.= 0.09, lods = 18.61
-3.23 10.23 17.56 18.60 17.76 16.09 13.90 11.36 8.58 5.64 2.68 0.00
D2S54 D2S21 rec. fracs.= 0.00, lods = 15.05
15.03 14.82 13.89 12.67 11.38 10.01 8.56 7.01 5.36 3.62 1.81 0.00
D2S54 D2S41 rec. fracs.= 0.09, lods = 6.41
0.32 4.15 6.18 6.39 6.05 5.46 4.71 3.84 2.89 1.88 0.89 0.00
D2S54 LCT rec. fracs.= 0.12, lods = 2.35
-4.19 -0.32 1.88 2.33 2.29 2.06 1.77 1.45 1.12 0.78 0.41 0.00
D2S54 Prot_C/pcr rec. fracs.= 0.06, lods = 14.03
7.24 11.93 14.00 13.66 12.63 11.27 9.69 7.95 6.09 4.13 2.09 0.00
D2S54 LCO rec. fracs.= 0.06, lods = 11.99
6.63 10.37 11.97 11.62 10.71 9.51 8.12 6.58 4.94 3.24 1.56 0.00
D2S54 GYPC rec. fracs.= 0.01, lods = 17.84
17.14 17.83 17.14 15.63 13.91 12.05 10.07 7.99 5.83 3.67 1.64 0.00
D2S43 CD8A rec. fracs.= 0.19, lods = 3.42
-17.37 -6.56 0.28 2.48 3.26 3.42 3.22 2.77 2.13 1.37 0.60 0.00
D2S43 D2S25 rec. fracs.= 0.13, lods = 8.75
-11.65 0.02 6.90 8.58 8.68 8.10 7.12 5.86 4.41 2.86 1.32 0.00
D2S43 D2S21 rec. fracs.= 0.14, lods = 6.42
-12.56 -1.85 4.54 6.18 6.40 6.00 5.27 4.34 3.31 2.22 1.08 0.00
D2S43 D2S41 rec. fracs.= 0.03, lods = 11.48
9.33 11.08 11.36 10.51 9.36 8.06 6.66 5.21 3.72 2.24 0.87 0.00
D2S43 D2S38_2 rec. fracs.= 0.15, lods = 9.10
-17.64 -2.98 6.00 8.54 9.10 8.79 7.93 6.69 5.16 3.42 1.61 0.00
D2S43 IL1-RN/pcr rec. fracs.= 0.00, lods = 6.62
6.61 6.51 6.07 5.48 4.86 4.20 3.51 2.77 2.00 1.23 0.51 0.00
D2S43 IL1A/pcr rec. fracs.= 0.00, lods = 3.61
3.61 3.55 3.28 2.93 2.55 2.16 1.75 1.32 0.88 0.47 0.13 0.00
D2S43 Prot_C/pcr rec. fracs.= 0.18, lods = 6.36
-23.65 -7.93 1.99 5.14 6.19 6.34 5.92 5.11 4.01 2.70 1.30 0.00
D2S43 LCO rec. fracs.= 0.08, lods = 13.73
0.35 8.93 13.34 13.62 12.69 11.24 9.50 7.59 5.57 3.50 1.52 0.00
D2S43 GYPC rec. fracs.= 0.11, lods = 8.30
-6.26 2.43 7.34 8.28 8.06 7.35 6.36 5.18 3.87 2.48 1.11 0.00
D2S62 TGFA_3 rec. fracs.= 0.14, lods = 4.26
-6.28 -0.42 3.13 4.09 4.26 4.06 3.64 3.05 2.33 1.51 0.69 0.00
D2S62 CD8A rec. fracs.= 0.00, lods = 9.03
9.02 8.89 8.30 7.52 6.70 5.83 4.91 3.93 2.91 1.85 0.85 0.00
D2S62 D2S25 rec. fracs.= 0.02, lods = 14.01
13.23 13.98 13.54 12.36 11.01 9.54 7.98 6.34 4.63 2.92 1.31 0.00
D2S62 D2S21 rec. fracs.= 0.29, lods = 2.00
-33.56 -16.73 -5.61 -1.50 0.43 1.44 1.90 2.00 1.81 1.39 0.78 0.00
D2S62 D2S41 rec. fracs.= 0.18, lods = 4.18
-14.37 -4.55 1.60 3.51 4.11 4.14 3.82 3.26 2.50 1.61 0.69 0.00
D2S62 D2S38_2 rec. fracs.= 0.01, lods = 19.03
18.34 19.02 18.27 16.70 14.91 12.99 10.95 8.79 6.55 4.26 2.05 0.00
D2S62 D2S30 rec. fracs.= 0.20, lods = 4.80
-29.35 -11.66 -0.46 3.16 4.47 4.80 4.58 3.98 3.12 2.11 1.03 0.00
D2S62 D2S31 rec. fracs.= 0.25, lods = 2.29
-23.97 -11.12 -2.75 0.23 1.53 2.12 2.29 2.18 1.85 1.36 0.73 0.00
D2S62 IL1-RN/pcr rec. fracs.= 0.08, lods = 2.12
0.61 1.56 2.07 2.11 2.01 1.85 1.64 1.39 1.10 0.77 0.41 0.00
D2S62 Prot_C/pcr rec. fracs.= 0.22, lods = 3.45
-31.15 -13.45 -2.19 1.52 2.95 3.42 3.37 2.99 2.40 1.67 0.86 0.00
D2S45 TGFA_3 rec. fracs.= 0.00, lods = 18.66
18.63 18.32 16.94 15.15 13.31 11.40 9.43 7.41 5.37 3.36 1.52 0.00
D2S45 CD8A rec. fracs.= 0.00, lods = 3.31
3.31 3.25 3.00 2.67 2.33 1.96 1.58 1.19 0.80 0.42 0.12 0.00
D2S45 D2S38_2 rec. fracs.= 0.08, lods = 3.86
0.91 2.82 3.79 3.83 3.58 3.20 2.73 2.18 1.57 0.93 0.34 0.00
D2S45 D2S30 rec. fracs.= 0.07, lods = 7.30
1.52 5.32 7.19 7.19 6.65 5.85 4.89 3.82 2.70 1.60 0.64 0.00
D2S45 LCO rec. fracs.= 0.26, lods = 2.72
-33.85 -16.07 -4.47 -0.32 1.53 2.40 2.70 2.64 2.29 1.72 0.95 0.00
D2S5_2 D2S34 rec. fracs.= 0.00, lods = 9.63
9.62 9.47 8.79 7.91 6.99 6.03 5.02 3.97 2.88 1.78 0.76 0.00
D2S5_2 D2S30 rec. fracs.= 0.15, lods = 5.29
-12.27 -2.51 3.40 5.00 5.29 5.01 4.39 3.56 2.61 1.61 0.68 0.00
D2S5_2 D2S31 rec. fracs.= 0.02, lods = 8.44
7.52 8.34 8.24 7.50 6.59 5.60 4.54 3.45 2.37 1.36 0.53 0.00
D2S5_2 D2S28 rec. fracs.= 0.08, lods = 4.20
1.21 3.12 4.11 4.17 3.95 3.60 3.15 2.63 2.04 1.40 0.72 0.00
D2S5_2 IMR-6 rec. fracs.= 0.02, lods = 9.29
8.42 9.22 9.01 8.16 7.15 6.06 4.93 3.77 2.63 1.56 0.66 0.00
D2S5_2 D2S17 rec. fracs.= 0.08, lods = 3.00
0.01 1.92 2.91 2.97 2.77 2.43 2.02 1.56 1.08 0.61 0.23 0.00
D2S6 POMC rec. fracs.= 0.22, lods = 3.01
-24.26 -10.47 -1.65 1.34 2.53 2.97 2.97 2.68 2.17 1.52 0.78 0.00
D2S6 D2S46 rec. fracs.= 0.16, lods = 7.87
-26.04 -7.47 3.86 7.08 7.86 7.62 6.83 5.69 4.34 2.87 1.38 0.00
D2S6 CALMOD rec. fracs.= 0.07, lods = 9.92
2.73 7.47 9.79 9.78 9.08 8.08 6.89 5.57 4.15 2.68 1.23 0.00
D2S6 D2S25 rec. fracs.= 0.30, lods = 2.81
-66.22 -33.56 -12.04 -4.12 -0.39 1.57 2.53 2.81 2.60 2.01 1.12 0.00
D2S6 D2S34 rec. fracs.= 0.24, lods = 2.03
-15.87 -6.99 -1.24 0.77 1.62 1.97 2.02 1.87 1.57 1.14 0.61 0.00
D2S6 D2S19 rec. fracs.= 0.04, lods = 14.82
11.43 14.11 14.73 13.73 12.29 10.63 8.83 6.94 5.01 3.10 1.32 0.00
D2S6 D2S38_2 rec. fracs.= 0.30, lods = 2.28
-62.03 -31.40 -11.34 -4.02 -0.59 1.19 2.04 2.28 2.09 1.57 0.84 0.00
D2S6 D2S30 rec. fracs.= 0.27, lods = 3.58
-65.35 -31.78 -9.95 -2.20 1.23 2.87 3.52 3.51 3.01 2.15 1.07 0.00
D2S6 D2S31 rec. fracs.= 0.13, lods = 4.00
-6.28 -0.44 3.03 3.89 3.97 3.72 3.28 2.73 2.10 1.42 0.69 0.00
D2S6 D2S27 rec. fracs.= 0.04, lods = 14.72
11.14 13.86 14.68 13.92 12.69 11.20 9.52 7.66 5.66 3.55 1.52 0.00
D2S6 D2S28 rec. fracs.= 0.14, lods = 6.64
-10.76 -1.01 4.86 6.40 6.63 6.27 5.57 4.62 3.52 2.30 1.08 0.00
D2S6 IMR-6 rec. fracs.= 0.07, lods = 3.18
0.31 2.20 3.13 3.12 2.85 2.47 2.04 1.60 1.17 0.76 0.36 0.00
D2S6 D2S16 rec. fracs.= 0.15, lods = 4.91
-11.07 -2.28 3.07 4.57 4.91 4.74 4.28 3.63 2.84 1.95 1.00 0.00
D2S6 D2S17 rec. fracs.= 0.18, lods = 4.20
-25.46 -9.76 0.04 3.07 4.05 4.18 3.83 3.19 2.37 1.49 0.65 0.00
D2S48 POMC rec. fracs.= 0.00, lods = 3.31
3.31 3.25 3.02 2.72 2.40 2.06 1.72 1.36 1.01 0.65 0.32 0.00
D2S48 D2S46 rec. fracs.= 0.15, lods = 6.51
-16.16 -3.49 4.12 6.14 6.50 6.17 5.46 4.51 3.45 2.33 1.19 0.00
D2S48 D2S25 rec. fracs.= 0.25, lods = 3.05
-39.25 -18.51 -5.02 -0.24 1.85 2.78 3.05 2.87 2.37 1.64 0.80 0.00
D2S48 D2S34 rec. fracs.= 0.19, lods = 3.01
-11.97 -4.12 0.83 2.40 2.93 3.00 2.81 2.43 1.91 1.31 0.66 0.00
D2S48 D2S19 rec. fracs.= 0.15, lods = 3.43
-7.18 -1.32 2.25 3.24 3.43 3.26 2.88 2.34 1.70 1.02 0.40 0.00
D2S48 D2S27 rec. fracs.= 0.09, lods = 6.23
0.02 3.87 5.95 6.22 5.95 5.43 4.74 3.93 3.02 2.03 1.00 0.00
D2S48 D2S16 rec. fracs.= 0.17, lods = 4.46
-10.17 -2.33 2.55 4.02 4.43 4.38 4.04 3.48 2.75 1.88 0.94 0.00
APOB_2 POMC rec. fracs.= 0.09, lods = 4.92
-1.18 2.65 4.68 4.91 4.60 4.06 3.40 2.67 1.92 1.18 0.48 0.00
APOB_2 D2S46 rec. fracs.= 0.10, lods = 7.19
-3.87 2.87 6.59 7.19 6.86 6.12 5.15 4.03 2.84 1.66 0.64 0.00
APOB_2 D2S19 rec. fracs.= 0.17, lods = 3.22
-13.30 -4.47 1.01 2.68 3.18 3.17 2.86 2.36 1.74 1.06 0.42 0.00
APOB_2 D2S27 rec. fracs.= 0.09, lods = 6.09
1.52 4.40 5.92 6.07 5.81 5.34 4.73 4.01 3.18 2.24 1.19 0.00
APOB_2 D2S16 rec. fracs.= 0.03, lods = 6.75
5.71 6.58 6.66 6.16 5.50 4.77 3.99 3.17 2.34 1.51 0.71 0.00
D2S70 POMC rec. fracs.= 0.06, lods = 2.86
1.51 2.45 2.86 2.78 2.56 2.27 1.92 1.53 1.11 0.68 0.29 0.00
D2S70 D2S16 rec. fracs.= 0.02, lods = 9.99
9.02 9.86 9.83 9.17 8.34 7.40 6.36 5.25 4.04 2.76 1.41 0.00
D2S47 TPO rec. fracs.= 0.03, lods = 35.74
30.39 34.76 35.41 33.20 30.17 26.67 22.79 18.56 14.00 9.15 4.23 0.00
D2S47 ACP1 rec. fracs.= 0.05, lods = 23.14
13.87 20.39 23.12 22.41 20.68 18.44 15.85 12.97 9.82 6.44 2.95 0.00
D2S47 D2S49 rec. fracs.= 0.01, lods = 30.31
29.76 30.30 28.90 26.46 23.73 20.78 17.61 14.22 10.60 6.82 3.09 0.00
D2S47 D2S1_2 rec. fracs.= 0.01, lods = 33.02
31.56 32.98 31.75 28.94 25.75 22.32 18.71 14.95 11.07 7.15 3.32 0.00
D2S47 D2S16 rec. fracs.= 0.29, lods = 2.19
-45.85 -23.08 -8.08 -2.54 0.05 1.40 2.04 2.19 1.99 1.53 0.86 0.00