ASD Peter Gwozdz Click sheet "ASD Doc" for instructions In this TRANSPOSE array, the "Years" are figured with ASD, copied from row 7, treating compound markers as individuals
Column A is input data But the "Mutations" are figured using "Infinite Alleles",  copied from row 42;  for compound markers the mutations are totaled in the "a" marker only
25 < Years per generation;  may be changed DYS 393 390 19 391 385a 385b 426 388 439 389-1 392 389-2 458 459a 459b 455 454 447 437 448 449 464a 464b 464c 464d 460 GATA YCa YCb 456 607 576 570 CDa CDb 442 438 531 578 395a 395b 590 537 641 472 406 511 425 413a 413b 557 594 436 490 534 450 444 481 520 446 617 568 487 572 640 492 565 DYS Copy this array over to the right;  use Paste, Special, Values The copy over here can be sorted by Rank
ASD 0,00000 0,80859 0,37109 0,05859 0,00000 2,58984 0,00000 0,00000 0,15234 0,10938 0,00000 0,12500 0,58984 0,10938 0,00000 0,00000 0,00000 0,10938 0,05859 0,05859 0,73438 0,96484 0,05859 0,10938 0,00000 0,05859 0,10938 0,00000 0,00000 0,30859 0,18750 0,65234 0,68359 1,55859 1,62500 0,65234 0,00000 0,00000 0,00000 0,23438 0,05859 0,00000 0,18750 0,00000 0,00000 0,00000 0,10938 0,00000 0,56250 0,31250 0,23438 0,00000 0,00000 0,00000 0,05859 0,00000 0,33984 0,68359 0,00000 0,05859 0,05859 0,05859 0,05859 0,00000 0,00000 0,00000 0,10938 ASD Do not sort this "TRANSPOSE" array Sort by Sequence to get back to standard order
Mutation Rates >>> Chandler Mutation Rates 0,00076 0,00311 0,00151 0,00265 0,00226 0,00226 0,00009 0,00022 0,00477 0,00186 0,00052 0,00242 0,00814 0,00132 0,00132 0,00016 0,00016 0,00264 0,00099 0,00135 0,00838 0,00566 0,00566 0,00566 0,00566 0,00402 0,00208 0,00123 0,00123 0,00735 0,00411 0,01022 0,00790 0,03531 0,03531 0,00324 0,00055 0,00037 0,00008 0,00031 0,00031 0,00054 0,00057 0,00018 0,00001 0,00154 0,00128 0,00018 0,00202 0,00202 0,00321 0,00029 0,00018 0,00019 0,00832 0,00020 0,00321 0,00544 0,00245 0,00365 0,00042 0,00053 0,00097 0,00212 0,00034 0,00042 0,00087 Chandler Mutation Rates Rank DYS Sequence Mutations Years Rank DYS Sequence Mutations Years Mask Notes
Age in generations = ASD divided by rate 0 260 246 22 0 1146 0 0 32 59 0 52 72 83 0 0 0 41 59 43 88 170 10 19 0 15 53 0 0 42 46 64 87 44 46 201 0 0 0 756 189 0 329 0 0 0 85 0 278 155 73 0 0 0 7 0 106 126 0 16 140 111 60 0 0 0 126 Age in generations = ASD divided by rate 41 393 1 0 0 1 385b 6 0 28 649 Yes recLOH in 3 samples;  misleading age
Years 0 6 500 6 144 553 0 28 649 0 0 798 1 470 0 1 291 1 812 2 071 0 0 0 1 036 1 480 1 085 2 191 4 262 259 483 0 364 1 315 0 0 1 050 1 141 1 596 2 163 1 104 1 151 5 034 0 0 0 18 901 4 725 0 8 224 0 0 0 2 136 0 6 962 3 868 1 825 0 0 0 176 0 2 647 3 142 0 401 3 488 2 764 1 510 0 0 0 3 143 Years 5 390 2 7 6 500 2 395a 40 2 18 901 Yes One double step out of 16 samples in this slow mutating marker provides a very old age estimate
Averages by various sets of markers: Average of first 12 markers Average of first 25 markers Average of first 37 markers Average of all 67 markers 6 19 3 8 6 144 3 537 43 4 8 224 This is due to the 11 value, perhaps ancestral from M458;  this is evidence that this marker, for PcB1, corresponds to a very old branch
Average ASD;  all 67 markers 0,23834 0,35124 0,28031 0,34713 0,23834 Average ASD 35 391 4 1 553 4 413a 49 6 6 962 Includes two double step and two single step mutations
Chandler Mutation Rates Average 0,00335 0,00187 0,00278 0,00492 0,00335 Chandler Mutation Rates Average 41 385a 5 4 0 5 390 2 7 6 500 I could not make credible clusters using this marker
Age in generations = ASD divided by rate 71 188 Generations 101 71 71 Age in generations = ASD divided by rate 1 385b 6 0 28 649 6 19 3 8 6 144 This is due to the 16 value, perhaps ancestral from M458;  this is evidence that this marker, for PcB2, corresponds to a very old branch
Age in years 1 780 4 698 2 520 1 763 1 780 Years 41 426 7 0 0 7 442 36 8 5 034 This one has less variation in PcAlt, and more variation in PcB4, so this one is evidence that PcAlt is valid, and that PcB4 is invalid
Thomas: 1 2 3 4 5 Average of markers 13-25 Average of markers 26-37 Average of markers 38-67 41 388 8 0 0 8 395b 41 0 4 725 Mutated instances counted at 395a, but age is calculated separately for a and b as individuals
Average ASD with the 5 Thomas markers 0,24766 (Compare to Thomas average = 0.2226) 0,21484 0,48633 0,10417 Average ASD 34 439 9 3 798 9 464a 22 4 4 262 Yes recLOH;  16-16-16-16 is misleading.  Number of mutated 464 sets are counted here, but each of the four have age calculated as individuals
Thomas Rate 0,00210 0,00362 0,00938 0,00141 Chandler Mutation Rates Average 25 389-1 10 2 1 470 10 413b 50 0 3 868 Mutated instances counted at 413a, but age is calculated separately for a and b as individuals
Age in generations = ASD divided by rate 118 59 52 74 Age in generations = ASD divided by rate 41 392 11 0 0 11 617 61 1 3 488 One mutation out of 16 samples in this slow mutating marker provides an old age estimate
Age in years 2 948 (Compare to Thomas 2,650) 1 482 1 296 1 850 Years 27 389-2 12 2 1 291 12 565 67 2 3 143 Two samples with the 13 value, which is ancestral for K, N, and P.  This is evidence against these two samples.   In fact, PcAlt excludes these two
Mask: 21 458 13 8 1 812 13 481 58 8 3 142 This marker provides evidence for the 4 clusters PcB1 through PcB4, because this marker does not vary much in those 4 clusters
Masks are explained in the Documentation Compound Markers;  Infinite Alleles 19 459a 14 2 2 071 14 568 62 1 2 764 One mutation out of 16 samples in this slow mutating marker provides an old age estimate
To specify which markers to use for ASD: Modal 0 = Not mutated;  1 - Mutated 41 459b 15 0 0 15 444 57 7 2 647 This marker provides evidence for the 4 clusters PcB1 through PcB4, because this marker does not vary much in those 4 clusters
Mask >>> Type or copy a mask into this row >> 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 Count 12 14 12 16 2 14 10 41 455 16 0 0 16 449 21 9 2 191 This marker provides evidence for the 4 clusters PcB1 through PcB4, because this marker does not vary much in those 4 clusters
Count 1 1 1 1 1 - 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 - - - - 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 385 459 464 YC CD 395 413 41 454 17 0 0 17 570 33 8 2 163
Number of Markers 62 1 0 0 0 1 0 1 33 447 18 2 1 036 18 511 47 2 2 136
ASD 0 0,80859 0,37109 0,05859 0 0 0 0,15234 0,10938 0 0,125 0,58984 0,10938 0 0 0 0,10938 0,05859 0,05859 0,73438 0,05859 0,10938 0 0 0,30859 0,1875 0,65234 0,68359 1,55859 1,625 0,65234 0 0 0 0,23438 0,05859 0 0,1875 0 0 0 0,10938 0 0,5625 0,3125 0,23438 0 0 0 0,05859 0 0,33984 0,68359 0 0,05859 0,05859 0,05859 0,05859 0 0 0 0,10938 1 0 0 0 1 0 1 24 437 19 1 1 480 19 459a 14 2 2 071
Rate 0,00076 0,00311 0,00151 0,00265 0,00226 0,00009 0,00022 0,00477 0,00186 0,00052 0,00242 0,00814 0,00132 0,00132 0,00016 0,00016 0,00264 0,00099 0,00135 0,00838 0,00402 0,00208 0,00123 0,00123 0,00735 0,00411 0,01022 0,0079 0,03531 0,03531 0,00324 0,00055 0,00037 0,00008 0,00031 0,00031 0,00054 0,00057 0,00018 0,00001 0,00154 0,00128 0,00018 0,00202 0,00202 0,00321 0,00029 0,00018 0,00019 0,00832 0,0002 0,00321 0,00544 0,00245 0,00365 0,00042 0,00053 0,00097 0,00212 0,00034 0,00042 0,00087 0 0 0 0 1 0 0 31 448 20 1 1 085 20 557 51 4 1 825
Average ASD;  selected markers 0,19752 0 0 0 0 0 0 1 16 449 21 9 2 191 21 458 13 8 1 812
Average rate 0,00322 0 0 0 0 1 0 0 9 464a 22 4 4 262 22 576 32 8 1 596
Generations 61 1 1 1 0 1 0 1 39 464b 23 0 259 23 487 63 1 1 510
Years 1 535 0 0 0 0 1 0 0 36 464c 24 0 483 24 437 19 1 1 480
0 0 0 0 1 0 0 41 464d 25 0 0 25 389-1 10 2 1 470
Mask Tool: Be sure to use "Paste Special, Values" when copying a mask to another location 1 0 0 0 1 1 0 38 460 26 1 364 26 GATA 27 2 1 315
5 000 < Set the limit for the number of years in the mask 0 0 0 0 1 0 0 26 GATA 27 2 1 315 27 389-2 12 2 1 291
Years Limit 0 1 1 0 1 1 0 41 YCa 28 0 0 28 CDb 35 0 1 151
Rank;  oldest = 1, 2, 3 … 41 5 6 35 41 1 41 41 34 25 41 27 21 19 41 41 41 33 24 31 16 9 39 36 41 38 26 41 41 32 29 22 17 30 28 7 41 41 41 2 8 41 3 41 41 41 18 41 4 10 20 41 41 41 40 41 15 13 41 37 11 14 23 41 41 41 12 0 0 0 0 1 0 0 41 YCb 29 0 0 29 607 31 4 1 141
Highlight > Limit - 6 500 6 144 - - 28 649 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 5 034 - - - 18 901 - - 8 224 - - - - - 6 962 - - - - - - - - - - - - - - - - - - 0 0 0 0 0 0 1 32 456 30 5 1 050 30 CDa 34 14 1 104
Mask for all markers below the "Years Limit" 4 0 0 4 4 0 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 0 4 4 4 0 4 4 0 4 4 4 4 4 0 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 0 0 1 0 1 0 1 29 607 31 4 1 141 31 448 20 1 1 085
0 0 1 0 1 0 0 22 576 32 8 1 596 32 456 30 5 1 050
DYS 393 390 19 391 385a 385b 426 388 439 389-1 392 389-2 458 459a 459b 455 454 447 437 448 449 464a 464b 464c 464d 460 GATA YCa YCb 456 607 576 570 CDa CDb 442 438 531 578 395a 395b 590 537 641 472 406 511 425 413a 413b 557 594 436 490 534 450 444 481 520 446 617 568 487 572 640 492 565 DYS 0 0 0 0 1 0 0 17 570 33 8 2 163 33 447 18 2 1 036
Infinite Alleles: 30 CDa 34 14 1 104 34 439 9 3 798
10% < Limit for Fraction Mutated Set the limit in the red cell to the left  for the percent of samples mutated (not the modal value) 28 CDb 35 0 1 151 35 391 4 1 553
Number of Samples 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 7 442 36 8 5 034 36 464c 24 0 483 Yes
Number Mutated (not modal value) 0 7 8 1 4 0 0 3 2 0 2 8 2 0 0 2 1 1 9 4 1 2 0 5 4 8 8 14 8 0 0 0 2 0 4 0 0 0 2 0 6 4 0 0 0 1 0 7 8 0 1 1 1 1 0 0 0 2 41 438 37 0 0 37 446 60 1 401
Fraction Mutated 0,00000 0,43750 0,50000 0,06250 0,00000 0,00000 0,00000 0,18750 0,12500 0,00000 0,12500 0,50000 0,12500 0,00000 0,00000 0,12500 0,06250 0,06250 0,56250 0,12500 0,06250 0,12500 0,00000 0,31250 0,25000 0,50000 0,50000 0,62500 0,50000 0,00000 0,00000 0,00000 0,06250 0,00000 0,25000 0,00000 0,00000 0,00000 0,12500 0,00000 0,25000 0,25000 0,00000 0,00000 0,00000 0,06250 0,00000 0,43750 0,50000 0,00000 0,06250 0,06250 0,06250 0,06250 0,00000 0,00000 0,00000 0,12500 41 531 38 0 0 38 460 26 1 364
Generations 0 141 331 24 0 0 0 39 67 0 52 61 47 0 0 47 63 46 67 6 16 60 0 43 61 49 63 9 154 0 0 0 101 0 439 0 0 0 98 0 62 78 0 0 0 8 0 136 92 0 17 149 118 64 0 0 0 144 41 578 39 0 0 39 464b 23 0 259
Years 0 3517 8278 590 0 0 0 983 1680 0 1291 1536 1184 0 0 1184 1578 1157 1678 138 389 1502 0 1063 1521 1223 1582 221 3858 0 0 0 2520 0 10965 0 0 0 2441 0 1547 1947 0 0 0 188 0 3407 2298 0 428 3720 2948 1611 0 0 0 3592 2 395a 40 2 18 901 40 534 55 1 176
Infinite Alleles / ASD 1,00 0,54 1,35 1,07 1,00 1,00 1,00 1,23 1,14 1,00 1,00 0,85 0,57 1,00 1,00 1,14 1,07 1,07 0,77 0,03 1,07 1,14 1,00 1,01 1,33 0,77 0,73 0,20 0,77 1,00 1,00 1,00 0,13 1,00 1,33 1,00 1,00 1,00 1,14 1,00 0,22 1,07 1,00 1,00 1,00 1,07 1,00 1,29 0,73 1,00 1,07 1,07 1,07 1,07 1,00 1,00 1,00 1,14 8 395b 41 0 4 725 41 393 1 0 0
Markers Less Than Limit 1 - - 1 1 1 1 - - 1 - - - 1 1 - 1 1 - - 1 - 1 - - - - - - 1 1 1 1 1 - 1 1 1 - 1 - - 1 1 1 1 1 - - 1 1 1 1 1 1 1 1 - 41 590 42 0 0 41 385a 5 4 0
Mask >>> Enter 1 to Exclude a Marker 3 537 43 4 8 224 41 426 7 0 0
Mask >>> Enter 1 to Add a Marker 41 641 44 0 0 41 388 8 0 0
Net Mask 1 0 0 1 1 1 1 0 0 1 0 0 0 1 1 0 1 1 0 0 1 0 1 0 0 0 0 0 0 1 1 1 1 1 0 1 1 1 0 1 0 0 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 0 41 472 45 0 0 41 392 11 0 0
Mutations 0 0 0 1 4 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 1 1 1 0 0 0 0 41 406 46 0 0 41 459b 15 0 0 Yes
Total Mutations (values not modal) 15 18 511 47 2 2 136 41 455 16 0 0
Number of Markers 34 41 425 48 0 0 41 454 17 0 0
Fraction 0,00000 0,00000 0,00000 0,06250 0,00000 0,00000 0,00000 0,00000 0,00000 0,00000 0,00000 0,00000 0,00000 0,00000 0,00000 0,00000 0,06250 0,06250 0,00000 0,00000 0,06250 0,00000 0,00000 0,00000 0,00000 0,00000 0,00000 0,00000 0,00000 0,00000 0,00000 0,00000 0,12500 0,00000 0,00000 0,00000 0,00000 0,00000 0,00000 0,00000 0,00000 0,00000 0,00000 0,00000 0,00000 0,06250 0,00000 0,00000 0,00000 0,00000 0,06250 0,06250 0,06250 0,06250 0,00000 0,00000 0,00000 0,00000 4 413a 49 6 6 962 41 464d 25 0 0 Yes
Average Fraction 0,02022 10 413b 50 0 3 868 41 YCa 28 0 0
Rate 0,00076 0,00000 0,00000 0,00265 0,00226 0,00009 0,00022 0,00000 0,00000 0,00052 0,00000 0,00000 0,00000 0,00016 0,00016 0,00000 0,00099 0,00135 0,00000 0,00000 0,00402 0,00000 0,00123 0,00000 0,00000 0,00000 0,00000 0,00000 0,00000 0,00055 0,00037 0,00008 0,00031 0,00054 0,00000 0,00018 0,00001 0,00154 0,00000 0,00018 0,00000 0,00000 0,00029 0,00018 0,00019 0,00832 0,00020 0,00000 0,00000 0,00245 0,00365 0,00042 0,00053 0,00097 0,00212 0,00034 0,00042 0,00000 20 557 51 4 1 825 41 YCb 29 0 0
Average Rate 0,00113 41 594 52 0 0 41 438 37 0 0
Generations 18 41 436 53 0 0 41 531 38 0 0
Years 449 41 490 54 0 0 41 578 39 0 0
40 534 55 1 176 41 590 42 0 0
41 450 56 0 0 41 641 44 0 0
15 444 57 7 2 647 41 472 45 0 0
13 481 58 8 3 142 41 406 46 0 0
41 520 59 0 0 41 425 48 0 0
37 446 60 1 401 41 594 52 0 0
11 617 61 1 3 488 41 436 53 0 0
14 568 62 1 2 764 41 490 54 0 0
23 487 63 1 1 510 41 450 56 0 0
41 572 64 0 0 41 520 59 0 0
41 640 65 0 0 41 572 64 0 0
41 492 66 0 0 41 640 65 0 0
12 565 67 2 3 143 41 492 66 0 0