Mercurial > repos > miller-lab > genome_diversity

comparison test-data/test_out/select_snps/select_snps.gdSnp @ 10:9b92372de9f6

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
rename snp to gsSnp, sap to gdSap
author Richard Burhans <burhans@bx.psu.edu>
date Tue, 04 Sep 2012 12:49:53 -0400
parents test-data/test_out/select_snps/select_snps.snp@e29f4d801bb0
children
comparison
equal deleted inserted replaced
9:22fe0154fa54 10:9b92372de9f6
1 #{"column_names":["scaf","pos","A","B","qual","ref","rpos","rnuc","1A","1B","1G","1Q","2A","2B","2G","2Q","3A","3B","3G","3Q","4A","4B","4G","4Q","5A","5B","5G","5Q","6A","6B","6G","6Q","pair","dist",
2 #"prim","rflp"],"dbkey":"canFam2","individuals":[["PB1",9],["PB2",13],["PB3",17],["PB4",21],["PB6",25],["PB8",29]],"pos":2,"rPos":7,"ref":6,"scaffold":1,"species":"bear"}
3 Contig161_chr1_4641264_4641879 115 C T 73.5 chr1 4641382 C 6 0 2 45 8 0 2 51 15 0 2 72 5 0 2 42 6 0 2 45 10 0 2 57 Y 54 0.323 0
4 Contig86_chr1_30984450_30985684 670 C T 365.0 chr1 30985133 C 9 0 2 54 10 0 2 57 13 0 2 66 3 0 2 36 9 0 2 54 7 0 2 48 Y 145 0.031 0
5 Contig21_chr1_60697952_60699446 307 G A 51.9 chr1 60698265 G 12 0 2 63 9 0 2 54 4 0 2 39 6 0 2 45 9 0 2 54 4 0 2 39 Y 98 0.507 0
6 Contig64_chr1_87343284_87345672 163 T A 3.76 chr1 87343443 C 0 2 2 1 0 0 -1 0 5 0 2 42 2 0 2 33 0 1 2 14 0 0 -1 0 N 3 0.039 2
7 Contig20_chr1_110679280_110679687 181 C T 87.4 chr1 110679454 - 1 0 2 30 7 0 2 48 4 0 2 39 2 0 2 33 2 0 2 33 0 0 -1 0 N 31 0.660 2
8 Contig222_chr2_9817738_9818143 220 C T 888.0 chr2 9817960 C 17 0 2 78 12 0 2 63 20 0 2 87 8 0 2 51 11 0 2 60 12 0 2 63 Y 76 0.093 1
9 Contig47_chr2_25470778_25471576 126 G A 888.0 chr2 25470896 G 12 0 2 63 14 0 2 69 14 0 2 69 10 0 2 57 18 0 2 81 13 0 2 66 N 11 0.289 1
10 Contig6_chr2_56859179_56859956 671 T C 999.9 chr2 56859851 T 15 0 2 72 18 0 2 81 20 0 2 90 19 0 2 84 19 0 2 84 24 0 2 99 N 28 5.308 1
11 Contig163_chr2_76402959_76404830 221 C T 127.0 chr2 76403181 C 4 0 2 42 10 0 2 57 9 0 2 54 11 0 2 60 7 0 2 48 9 0 2 54 Y 54 0.178 1
12 Contig56_chr3_17326225_17327548 387 G C 91.2 chr3 17326591 G 14 0 2 69 13 0 2 66 15 0 2 72 15 0 2 72 13 0 2 66 12 0 2 63 Y 20 0.225 3
13 Contig108_chr3_46210055_46210874 367 A G 21.0 chr3 46210423 A 19 0 2 84 10 0 2 57 16 0 2 75 14 0 2 69 20 0 2 87 11 0 2 60 N 236 0.028 1
14 Contig1_chr3_51588422_51589409 926 A G 51.0 chr3 51589353 G 2 0 2 33 2 0 2 33 6 0 2 45 4 0 2 39 9 0 2 54 11 0 2 60 N 21 1.147 0
15 Contig65_chr3_80727952_80728283 39 T C 71.2 chr3 80727990 T 7 0 2 48 3 0 2 36 8 0 2 51 6 0 2 45 8 0 2 51 11 0 2 60 N 22 7.078 0
16 Contig134_chr4_12145648_12148225 1326 C T 164.0 chr4 12146961 C 9 0 2 54 8 0 2 51 7 0 2 48 3 0 2 36 5 0 2 42 5 0 2 42 Y 4 0.080 1
17 Contig19_chr4_26233601_26233991 146 G C 51.6 chr4 26233744 G 10 0 2 57 8 0 2 51 9 0 2 54 5 0 2 42 9 0 2 54 4 0 2 39 N 41 0.163 3
18 Contig17_chr4_61310346_61311158 267 C T 49.9 chr4 61310604 T 10 0 2 57 7 0 2 48 9 0 2 54 10 0 2 57 14 0 2 69 7 0 2 48 Y 219 0.098 0
19 Contig31_chr5_4734956_4736547 1166 C T 133.0 chr5 4736132 C 14 0 2 69 8 0 2 51 17 0 2 78 4 0 2 39 9 0 2 54 12 0 2 63 Y 1 0.021 0
20 Contig6_chr5_26899813_26900498 97 A C 88.6 chr5 26899910 A 15 0 2 72 14 0 2 69 27 0 2 108 15 0 2 72 13 0 2 69 12 0 2 63 Y 92 7.370 3
21 Contig45_chr5_50892738_50892968 169 C A 25.8 chr5 50892911 C 10 0 2 57 7 0 2 48 10 0 2 60 6 0 2 45 6 0 2 45 13 0 2 66 N 244 0.497 1
22 Contig45_chr5_76133561_76134403 388 A G 103.0 chr5 76133941 G 3 0 2 36 8 0 2 51 8 0 2 51 5 0 2 42 6 0 2 45 7 0 2 48 Y 57 0.038 0
23 Contig111_chr6_5821219_5822519 1060 A G 68.1 chr6 5822321 T 7 0 2 48 6 0 2 45 11 0 2 60 9 0 2 54 3 0 2 36 12 0 2 63 Y 7 0.231 1
24 Contig102_chr6_30271329_30271577 39 T G 139.0 chr6 30271371 G 3 0 2 36 4 0 2 39 6 0 2 45 1 0 2 30 4 0 2 39 4 0 2 39 N 15 1.159 0
25 Contig112_chr6_51024554_51024851 100 A G 121.0 chr6 51024654 A 10 0 2 57 12 0 2 63 9 0 2 54 13 0 2 66 14 0 2 69 17 0 2 78 N 75 4.287 0
26 Contig84_chr7_6648683_6650255 1297 G A 110.0 chr7 6649988 G 18 0 2 81 9 0 2 54 22 0 2 77 16 0 2 75 20 0 2 87 6 0 2 45 Y 83 0.166 0
27 Contig206_chr7_26281823_26282074 103 C A 101.0 chr7 26281925 T 11 0 2 60 16 0 2 61 19 0 2 84 6 0 2 45 19 0 2 84 16 0 2 75 N -1 0.947 1
28 Contig38_chr7_50681997_50682600 42 T C 92.4 chr7 50682037 G 6 0 2 45 2 0 2 33 10 0 2 57 12 0 2 63 5 0 2 42 6 0 2 45 Y 94 0.146 0
29 Contig91_chr8_12804505_12805470 409 C A 111.0 chr8 12804906 C 8 0 2 51 10 0 2 57 15 0 2 72 12 0 2 63 14 0 2 69 15 0 2 72 N 145 0.175 0
30 Contig8_chr8_27811135_27812620 333 C T 37.9 chr8 27811458 C 4 0 2 39 11 0 2 60 18 0 2 81 5 0 2 42 6 0 2 45 5 0 2 42 Y 1 0.272 0
31 Contig17_chr8_57490059_57490498 69 G T 97.4 chr8 57490127 A 2 0 2 33 11 0 2 60 15 0 2 72 16 0 2 75 8 0 2 51 10 0 2 57 N 40 0.522 5
32 Contig73_chr9_29451535_29452248 616 A G 24.7 chr9 29452127 G 4 0 2 39 7 0 2 48 1 0 2 30 4 0 2 39 7 0 2 48 6 0 2 45 N 49 0.448 4
33 Contig96_chr9_39008495_39009278 215 A C 98.7 chr9 39008708 C 7 0 2 48 13 0 2 66 28 0 2 111 16 0 2 75 17 0 2 78 17 0 2 78 Y 8 0.427 1
34 Contig22_chr10_15505382_15505589 172 T C 38.5 chr10 15505548 T 2 0 2 33 6 0 2 45 8 0 2 51 8 0 2 51 9 0 2 54 12 0 2 63 N 284 2.861 0
35 Contig69_chr10_40547265_40548153 371 G A 58.1 chr10 40547649 A 9 0 2 54 8 0 2 51 8 0 2 51 9 0 2 54 4 0 2 39 5 0 2 42 Y 20 0.138 4
36 Contig9_chr10_51475063_51476054 770 C T 57.3 chr10 51475839 C 6 0 2 45 16 0 2 75 16 0 2 75 13 0 2 66 9 0 2 54 9 2 2 21 N 80 0.394 0
37 Contig72_chr11_7142765_7143772 146 G A 152.0 chr11 7142911 A 8 0 2 51 8 0 2 51 24 0 2 99 10 0 2 57 17 0 2 78 11 0 2 60 Y 90 1.137 0
38 Contig7_chr11_40017076_40017630 352 C T 46.3 chr11 40017422 C 7 0 2 48 9 0 2 54 6 0 2 45 8 0 2 51 16 0 2 75 9 0 2 54 Y 44 0.336 0
39 Contig16_chr11_53408448_53408790 187 A G 153.0 chr11 53408638 A 7 0 2 48 9 0 2 54 18 0 2 81 10 0 2 57 11 0 2 60 12 0 2 63 Y 116 1.367 0
40 Contig21_chr12_18403415_18404381 586 G T 34.5 chr12 18403983 - 13 0 2 66 16 0 2 75 25 0 2 102 12 0 2 63 12 0 2 63 14 0 2 69 Y 12 0.068 0
41 Contig41_chr12_25565452_25566993 475 G T 6.29 chr12 25565926 G 15 0 2 72 14 0 2 69 10 0 2 57 15 0 2 72 18 0 2 81 19 0 2 84 N 10 2.231 1
42 Contig5_chr12_53880670_53882675 1221 A C 99.4 chr12 53881888 A 16 0 2 75 18 0 2 81 23 0 2 96 10 0 2 57 15 0 2 72 17 0 2 78 Y 31 0.061 0
43 Contig107_chr13_26045881_26046290 341 C G 81.4 chr13 26046230 C 16 0 2 75 20 0 2 90 14 0 2 69 15 0 2 72 9 0 2 54 9 0 2 54 Y 51 4.510 0
44 Contig251_chr13_28498333_28501066 864 T G 296.0 chr13 28499180 T 3 0 2 36 5 0 2 42 4 0 2 39 2 0 2 33 5 0 2 42 6 0 2 45 Y 9 0.068 0
45 Contig55_chr13_53467708_53468101 221 T G 132.0 chr13 53467925 T 25 0 2 102 12 0 2 63 26 0 2 105 7 0 2 48 16 0 2 75 16 0 2 75 N 20 5.717 1
46 Contig48_chr14_11839435_11843272 3014 A G 163.0 chr14 11842446 A 10 0 2 57 8 0 2 51 13 0 2 66 10 0 2 57 5 0 2 42 10 0 2 57 Y 31 0.908 0
47 Contig28_chr14_26905747_26909514 975 G C 3.13 chr14 26906723 G 16 0 2 75 10 0 2 57 12 0 2 63 15 0 2 72 10 0 2 57 7 0 2 48 N 287 0.117 2
48 Contig64_chr14_56768376_56768902 473 C T 29.0 chr14 56768832 C 15 0 2 72 11 0 2 60 14 0 2 69 14 0 2 69 7 0 2 48 9 0 2 54 Y 91 8.281 0
49 Contig60_chr15_18493036_18494316 150 G A 92.6 chr15 18493188 G 9 0 2 54 13 0 2 66 9 0 2 54 6 0 2 45 5 0 2 42 12 0 2 63 Y 45 0.125 0
50 Contig112_chr15_26772864_26773267 374 C T 21.6 chr15 26773244 C 4 0 2 39 4 0 2 39 5 0 2 42 2 0 2 33 4 0 2 39 3 0 2 36 N 18 +99. 0
51 Contig119_chr16_6160274_6160477 180 G A 54.8 chr16 6160457 G 7 0 2 48 6 0 2 45 12 0 2 63 3 0 2 36 11 0 2 60 10 0 2 57 N 42 +99. 0
52 Contig60_chr16_28079136_28080263 588 T G 157.0 chr16 28079739 T 22 0 2 93 20 0 2 87 22 0 2 93 17 0 2 78 12 0 2 63 10 0 2 57 Y 105 5.999 1
53 Contig31_chr17_12128267_12129637 205 G A 90.5 chr17 12128484 G 7 0 2 48 6 0 2 45 6 0 2 45 11 0 2 60 7 0 2 48 4 0 2 39 Y 10 0.246 0
54 Contig99_chr17_26021506_26022200 505 C T 88.8 chr17 26022017 T 15 0 2 72 13 0 2 66 19 0 2 84 9 0 2 54 10 0 2 57 11 0 2 60 Y 1 0.172 1
55 Contig27_chr17_61713766_61716585 1056 G C 40.0 chr17 61714821 G 4 0 2 39 8 0 2 51 10 0 2 57 6 0 2 45 6 0 2 45 3 0 2 36 N 6 2.200 4
56 Contig229_chr18_3706523_3708577 1076 A G 83.9 chr18 3707630 A 11 0 2 60 13 0 2 66 26 0 2 105 11 0 2 60 15 0 2 72 17 0 2 78 Y 63 0.445 0
57 Contig82_chr18_27305489_27306229 566 C T 49.5 chr18 27306051 A 6 0 2 45 6 0 2 45 10 0 2 57 11 0 2 60 6 0 2 45 7 0 2 48 N 1 0.349 0
58 Contig64_chr18_55979770_55980315 49 G A 89.1 chr18 55979824 G 3 0 2 36 9 0 2 54 7 0 2 51 4 0 2 39 3 0 2 36 3 0 2 36 Y -1 2.124 0
59 Contig146_chr19_5221790_5223013 143 A G 114.0 chr19 5221916 - 1 0 2 30 4 0 2 39 3 0 2 36 5 0 2 42 2 0 2 33 5 0 2 42 Y 12 0.870 0
60 Contig129_chr19_25541958_25542221 202 T C 68.1 chr19 25542154 C 11 0 2 60 19 0 2 84 10 0 2 60 17 0 2 78 9 0 2 54 12 0 2 63 N -1 2.551 1
61 Contig60_chr19_54013816_54014398 281 A G 138.0 chr19 54014103 C 6 0 2 45 15 0 2 72 7 0 2 48 10 0 2 57 15 0 2 72 10 0 2 57 Y 188 1.271 0
62 Contig50_chr20_12138509_12141975 3206 C A 248.0 chr20 12141763 C 8 0 2 51 15 0 2 72 14 0 2 69 6 0 2 45 10 0 2 57 7 0 2 48 Y 2 0.384 0
63 Contig36_chr20_32631363_32632049 176 G A 24.1 chr20 32631526 G 7 0 2 48 14 0 2 69 19 0 2 84 14 0 2 69 15 0 2 72 16 0 2 75 N 50 1.150 0
64 Contig50_chr21_4178523_4178687 121 G A 362.0 chr21 4178640 G 8 0 2 51 14 0 2 69 5 0 2 42 3 0 2 36 11 0 2 60 4 0 2 39 N 392 0.483 0
65 Contig129_chr21_31045749_31046924 381 A G 129.0 chr21 31046141 A 19 0 2 84 8 0 2 51 23 0 2 96 12 0 2 63 15 0 2 72 18 0 2 81 Y 69 0.028 2
66 Contig159_chr22_7896450_7896974 109 G C 151.0 chr22 7896570 G 16 0 2 75 5 7 1 62 14 0 2 69 16 0 2 75 13 0 2 66 13 0 2 66 Y 16 0.465 0
67 Contig23_chr22_34612023_34612568 167 C G 92.3 chr22 34612181 C 11 0 2 60 18 0 2 81 13 0 2 66 8 0 2 51 12 0 2 63 14 0 2 69 Y 7 0.409 0
68 Contig26_chr22_57817664_57819633 1453 A G 150.0 chr22 57819121 G 9 0 2 54 9 0 2 54 13 0 2 66 15 0 2 72 11 0 2 60 14 0 2 69 N 15 0.471 1
69 Contig133_chr23_3525134_3526502 1223 A G 201.0 chr23 3526387 A 11 0 2 60 13 0 2 66 23 0 2 96 21 0 2 90 13 0 2 66 10 0 2 57 Y 61 1.359 0
70 Contig35_chr23_28447813_28449115 70 T A 21.3 chr23 28447881 T 9 0 2 54 8 0 2 51 10 0 2 57 9 0 2 54 10 0 2 57 12 0 2 63 N 251 0.163 1
71 Contig50_chr24_22515247_22516072 761 C T 243.0 chr24 22515981 T 11 0 2 60 10 0 2 57 8 0 2 51 9 0 2 54 18 0 2 81 8 0 2 51 Y 1 0.190 0
72 Contig84_chr24_29196623_29199644 466 C T 126.0 chr24 29197091 T 7 0 2 48 11 0 2 60 8 0 2 51 7 0 2 48 11 0 2 60 15 0 2 72 Y 42 0.215 0
73 Contig144_chr25_4011170_4013134 541 A G 160.0 chr25 4011690 A 12 0 2 63 17 0 2 78 13 0 2 66 13 0 2 66 13 0 2 66 13 0 2 66 Y 5 0.087 0
74 Contig103_chr25_38891221_38892140 407 G A 131.0 chr25 38891644 G 8 0 2 51 14 0 2 69 18 0 2 81 8 0 2 51 8 0 2 51 11 0 2 60 Y 149 0.167 4
75 Contig204_chr26_4311195_4311778 170 C T 16.9 chr26 4311363 T 20 0 2 87 8 0 2 51 13 0 2 66 18 0 2 81 11 0 2 60 14 0 2 69 N 35 0.085 0
76 Contig146_chr26_26622638_26623906 574 G A 186.0 chr26 26623219 A 11 0 2 60 12 0 2 63 9 0 2 54 11 0 2 60 9 0 2 54 12 0 2 63 Y 1 0.318 0
77 Contig135_chr27_6853874_6854079 158 C T 116.0 chr27 6854032 T 18 0 2 81 19 0 2 84 13 0 2 66 7 0 2 48 8 0 2 51 11 0 2 60 N 4 0.060 1
78 Contig64_chr27_34654435_34654621 132 C A 115.0 chr27 34654567 T 2 0 2 33 2 0 2 33 5 0 2 42 3 0 2 36 3 0 2 36 8 0 2 51 N 12 0.297 1
79 Contig131_chr28_6481806_6483783 138 C T 36.2 chr28 6481953 C 12 0 2 63 12 0 2 63 20 0 2 87 11 0 2 60 10 0 2 57 12 0 2 63 Y 10 0.387 0
80 Contig60_chr28_30197166_30197364 92 T C 164.0 chr28 30197258 T 10 0 2 57 13 0 2 66 15 0 2 72 16 0 2 75 12 0 2 63 11 0 2 60 N 369 1.139 0
81 Contig29_chr29_4726399_4727143 559 A T 163.0 chr29 4726955 A 15 0 2 72 18 0 2 81 18 0 2 81 16 0 2 75 11 0 2 60 14 0 2 72 Y 161 3.114 0
82 Contig1_chr30_5992217_5993068 106 C T 129.0 chr30 5992319 C 10 0 2 57 11 0 2 60 7 0 2 48 11 0 2 60 10 0 2 57 12 0 2 63 Y 76 1.079 0
83 Contig165_chr30_25804389_25804926 190 T C 126.0 chr30 25804592 C 3 0 2 36 8 0 2 51 7 0 2 48 10 0 2 57 7 0 2 48 4 0 2 39 Y 113 0.329 0
84 Contig38_chr31_5164423_5166573 2074 C T 134.0 chr31 5166501 T 13 0 2 66 10 0 2 57 17 0 2 78 11 0 2 60 17 0 2 78 10 0 2 57 Y 58 +99. 0
85 Contig17_chr31_26433828_26434459 498 T C 9.79 chr31 26434322 T 18 0 2 81 10 0 2 57 15 0 2 72 13 0 2 66 16 0 2 75 15 0 2 72 Y 137 4.814 0
86 Contig9_chr32_19479532_19479735 12 A G 20.7 chr32 19479544 A 1 0 2 30 2 0 2 33 1 0 2 30 5 0 2 42 3 0 2 36 3 0 2 36 N 17 +99. 0
87 Contig30_chr32_25902721_25905783 208 C G 162.0 chr32 25902927 G 11 0 2 60 13 0 2 66 11 0 2 60 12 0 2 63 7 0 2 48 11 0 2 60 Y 145 0.322 2
88 Contig18_chr33_22207246_22209159 1363 G T 51.5 chr33 22208619 - 16 0 2 75 8 0 2 51 11 0 2 60 10 0 2 57 15 0 2 72 12 0 2 63 Y 59 2.560 0
89 Contig170_chr33_26189421_26189940 292 T C 98.4 chr33 26189703 T 21 0 2 90 13 0 2 66 15 0 2 72 13 0 2 66 19 0 2 84 13 0 2 66 Y 23 0.307 0
90 Contig113_chr34_13341080_13341643 236 C T 90.7 chr34 13341316 C 4 0 2 39 2 0 2 33 8 0 2 51 4 0 2 39 8 0 2 51 3 0 2 36 Y 47 0.412 3
91 Contig152_chr34_31794848_31795540 242 G A 93.2 chr34 31795093 G 11 0 2 60 24 0 2 99 17 0 2 78 15 0 2 72 18 0 2 81 17 0 2 78 Y 123 2.780 0
92 Contig47_chr35_3666773_3667898 348 G T 124.0 chr35 3667121 G 9 0 2 54 20 0 2 87 18 0 2 81 15 0 2 72 12 0 2 63 14 0 2 69 Y 285 0.235 0
93 Contig74_chr35_25394343_25394813 303 A T 221.0 chr35 25394646 G 23 0 2 96 15 0 2 72 25 0 2 105 7 7 1 49 18 0 2 81 16 0 2 75 Y 58 4.298 0
94 Contig5_chr36_4562983_4563634 343 C T 151.0 chr36 4563324 T 20 0 2 87 20 0 2 87 23 0 2 96 24 0 2 99 9 0 2 54 8 0 2 51 Y 40 1.169 0
95 Contig133_chr36_32954045_32955409 136 A G 116.0 chr36 32954182 A 16 0 2 75 15 0 2 72 20 0 2 87 11 0 2 60 18 0 2 81 13 0 2 66 Y 74 3.772 1
96 Contig53_chr37_6665763_6665919 116 C T 111.0 chr37 6665875 C 9 0 2 54 9 0 2 54 5 0 2 42 9 0 2 54 8 0 2 51 10 0 2 57 N 15 10.875 1
97 Contig2_chr37_31197993_31198256 182 C T 39.6 chr37 31198171 T 6 0 2 45 10 0 2 57 7 0 2 48 9 0 2 54 10 0 2 57 12 0 2 63 N 2 0.595 0
98 Contig7_chr38_12217200_12218387 1163 A T 44.4 chr38 12218353 A 11 0 2 60 13 0 2 66 17 0 2 78 10 0 2 57 11 0 2 60 11 0 2 60 Y 67 +99. 0
99 Contig265_chrX_2689247_2689484 114 C G 103.0 chrX 2689356 C 11 0 2 60 9 0 2 54 13 0 2 66 16 0 2 75 14 0 2 69 10 0 2 57 N 2 9.232 1
100 Contig113_chrX_26287829_26288398 385 C T 59.6 chrX 26288213 C 9 0 2 54 9 0 2 54 17 0 2 78 11 0 2 60 3 8 1 44 4 0 2 39 N 13 0.077 0
101 Contig90_chrX_57430715_57431566 548 C T 116.0 chrX 57431266 T 9 0 2 54 18 0 2 81 13 0 2 66 14 0 2 69 8 0 2 54 7 0 2 48 Y 261 0.154 1
102 Contig133_chrX_84833782_84834125 182 G A 69.7 chrX 84833962 G 5 0 2 42 18 0 2 81 12 0 2 63 19 0 2 84 6 3 1 27 7 0 2 48 N 619 0.278 0