*EVERYTHING ON IMPUTED DATA
MAC Histograms
CC BXD BXP HS CC BXD BXP HS
0 617966 6929819 3789826 5299681 0 0.074778 0.838553 0.458594 0.641296
0.125 3705293 0 0 1206160 0.125 0.448365 0 0 0.145953
0.25 2233271 0 0 754332 0.25 0.27024 0 0 0.091279
0.375 1202641 0 0 694626 0.375 0.145527 0 0 0.084054
0.5 504845 1334197 4474190 309217 0.5 0.06109 0.161447 0.541406 0.037417
Sanity 8264016 8264016 8264016 8264016 Sanity 1 1 1 1
SDP Histogram
Strain Ordering: ['129S1/SvImJ', 'A/J', 'C57BL/6J', 'CAST/Ei', 'NOD/LtJ', 'NZW/LacJ', 'PWD/PhJ', 'WSB/Ei'] IMPUTED
SDP Frequency Log-Frequency Subset Size Max Min Avg var
'00000010' 1613074 6.207654291 2 0.565002 0.078564 0.287773 0.179989
'00010000' 1437778 6.157691834 3 0.794451 0.134785 0.43166 0
'00010010' 1212500 6.083681747 4 0.864421 0.188208 0.532118 0.202348
'00000001' 267703 5.427653238 5 0.923444 0.23204 0.610862 0
'00010011' 214373 5.331170086 6 0.948825 0.267831 0.67567 0
'00010001' 139272 5.143863812 7 0.962964 0.295803 0.730431 0
'00000110' 105220 5.022098297 8 0.973275 0.328205 0.777474 0.147816
'00010110' 98837 4.994919555 9 0.980745 0.353153 0.818346 0
'00000100' 84911 4.928963956 10 0.986785 0.375338 0.854158 0
'10000000' 81869 4.913119486 11 0.99094 0.406877 0.885751 0
'00100010' 81743 4.912450572 12 0.994385 0.434224 0.91379 0
'00001000' 79800 4.902002891 13 0.997154 0.494405 0.938816 0
'00110010' 78243 4.893445494 14 0.998995 0.780636 0.96128 0
'01000000' 76910 4.885982811 15 1 0.865899 0.981565 0
'00100000' 63248 4.801046797 16 1 1 1 0
'10010010' 61867 4.791459057
'00000011' 60451 4.781403489
'10000010' 58726 4.768830421
'00011010' 50914 4.706837218
'00001010' 46849 4.670700325
'01000010' 45224 4.655368972
'00110011' 44414 4.647519888
'01010010' 39416 4.595672549
'01001000' 38187 4.581915541
'11101000' 36991 4.568096072
'10000100' 36730 4.565020928
'00011011' 35300 4.547774705
'10000110' 34363 4.536091072
'01101001' 33978 4.531197812
'10010011' 33671 4.527256015
'00001001' 32610 4.513350799
'00110000' 29535 4.470336975
'01010011' 28450 4.454082271
'01101000' 27292 4.436035363
'00100001' 27150 4.433769834
'01001001' 26399 4.421587476
'01000001' 26347 4.420731171
'10000001' 25567 4.407679771
'00010100' 25257 4.402381764
'00000101' 23816 4.376868822
'10100100' 23412 4.369438515
'01100000' 23100 4.36361198
'10100000' 23078 4.363198169
'00101000' 23075 4.36314171
'11000000' 22981 4.361368923
'01011001' 22034 4.343093345
'11001000' 21770 4.337858429
'11100001' 21753 4.33751916
'00100100' 21590 4.334252642
'01001100' 21078 4.3238294
'11001001' 20455 4.310799484
'00001100' 19446 4.288830281
'11000100' 19020 4.279210513
'00001110' 18568 4.268765127
'10001000' 18229 4.260762845
'10010000' 18111 4.257942431
'01011010' 18096 4.257582588
'00011001' 17870 4.252124553
'00110001' 17499 4.243013231
'00011000' 17342 4.239099182
'10001100' 17029 4.231189145
'00100110' 16338 4.213198892
'01110010' 16234 4.210425542
'10000101' 16232 4.210372034
'01000100' 15883 4.200932536
'00101100' 15660 4.194791758
'10110010' 15491 4.190079454
'11100000' 15287 4.184322266
'01010000' 15252 4.183326797
'01100001' 14930 4.174059808
'00111010' 14154 4.150879191
'01010001' 14153 4.150848507
'00101001' 13919 4.143608035
'01001010' 13845 4.14129296
'10101000' 13785 4.13940677
'11010010' 13718 4.137290799
'10101001' 13715 4.137195812
'10100001' 13527 4.13120149
'01100010' 13504 4.130462429
'00010101' 13247 4.122117536
'10010001' 12967 4.112839511
'01110001' 12948 4.112202691
'01100100' 12684 4.103256233
'11000001' 12108 4.083072412
'01101010' 11727 4.069186925
'10100010' 11649 4.066288645
'00100011' 11364 4.055531225
'11000010' 10865 4.036029731
'10011010' 10848 4.035349677
'00000111' 10751 4.031448862
'00100101' 10466 4.01978073
'00101010' 10086 4.003718964
'01000110' 9978 3.9990435
'10001001' 9721 3.987710943
'00001011' 9639 3.98403198
'10010100' 9636 3.983896791
'10110001' 9443 3.97510999
'00111001' 9433 3.974649834
'01000101' 9319 3.969369312
'01000011' 9225 3.964966375
'00001101' 8985 3.953518081
'10000011' 8742 3.941610802
'10001010' 8737 3.941362336
'01011000' 7945 3.900093902
'01001011' 7228 3.859018144
'01111000' 7210 3.857935265
'01110000' 6977 3.843668723
'11001010' 6968 3.843108142
'00110100' 6649 3.822756333
'00111000' 6626 3.821251432
'00011100' 6567 3.817367016
'11100010' 6470 3.810904281
'11010001' 6230 3.794488047
'10101010' 5816 3.764624398
'10110000' 5440 3.7355989
'10111000' 5408 3.733036683
'10011001' 5322 3.72607487
'11011000' 5267 3.721563318
'00101011' 4922 3.692141609
'11010000' 4771 3.678609417
'10100011' 4699 3.672005445
'01100011' 4513 3.654465334
'10011000' 4486 3.651859269
'11000011' 4168 3.61992771
'10001011' 3975 3.599337133
'01010100' 3881 3.588943643
'11110000' 3796 3.579326204
1 MB Sliding Windows (over 100 KB Bins): Fraction Captured by
1 MB Sliding Windows (over 100 KB Bins): MAC (divided by all SNPs)
CC BXD BXP HS Classical + WSB CC BXD BXP HS Classical + WSB Loc CC BXD BXP HS Classical + WSB
0 0 4531 162 175 11 0 0.177283 0.006339 0.006847 0.00043 90 0.191541 0.033562 0.303151 0.078801 0.102592
1 0 1610 77 428 8 0 0.062994 0.003013 0.016746 0.000313 91 0.190507 0.041014 0.302174 0.076775 0.100312
2 0 818 33 314 9 0 0.032006 0.001291 0.012286 0.000352 92 0.190688 0.046986 0.301391 0.074961 0.097468
3 0 608 27 279 13 0 0.023789 0.001056 0.010916 0.000509 93 0.185905 0.044829 0.294829 0.069384 0.091724
4 0 611 27 210 11 0 0.023906 0.001056 0.008217 0.00043 94 0.179362 0.044829 0.294085 0.061105 0.08465
5 0 635 36 249 37 0 0.024845 0.001409 0.009743 0.001448 95 0.17493 0.046367 0.29727 0.04717 0.067134
6 0 662 44 250 46 0 0.025902 0.001722 0.009782 0.0018 96 0.182974 0.059287 0.289869 0.052392 0.073921
7 0 668 44 276 60 0 0.026137 0.001722 0.010799 0.002348 97 0.187116 0.059255 0.274932 0.059213 0.082282
8 0 642 45 263 55 0 0.025119 0.001761 0.01029 0.002152 98 0.189987 0.05901 0.268639 0.061978 0.084947
9 0 685 82 294 67 0 0.026802 0.003208 0.011503 0.002621 99 0.195037 0.056769 0.276621 0.061639 0.085037
10 0 726 80 341 89 0 0.028406 0.00313 0.013342 0.003482 100 0.196733 0.042405 0.295447 0.05557 0.078073
11 0 731 89 365 70 0 0.028602 0.003482 0.014281 0.002739 101 0.198807 0.032341 0.289625 0.048191 0.076701
12 0 754 111 341 103 0 0.029502 0.004343 0.013342 0.00403 102 0.199127 0.023976 0.28953 0.048938 0.080285
13 0 783 98 364 109 0 0.030636 0.003834 0.014242 0.004265 103 0.200285 0.023545 0.290942 0.05099 0.079715
14 0 771 118 396 143 0 0.030167 0.004617 0.015494 0.005595 104 0.200265 0.024516 0.283573 0.053287 0.0818
15 0 714 104 431 167 0 0.027936 0.004069 0.016864 0.006534 105 0.198208 0.022934 0.248937 0.061209 0.090125
16 0 714 97 441 172 0 0.027936 0.003795 0.017255 0.00673
17 0 655 93 514 158 0 0.025628 0.003639 0.020111 0.006182 (divided by captured SNPs)
18 0 656 78 499 193 0 0.025667 0.003052 0.019524 0.007551 Loc CC BXD BXP HS Classical + WSB
19 0 621 84 559 222 0 0.024298 0.003287 0.021872 0.008686 90 0.203175 0.5 0.5 0.336404 0.293695
20 0 577 83 542 208 0 0.022576 0.003248 0.021207 0.008138 91 0.20273 0.5 0.5 0.328629 0.287918
21 0 524 88 638 253 0 0.020502 0.003443 0.024963 0.009899 92 0.203388 0.5 0.5 0.322045 0.286383
22 0 483 60 600 298 0 0.018898 0.002348 0.023476 0.01166 93 0.201465 0.5 0.5 0.323357 0.272337
23 0 379 73 648 316 0 0.014829 0.002856 0.025354 0.012364 94 0.197108 0.5 0.5 0.318314 0.247594
24 0 335 61 624 335 0 0.013107 0.002387 0.024415 0.013107 95 0.190533 0.5 0.5 0.298223 0.226907
25 0 274 80 586 346 0 0.010721 0.00313 0.022928 0.013538 96 0.19718 0.5 0.5 0.289678 0.250955
26 0 238 47 609 405 0 0.009312 0.001839 0.023828 0.015846 97 0.202243 0.5 0.5 0.295862 0.252805
27 0 188 69 594 425 0 0.007356 0.0027 0.023241 0.016629 98 0.205218 0.5 0.5 0.29851 0.257685
28 0 175 79 615 512 0 0.006847 0.003091 0.024063 0.020033 99 0.211213 0.5 0.5 0.29886 0.254426
29 0 155 75 654 522 0 0.006065 0.002935 0.025589 0.020424 100 0.213183 0.5 0.5 0.308639 0.246559
30 0 118 63 564 563 0 0.004617 0.002465 0.022067 0.022028 101 0.214391 0.5 0.5 0.31095 0.228567
31 0 121 65 551 569 0 0.004734 0.002543 0.021559 0.022263 102 0.213931 0.5 0.5 0.33043 0.225908
32 0 116 47 480 554 0 0.004539 0.001839 0.018781 0.021676 103 0.21368 0.5 0.5 0.333333 0.232927
33 0 114 74 436 566 0 0.00446 0.002895 0.017059 0.022146 104 0.214896 0.5 0.5 0.333252 0.241181
34 0 97 75 452 573 0 0.003795 0.002935 0.017685 0.02242 105 0.218154 0.5 0.5 0.341525 0.251861
35 0 91 95 415 644 0 0.003561 0.003717 0.016238 0.025198
36 0 80 74 346 603 0 0.00313 0.002895 0.013538 0.023593
37 0 72 89 329 639 0 0.002817 0.003482 0.012873 0.025002
38 0 71 89 333 626 0 0.002778 0.003482 0.013029 0.024493
39 0 76 88 281 600 0 0.002974 0.003443 0.010995 0.023476
40 0 59 99 265 573 0 0.002308 0.003874 0.010369 0.02242
41 0 65 93 213 529 0 0.002543 0.003639 0.008334 0.020698
42 0 60 118 188 501 0 0.002348 0.004617 0.007356 0.019602
43 2 53 134 182 448 7.83E-05 0.002074 0.005243 0.007121 0.017529
44 0 72 157 181 415 0 0.002817 0.006143 0.007082 0.016238
45 1 53 163 161 348 3.91E-05 0.002074 0.006378 0.006299 0.013616
46 3 48 198 175 334 0.000117 0.001878 0.007747 0.006847 0.013068
47 1 50 225 134 265 3.91E-05 0.001956 0.008804 0.005243 0.010369
48 1 56 260 122 270 3.91E-05 0.002191 0.010173 0.004773 0.010564
49 2 57 347 140 261 7.83E-05 0.00223 0.013577 0.005478 0.010212
50 4 67 497 143 227 0.000157 0.002621 0.019446 0.005595 0.008882
51 1 53 507 138 220 3.91E-05 0.002074 0.019837 0.005399 0.008608
52 1 55 666 128 195 3.91E-05 0.002152 0.026058 0.005008 0.00763
53 0 65 844 121 202 0 0.002543 0.033023 0.004734 0.007904
54 3 94 1061 124 159 0.000117 0.003678 0.041513 0.004852 0.006221
55 3 79 1150 129 146 0.000117 0.003091 0.044996 0.005047 0.005712
56 2 102 1389 111 162 7.83E-05 0.003991 0.054347 0.004343 0.006339
57 2 106 1493 117 169 7.83E-05 0.004147 0.058416 0.004578 0.006612
58 4 137 1582 115 150 0.000157 0.00536 0.061898 0.0045 0.005869
59 5 145 1474 113 161 0.000196 0.005673 0.057673 0.004421 0.006299
60 5 127 1370 140 139 0.000196 0.004969 0.053604 0.005478 0.005439
61 7 135 1435 131 153 0.000274 0.005282 0.056147 0.005126 0.005986
62 3 130 1248 162 160 0.000117 0.005086 0.04883 0.006339 0.00626
63 8 123 1054 179 168 0.000313 0.004813 0.04124 0.007004 0.006573
64 13 103 966 208 164 0.000509 0.00403 0.037796 0.008138 0.006417
65 11 102 836 206 177 0.00043 0.003991 0.03271 0.00806 0.006925
66 18 90 625 253 206 0.000704 0.003521 0.024454 0.009899 0.00806
67 31 92 523 258 248 0.001213 0.0036 0.020463 0.010095 0.009703
68 25 73 430 302 256 0.000978 0.002856 0.016824 0.011816 0.010016
69 38 57 342 307 277 0.001487 0.00223 0.013381 0.012012 0.010838
70 53 62 206 285 276 0.002074 0.002426 0.00806 0.011151 0.010799
71 51 34 167 317 334 0.001995 0.00133 0.006534 0.012403 0.013068
72 62 14 143 302 351 0.002426 0.000548 0.005595 0.011816 0.013733
73 79 10 117 280 422 0.003091 0.000391 0.004578 0.010955 0.016511
74 69 7 110 259 452 0.0027 0.000274 0.004304 0.010134 0.017685
75 74 8 80 211 492 0.002895 0.000313 0.00313 0.008256 0.01925
76 93 3 76 200 493 0.003639 0.000117 0.002974 0.007825 0.019289
77 89 5 54 181 472 0.003482 0.000196 0.002113 0.007082 0.018468
78 80 0 57 148 430 0.00313 0 0.00223 0.005791 0.016824
79 110 7 34 135 392 0.004304 0.000274 0.00133 0.005282 0.015338
80 89 6 28 129 367 0.003482 0.000235 0.001096 0.005047 0.014359
81 165 1 27 118 297 0.006456 3.91E-05 0.001056 0.004617 0.011621
82 178 0 18 118 275 0.006965 0 0.000704 0.004617 0.01076
83 211 2 13 84 251 0.008256 7.83E-05 0.000509 0.003287 0.009821
84 289 2 18 66 259 0.011308 7.83E-05 0.000704 0.002582 0.010134
85 390 0 16 60 191 0.015259 0 0.000626 0.002348 0.007473
86 474 0 16 42 163 0.018546 0 0.000626 0.001643 0.006378
87 658 0 18 37 99 0.025745 0 0.000704 0.001448 0.003874
88 876 0 19 33 106 0.034275 0 0.000743 0.001291 0.004147
89 1154 0 23 31 93 0.045152 0 0.0009 0.001213 0.003639
90 1509 0 10 23 60 0.059042 0 0.000391 0.0009 0.002348
91 1871 0 8 27 66 0.073206 0 0.000313 0.001056 0.002582
92 2183 0 8 12 72 0.085414 0 0.000313 0.00047 0.002817
93 2652 0 2 7 47 0.103764 0 7.83E-05 0.000274 0.001839
94 2941 0 1 4 32 0.115072 0 3.91E-05 0.000157 0.001252
95 2861 0 0 4 29 0.111941 0 0 0.000157 0.001135
96 2234 0 0 0 13 0.087409 0 0 0 0.000509
97 1712 0 0 2 11 0.066985 0 0 7.83E-05 0.00043
98 1164 0 0 0 13 0.045543 0 0 0 0.000509
99 938 0 0 0 0 0.036701 0 0 0 0
100 55 10 0 11 17 0.002152 0.000391 0 0.00043 0.000665
25558 25558 25558 25558 25558 1 1 1 1 1