Washington University School of Medicine SNP Research Facility
Google Research
FP-TDI SNP genotyping
HOME               SNPS               INFORMATICS               SERVICES               RESEARCH               RESOURCES      


: : QC Tools

: : Technician Tools

: : General Tools

HapMap Project Genotyping on Chr 7p (UCSF-WU)

Note: This page contains HapMap data for UCSF-WU's region, chromosome 7p. To access the complete set of HapMap frequencies, use SNPseek.

Our allocated region on 7p has been divided into six sections of ~10,000K for easier viewability. The key that describes column headings is below.

Last updated Nov 27 2007

SNPs per 100 kb Bin
0 - 10 mb10 - 20 mb20 - 30 mb30 - 40 mb40 - 50 mb50 - 57 mb

Bin (kb)AllocationCEUYRIHCBJPT
Tot DH SHPoly Mon AF QF IPPoly Mon AF QF IPPoly Mon AF QF IPPoly Mon AF QF IP
0-99312 8 1501 0 0 3 00 0 0 0 00 0 0 0 00 0 0 0 0
100-199523 127 1139 4 3 3 010 2 1 0 08 3 0 1 08 3 0 1 0
200-299457 218 3613 4 3 7 09 5 0 2 07 6 0 2 07 6 0 2 0
300-3990 0 00 0 0 0 00 0 0 0 00 0 0 0 00 0 0 0 0
400-49927 11 71 4 0 0 03 0 0 2 02 1 0 2 02 1 0 2 0
500-599196 58 608 4 2 6 07 1 1 3 06 3 0 2 06 3 0 2 0
600-699346 145 625 4 0 2 05 1 1 2 04 3 0 2 04 3 0 2 0
700-799357 144 485 4 3 15 04 3 0 2 04 3 0 2 05 2 0 2 0
800-899374 145 587 0 5 14 05 0 0 0 04 0 0 0 04 0 0 0 0
900-999480 241 4011 4 0 7 011 2 0 2 09 3 0 3 09 3 0 3 0
1000-1099403 146 678 7 2 8 08 4 0 1 08 3 0 2 08 3 0 2 0
1100-1199321 126 536 4 4 8 04 1 1 3 03 2 0 4 03 2 0 4 0
1200-1299212 94 362 6 3 9 01 0 0 7 02 4 0 2 02 4 0 2 0
1300-1399376 196 359 4 1 17 08 2 2 1 07 3 0 1 07 3 0 1 0
1400-1499277 103 529 1 4 5 05 2 0 3 07 0 0 3 07 0 0 3 0
1500-1599304 132 3210 8 2 3 013 4 0 1 06 8 0 2 07 7 0 2 0
1600-1699433 201 5110 4 4 4 08 3 0 3 08 1 1 4 08 1 1 4 0
1700-1799411 208 469 7 2 2 011 3 0 2 07 6 0 2 08 5 0 2 0
1800-1899358 177 608 7 2 8 08 0 0 6 010 1 0 3 010 1 0 3 0
1900-1999338 196 674 13 3 15 03 10 1 1 06 8 0 1 06 8 0 1 0
2000-2099301 142 3614 11 2 9 014 8 1 2 015 5 0 5 015 5 0 5 0
2100-2199313 136 319 9 0 3 08 5 0 4 07 4 0 5 07 4 0 5 0
2200-2299318 150 4913 4 1 8 010 4 1 2 06 6 0 5 05 7 0 5 0
2300-2399419 164 1159 3 3 8 08 4 0 1 07 4 0 2 07 4 0 2 0
2400-2499419 191 649 7 4 11 09 6 1 0 08 7 0 0 08 7 0 0 0
2500-2599392 218 7016 5 1 5 013 4 1 3 016 3 0 2 017 2 0 2 0
2600-2699346 202 5515 12 3 1 014 7 0 5 015 5 0 6 015 5 0 6 0
2700-2799390 193 7515 6 3 7 010 5 3 2 011 6 1 2 011 6 1 2 0
2800-2899397 207 6711 5 0 2 013 2 0 1 011 2 0 3 011 2 0 3 0
2900-2999505 255 7114 5 0 4 011 4 1 2 012 6 0 0 013 5 0 0 0
3000-3099418 238 4012 5 0 2 011 3 0 2 08 5 0 3 09 4 0 3 0
3100-3199469 265 6511 9 0 5 010 5 1 2 07 8 0 3 07 8 0 3 0
3200-3299290 153 4214 10 2 3 017 5 1 1 013 8 0 3 013 8 0 3 0
3300-3399287 146 4617 4 0 2 015 3 0 3 014 3 0 3 015 2 0 3 0
3400-3499417 208 6817 4 1 3 010 5 3 3 014 4 1 2 015 3 1 2 0
3500-3599292 155 338 11 0 3 013 1 1 4 06 11 0 2 06 11 0 2 0
3600-3699398 207 4214 9 2 2 016 4 0 3 013 8 0 1 012 9 0 1 0
3700-3799282 128 4316 10 0 1 017 4 2 3 016 7 0 3 016 7 0 3 0
3800-3899400 218 5114 5 2 4 012 3 0 3 011 5 0 2 09 7 0 2 0
3900-3999439 225 7316 6 2 8 018 2 0 2 010 11 0 1 013 8 0 1 0
4000-4099428 217 607 6 1 9 010 3 0 0 08 3 0 2 08 3 0 2 0
4100-4199472 277 6713 6 2 3 015 3 1 1 014 6 0 0 015 5 0 0 0
4200-4299473 183 7613 5 0 4 013 4 0 1 013 2 0 2 013 2 0 2 0
4300-4399332 169 4610 5 0 1 09 5 0 1 011 4 0 0 011 4 0 0 0
4400-4499208 80 344 3 1 3 06 1 0 1 06 0 0 2 06 0 0 2 0
4500-4599276 110 364 8 3 13 03 6 0 3 05 4 0 3 04 5 0 3 0
4600-4699369 155 726 7 2 6 06 3 1 3 04 6 0 2 04 6 0 2 0
4700-4799332 126 786 9 0 6 05 6 0 3 04 8 0 2 04 8 0 2 0
4800-4899322 153 4113 4 1 4 011 5 0 1 07 6 0 4 08 5 0 4 0
4900-4999434 153 698 5 0 3 05 2 2 3 05 3 0 4 05 3 0 4 0
5000-5099357 148 5010 9 1 3 06 8 2 1 05 8 1 2 08 5 1 2 0
5100-5199326 120 527 3 2 7 05 2 0 3 06 3 0 1 06 3 0 1 0
5200-5299339 157 5212 5 0 1 06 3 3 4 011 3 0 1 08 6 0 1 0
5300-5399393 186 727 5 1 12 06 2 1 3 06 4 0 2 06 4 0 2 0
5400-5499279 128 6212 16 1 10 016 6 1 3 010 13 0 3 09 14 0 3 0
5500-5599308 117 609 15 0 6 010 7 2 3 010 8 0 4 011 7 0 4 0
5600-5699452 124 9411 4 0 9 06 5 0 3 011 2 0 1 010 3 0 1 0
5700-5799268 46 1224 6 3 9 03 3 0 3 02 5 0 2 03 4 0 2 0
5800-5899351 165 5618 11 0 2 013 11 0 4 017 7 0 4 013 11 0 4 0
5900-5999225 92 368 6 0 6 09 0 1 3 06 5 0 1 06 5 0 1 0
6000-6099236 86 315 14 1 3 012 3 0 4 01 15 0 3 02 14 0 3 0
6100-6199361 126 5814 8 0 2 014 3 3 1 016 3 0 1 016 3 0 1 0
6200-6299378 168 6012 9 0 2 015 2 0 2 010 7 0 2 010 7 0 2 0
6300-6399243 82 3312 3 0 9 05 8 2 0 010 4 0 1 011 3 0 1 0
6400-6499306 108 7220 6 1 3 018 6 2 1 021 5 0 0 021 5 0 0 0
6500-6599211 63 475 4 1 5 07 2 0 0 03 4 0 2 03 4 0 2 0
6600-6699494 132 1355 2 0 8 02 0 0 4 03 1 0 2 03 1 0 2 0
6700-6799541 205 1027 6 1 6 05 3 0 5 07 2 0 3 07 2 0 3 0
6800-6899505 220 978 6 0 2 09 2 2 1 010 1 0 1 010 1 0 1 0
6900-6999365 203 5513 8 0 4 012 5 0 3 08 8 0 3 09 7 0 3 0
7000-7099388 182 5514 5 0 4 013 3 0 3 011 4 0 3 012 3 0 3 0
7100-7199419 266 6719 3 1 4 016 3 0 3 012 4 1 5 012 4 1 5 0
7200-7299236 120 3913 6 0 3 011 4 0 2 011 6 0 1 08 9 0 1 0
7300-7399281 154 3117 7 0 3 014 7 0 2 08 11 0 4 07 12 0 4 0
7400-7499422 234 4820 5 2 5 014 9 1 1 015 8 0 2 014 9 0 2 0
7500-7599285 174 4320 4 1 3 020 2 0 2 013 8 0 2 013 8 0 2 0
7600-7699421 271 4222 2 2 1 019 3 0 1 018 1 0 3 018 1 0 3 0
7700-7799322 158 6121 2 0 5 017 4 0 1 013 7 0 0 014 6 0 0 0
7800-7899241 124 3617 4 1 3 012 1 3 3 014 3 0 1 015 2 0 1 0
7900-7999360 210 5118 8 2 6 016 3 2 3 016 4 0 4 016 4 0 4 0
8000-8099311 199 3219 13 0 6 019 9 0 3 021 5 0 3 020 6 0 3 0
8100-8199312 158 319 7 1 0 010 5 0 0 05 9 0 0 06 8 0 0 0
8200-8299327 185 4115 8 0 8 013 4 0 4 016 2 1 2 018 0 1 2 0
8300-8399273 181 2718 6 1 3 018 6 0 0 014 7 2 1 014 7 2 1 0
8400-8499495 317 4517 11 0 6 020 5 1 1 011 12 0 4 011 12 0 4 0
8500-8599309 180 3817 5 0 5 013 6 0 2 013 7 0 0 013 7 0 0 0
8600-8699288 149 4210 12 1 5 012 5 0 2 011 5 0 2 011 5 0 2 0
8700-8799435 282 3515 8 1 5 013 2 0 5 012 4 0 4 011 5 0 4 0
8800-8899484 267 5713 7 2 7 014 5 0 1 013 6 1 0 014 5 1 0 0
8900-8999470 282 8614 4 0 11 010 4 2 2 010 4 0 3 010 4 0 3 0
9000-9099432 241 9424 6 0 3 019 6 0 5 020 3 0 5 019 4 0 5 0
9100-9199294 132 4812 5 0 2 010 6 1 0 09 6 0 1 09 6 0 1 0
9200-9299322 153 5611 4 0 0 08 3 0 2 011 3 0 0 011 3 0 0 0
9300-9399418 247 6925 5 0 2 021 5 1 3 022 7 0 1 023 6 0 1 0
9400-9499488 289 6622 5 0 3 019 5 2 1 017 10 0 0 016 11 0 0 0
9500-9599322 148 7924 3 1 7 021 3 0 4 018 6 0 3 018 6 0 3 0
9600-9699397 178 8519 9 0 5 017 7 0 3 017 7 0 2 018 6 0 2 0
9700-9799368 232 4717 6 0 5 015 5 3 0 016 5 0 2 015 6 0 2 0
9800-9899493 310 7213 9 1 5 015 3 2 1 016 1 1 3 016 1 1 3 0
9900-9999345 183 6514 10 2 6 015 4 1 5 016 6 1 1 016 6 1 1 0

Key - Column Headings
TotThe total number SNPs in the DCC allocation that map to this bin (dbSNP build 124, reference assembly).
DHDouble-hit SNPs in the DCC allocation. These include validated, two-hit, perlegen-verified, and jsnp-verified SNPs as well as cSNPs.
SHSingle-hit SNPs of sufficient class in allocation. These include tsc- and bac- overlap project SNPs.
PolySNPs genotyped at UCSF-WU that passed quality control and consistency tests, whose minor allele frequency was at least 5%.
MonSNPs genotyped at UCSF-WU that passed quality control and consistency tests, whose minor allele frequency was less than 5%.
AFAutomatic Failure - SNPs genotyped at UCSF-WU that passed quality control but had blank, duplicate, mendel, callrate, or HW failures.
QFQuality Control Failure - SNPs failed by human quality control personnel at UCSF-WU.
IPIn Progress - SNPs whose data is not yet finalized and submitted (mop-ups).
Sequencing Services Genotyping Services HapMap Project Informatics Services

Copyright 2007, Washington University School of Medicine SNP Research Facility. All rights reserved.
Legal   Contact   Site Map