ordering markers on LGs

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Ian Bremen

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Jan 26, 2022, 7:16:16 AM1/26/22

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Dear Karl,

below is the initial order for Grapevine (19 chromosomes) initial LGs. The initial order is in sequence but the others, i dont know how to order and what to switch with what?.

40. summary(rip19lik)

Initial1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19

1 1 2 3 4 5 6 7 8 9 10 11 12 14 15 13 16 17 18 19

2 1 2 3 4 5 6 7 8 9 10 11 12 15 14 13 16 17 18 19

3 1 2 3 4 5 6 7 8 9 10 11 14 12 15 13 16 17 18 19

4 1 2 3 4 5 6 7 8 9 10 11 15 12 14 13 16 17 18 19

5 1 2 3 4 5 6 7 8 9 10 11 14 15 12 13 16 17 18 19

Initial 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35

1 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35

2 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35

3 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35

4 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35

5 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35

Initial 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51

1 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51

2 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51

3 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51

4 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51

5 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51

Initial 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67

1 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67

2 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67

3 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67

4 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67

5 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67

LOD chrlen

Initial 68 69 70 71 72 73 74 75 76 0 50.7

1 68 69 70 71 72 73 74 75 76 0 50.7

2 68 69 70 71 72 73 74 75 76 0 50.7

3 68 69 70 71 72 73 74 75 76 0 50.7

4 68 69 70 71 72 73 74 75 76 0 50.7

5 68 69 70 71 72 73 74 75 76 0 50.7

... [ 489 additional rows] ...

Karl Broman

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Jan 26, 2022, 10:59:54 AM1/26/22

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The orders all have the same likelihood, so they can’t be distinguished. Likely, this is a block of markers with no recombination events.