Locus choices for ordered_loci

There are 30 loci known to map to the p arm of chromosome 2, 14 on the q arm, and 34 that could be on either (two of these 34 having a limited band assignment that crosses the centromere).

p arm loci:

locus name	index#		inf rank	where?
----------	-------         --------	---------
D2S54		1		18
D2S54_2		3		42
ACP1		5		12		p25
CPS1		9		39
D2S62		33		24		p13-q14
D2S5		39		68		p16-p15
D2S5_2		40		66		p16-p15
D2S1		41		59		p25
D2S1_2		42		45		p25
TPO		44		8		pter-p12
TPO_2		45		40		pter-p12
D2S70		50		26		pter-p22
APOB		53		62		p24-p13
APOB_2		54		48		p24-p13
D2S51		55		37
D2S48		56		27		pter-q32
D2S45		59		29
D2S12		60		78		pter-p23
POMC		62		31		p23
D2S61		63		64
D2S61_2		64		9
D2S47		65		6
D2S6		66		22		p23-p15
D2S49		67		16		pter-p23
D2S44		68		1
D2S43		69		17		p12-cen
D2S46		70		34
CD8A		71		67		p12
TGFA		72		73		p13
TGFA_2		73		58		p13
TGFA_3		75		36		p13
TGFA_4		76		75		p13

Note that the most meiotically informative locus (D2S44) has no precise cyto-location data!

Below are four sets of ordered loci, with corresponding sets of inserted loci. Given that the meiotic information content of a locus is not always matched by the precision of its cytological location data, I've chosen these locus sets to maximise one or the other quality. These choices are naïve, in that they assume the chr2.gen dataset holds mapping information for each locus relative to every other locus; this assumption is not true.

Try1 - maximising meiotic informativeness

Of the 30 loci on the p arm, 19 rank in the top 40 for meiotic informativeness, and 13 are in the first 30. Using only these "best" 13, choose the top two as ordered loci, with the other 11 as loci to be inserted.
ordered_loci 68 65  *                           (D2S44 & D2S47)
inserted_loci 44 64 5 67 69 1 66 33 50 56 59  * (TPO ... D2S45)

Try2 - loci near the centromere

Nine loci on the p arm are found near the centromere. Choose two close together as ordered loci, with the other seven to be inserted. Add the inserted loci in their order of meiotic informativeness.
ordered_loci 69 33  *                           (D2S43 & D2S62)
inserted_loci 75 73 40 71 39 72 76  *           (TGFA_3 ... TGFA_4)

Try3 - loci near the telomere

Five loci on the p arm are found near the telomere. Choose two close together as ordered loci, with the other three to be inserted. Add the inserted loci in their order of meiotic informativeness.
ordered_loci 67 50  *                           (D2S49 & D2S70)
inserted_loci 44 45 60  *                       (TPO TPO_2 D2S12)

Try4 - loci in the middle

Seven loci on the p arm are found in the middle. Choose two close together as ordered loci, with the other five to be inserted. Add the inserted loci in their sequence of cyto-location.
ordered_loci 5 41  *                            (ACP1 & D2S1)
inserted_loci 42 53 54 62 66  *                 (D2S1_2 APOB APOB_2 POMC D2S6)