You may have noted that MAPMAKER's "sequence" command continues to display the name of the chromosome we had been working on, now with the new sequence of loci. In fact, once we select a chromosome for analysis (as we did using the sequence command on page 27), MAPMAKER will restrict all following analyses to that chromosome until explicitly told otherwise. These uses of the "sequence" command are discussed in the "Genome Analysis" section in the Reference Manual.
We will continue mapping this data set by performing an "order" analysis on chromosome 12.
67> sequence chrom12 sequence #25= chrom12: assigned68> three point Linkage Groups at min LOD 3.00, max Distance 50.0 Triplet criteria: LOD 3.00, Max-Dist 50.0, #Linkages 2 'triple error detection' is on. counting...91 linked triplets in 1 linkage group
log-likelihood differences count markers a-b-c b-a-c a-c-b 1: L016 L041 L058 -1.03 -6.65 0.00 2: L016 L041 T002 -3.20 0.00 -6.32 3: L016 L041 T051 0.00 -6.73 -2.86 4: L016 L041 M027 0.00 -5.34 -3.78 .
<< More Output Follows .
69> order Linkage Groups at min LOD 3.00, max Distance 50.0 Starting Orders: Size 5, Log-Likelihood 3.00, Searching up to 50 subsets Informativeness: min #Individuals 44 (codominant only), min Distance 4.0 Placement Threshold-1 3.00, Threshold-2 2.00, Npt-Window 7 ===============================================================================<> Linkage group 1, 12 Markers: 3 L016 21 L041 53 L058 65 T002 85 T051 127 M027 132 M050 140 M062 188 T064 237 D007 243 T001 283 A064Most informative subset: 3 188 53 65 85 140 Searching for a unique starting order containing 5 of 6 informative loci... Got one using three-point analysis alone.
Placing at log-likelihood threshold 3.00... Start: 188 85 53 140 65 Npt: 188 85 (21) 53 140 65 Npt: 188 (127) 85 21 53 140 65 Npt: 188 127 85 21 53 (3) 140 65 Npt-End: 188 127 85 21 53 3 140 65 (243) No unique placements for 3 remaining markers
Map: Markers Distance 188 T064 14.3 cM 127 M027 3.7 cM 85 T051 7.3 cM 21 L041 4.7 cM 53 L058 10.0 cM 3 L016 5.2 cM 140 M062 17.5 cM 65 T002 0.0 cM 243 T001 ---------- 62.8 cM 9 markers log-likelihood= -85.08
Markers placed relative to above map: 188 127 85 21 53 3 140 65 243 :-14-:--4-:--7-:--5-:-10-:--5-:-17-:--0-: 132 2 **.:..*.:....:....:....:....:....:....:....:... 283 2 ...:....:....:..*.:.**.:....:....:....:....:... 237 2 ...:....:....:....:....:....:....:.**.:....:.*. -------------------------------------------------------------------------------
In this case, MAPMAKER has uniquely ordered 10 of the 12 markers assigned to chromosome 12. The other two markers (D007 and M050) place near the two ends of the 10 marker order.
Placing at log-likelihood threshold 2.00... Start: 188 127 85 21 53 3 140 65 243 Npt: 188 127 85 21 (283) 53 3 140 65 243 No unique placements for 2 remaining markers
Map: Markers Distance 188 T064 14.3 cM 127 M027 3.7 cM 85 T051 7.3 cM 21 L041 1.1 cM 283 A064 3.4 cM 53 L058 10.0 cM 3 L016 5.2 cM 140 M062 17.5 cM 65 T002 0.0 cM 243 T001 ---------- 62.6 cM 10 markers log-likelihood= -86.08
Markers placed relative to above map: 188 127 85 21 283 53 3 140 65 243 :-14-:--4-:--7-:--1-:--3-:-10-:--5-:-17-:--0-: 132 2 **.:..*.:....:....:....:....:....:....:....:....:... 237 2 ...:....:....:....:....:....:....:....:.**.:....:.*. order1= T064 M027 T051 L041 A064 L058 L016 M062 T002 T001 other1= M050 D007 ------------------------------------------------------------------------------- Best placement of D007: Markers Distance 188 T064 14.3 cM 127 M027 3.7 cM 85 T051 7.3 cM 21 L041 1.1 cM 283 A064 3.4 cM 53 L058 10.0 cM 3 L016 5.4 cM 140 M062 13.9 cM (237) D007 2.3 cM 65 T002 0.0 cM 243 T001 ---------- 61.4 cM 11 markers log-likelihood= -88.63 ------------------------------------------------------------------------------- Best placement of M050: Markers Distance (132) M050 3.5 cM 188 T064 14.3 cM 127 M027 3.7 cM 85 T051 7.3 cM 21 L041 1.1 cM 283 A064 3.4 cM 53 L058 10.0 cM 3 L016 5.2 cM 140 M062 17.5 cM 65 T002 0.0 cM 243 T001 ---------- 66.1 cM 11 markers log-likelihood= -91.48 ===============================================================================