Table 4

Gene deletion calls in the SC dataset
Population Sample Gene name Gene function Chr Start [bp] End [bp] Posterior probability RDobserved RDexpected
YRI NA18523 BCL2L15 BCL2-like 15 1 114225268 114231520 1.000 533 1158
YRI NA18523 HIPK1 homeodomain interacting protein kinase 1 1 114298778 114317657 1.000 2539 5272
TSI NA20533 GLOD4 glyoxalase domain containing 4 17 610163 632245 1.000 1322 2295
TSI NA20533 C1QBP complement component 1, q subcomponent binding protein 17 5277059 5282317 1.000 793 1416
TSI NA20533 C17orf91 chromosome 17 open reading frame 91 17 1562414 1563890 1.000 369 574
YRI NA18523 NRAS neuroblastoma RAS viral (v-ras) oncogene homolog 1 115052679 115060304 1.000 702 1462
YRI NA18523 TRI3 tripartite motif-containing 33 1 114741793 114808533 1.000 2610 5225
TSI NA20533 TRPV3 transient receptor potential cation channel, subfamily V, member 3 17 3363961 3404894 1.000 3365 5275
TSI NA20774 PTMAP1 prothymosin, alpha pseudogene 1 (gene sequence 26) 6 30725671 30728671 1.000 132 260
TSI NA20796 SNRNP27 small nuclear ribonucleoprotein 27 kDa (U4/U6.U5) 2 69974621 69977184 0.998 105 194
TSI NA20807 HIST1H2BC histone cluster 1, H2bc 6 26231731 26232111 0.998 42 90
TSI NA20772 ULBP1 UL16 binding protein 1 6 150331436 150332954 0.997 104 205
TSI NA20807 CYP2A13 cytochrome P450, family 2, subfamily A, polypeptide 13 19 46291375 46293686 0.996 126 204
YRI NA18508 PTMAP1 prothymosin, alpha pseudogene 1 (gene sequence 26) 6 30725671 30728671 0.992 145 230
CEU NA07000 PSG8 pregnancy specific beta-1-glycoprotein 8 19 47950287 47960273 0.990 29 70
CEU NA11893 PSG8 pregnancy specific beta-1-glycoprotein 8 19 47950287 47960273 0.985 43 86
TSI NA20771 PTMAP1 prothymosin, alpha pseudogene 1 (gene sequence 26) 6 30725671 30728671 0.980 533 862
TSI NA20773 CCK cholecystokinin 3 42274594 42280126 0.971 282 474
CEU NA07000 HMGN4 high mobility group nucleosomal binding domain 4 6 26653414 26653686 0.966 68 132
CEU NA12749 HMGN4 high mobility group nucleosomal binding domain 4 6 26653414 26653686 0.966 156 286
TSI NA20772 AIF1 allograft inflammatory factor 1 6 31692086 31692262 0.964 51 124
CEU NA12348 DUSP10 dual specificity phosphatase 10 1 219942377 219946216 0.962 155 242
YRI NA18508 ULBP1 UL16 binding protein 1 6 150331436 150332954 0.941 40 79
YRI NA18523 PPM1J protein phosphatase, Mg2+/Mn2+ dependent, 1 J 1 113056116 113057756 0.891 560 924
TSI NA20807 POU5F1 POU class 5 homeobox 1 6 31240884 31241803 0.891 124 193
TSI NA20772 SERPINA11 serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 11 14 93978696 93984864 0.889 786 1243
CEU NA07000 KRT18P19 keratin 18 pseudogene 19 12 51630379 51632393 0.887 85 174
CEU NA12348 ULBP1 UL16 binding protein 1 6 150331436 150332954 0.879 49 88
YRI NA18523 RHOC ras homolog gene family, member C 1 113054308 113055529 0.867 557 955
CEU NA12348 STBD1 starch binding domain 1 4 77446947 77450177 0.839 246 395
CEU NA07000 POU5F1 POU class 5 homeobox 1 6 31240884 31241803 0.823 106 169
CEU NA12749 SNRNP27 small nuclear ribonucleoprotein 27 kDa (U4/U6.U5) 2 69974621 69977184 0.775 142 216
TSI NA20752 POU5F1 POU class 5 homeobox 1 6 31240884 31241803 0.723 76 142
TSI NA20807 HIST1H2BO histone cluster 1, H2bo 6 27969220 27969600 0.723 48 88
TSI NA20589 POU5F1 POU class 5 homeobox 1 6 31240884 31241803 0.697 61 117
TSI NA20786 NPSR1 neuropeptide S receptor 1 7 34884213 34884321 0.678 51 88

Wu et al.

Wu et al. BMC Bioinformatics 2012 13:305   doi:10.1186/1471-2105-13-305

Open Data