Appendix E | Mapping Tool Algorithms
381
ALLELE FREQUENCY
The allele frequency for the A allele is calculated as
where the Total Number Calls does not include the no call samples,
i.e.
Total Number of Calls = Number of AA Calls + Number of BB Calls
+ Number of AB Calls
The B allele frequency is
.
The minor allele frequency is used for filtering. The minor allele
frequency is the Min(
p
A
,
p
B
).
HARDY-WEINBERG PROBABILITY
The Hardy/Weinberg probability is a measure of the significance of
the discrepancy between the observed ratio of heterozygote calls in a
population and the ratio expected if the population was in Hardy/
Weinberg equilibrium.
Hardy-Weinberg is calculated from the likelihood ratio
p
A
Number of AA calls + 0.5 * Number of AB Calls
(
)
Total Number of Calls
---------------------------------------------------------------------------------------------------------------
=
p
B
1
p
A
–
=
x
2
f
2
aa
f
a
–
(
)
2
f
2
aa
--------------------------
2
f
aa
f
bb
f
ab
–
(
)
2
2
f
aa
f
bb
-------------------------------------
f
2
bb
f
b
–
(
)
f
2
bb
------------------------
+
+
=
GTYPE_manual.book Page 381 Wednesday, August 2, 2006 11:31 AM
Summary of Contents for iServer MicroServer iTHX-M
Page 9: ...Introduction GTYPE_manual book Page 1 Wednesday August 2 2006 11 31 AM...
Page 10: ...GTYPE_manual book Page 2 Wednesday August 2 2006 11 31 AM...
Page 19: ...Chapter 1 GTYPE Overview GTYPE_manual book Page 11 Wednesday August 2 2006 11 31 AM...
Page 20: ...Chapter 1 GTYPE_manual book Page 12 Wednesday August 2 2006 11 31 AM...
Page 55: ...Chapter 2 Getting Started GTYPE_manual book Page 47 Wednesday August 2 2006 11 31 AM...
Page 56: ...Chapter 2 GTYPE_manual book Page 48 Wednesday August 2 2006 11 31 AM...
Page 85: ...Chapter 3 Working with Images GTYPE_manual book Page 77 Wednesday August 2 2006 11 31 AM...
Page 86: ...Chapter 3 GTYPE_manual book Page 78 Wednesday August 2 2006 11 31 AM...
Page 114: ...Chapter 4 GTYPE_manual book Page 106 Wednesday August 2 2006 11 31 AM...
Page 145: ...Chapter 5 Mapping Analysis Window GTYPE_manual book Page 137 Wednesday August 2 2006 11 31 AM...
Page 146: ...Chapter 5 GTYPE_manual book Page 138 Wednesday August 2 2006 11 31 AM...
Page 188: ...Chapter 6 GTYPE_manual book Page 180 Wednesday August 2 2006 11 31 AM...
Page 259: ...Chapter 7 Universal Tag Window GTYPE_manual book Page 251 Wednesday August 2 2006 11 31 AM...
Page 260: ...Chapter 7 GTYPE_manual book Page 252 Wednesday August 2 2006 11 31 AM...
Page 269: ...Chapter 8 Probe Intensity Window GTYPE_manual book Page 261 Wednesday August 2 2006 11 31 AM...
Page 270: ...Chapter 8 GTYPE_manual book Page 262 Wednesday August 2 2006 11 31 AM...
Page 283: ...Chapter 9 NetAffx Annotations GTYPE_manual book Page 275 Wednesday August 2 2006 11 31 AM...
Page 284: ...Chapter 9 GTYPE_manual book Page 276 Wednesday August 2 2006 11 31 AM...
Page 297: ...Chapter 10 Reports GTYPE_manual book Page 289 Wednesday August 2 2006 11 31 AM...
Page 298: ...Chapter 10 GTYPE_manual book Page 290 Wednesday August 2 2006 11 31 AM...
Page 314: ...Appendix A GTYPE_manual book Page 306 Wednesday August 2 2006 11 31 AM...
Page 325: ...Appendix B MPAM Mapping Algorithm GTYPE_manual book Page 317 Wednesday August 2 2006 11 31 AM...
Page 326: ...Appendix B GTYPE_manual book Page 318 Wednesday August 2 2006 11 31 AM...
Page 344: ...Appendix C GTYPE_manual book Page 336 Wednesday August 2 2006 11 31 AM...
Page 362: ...Appendix D GTYPE_manual book Page 354 Wednesday August 2 2006 11 31 AM...
Page 385: ...Appendix E Mapping Tool Algorithms GTYPE_manual book Page 377 Wednesday August 2 2006 11 31 AM...
Page 386: ...Appendix E GTYPE_manual book Page 378 Wednesday August 2 2006 11 31 AM...
Page 393: ...Appendix F IUPAC Base Codes GTYPE_manual book Page 385 Wednesday August 2 2006 11 31 AM...
Page 394: ...Appendix F GTYPE_manual book Page 386 Wednesday August 2 2006 11 31 AM...
Page 397: ...Appendix G File Types GTYPE_manual book Page 389 Wednesday August 2 2006 11 31 AM...
Page 398: ...Appendix G GTYPE_manual book Page 390 Wednesday August 2 2006 11 31 AM...
Page 402: ...Appendix H GTYPE_manual book Page 394 Wednesday August 2 2006 11 31 AM...
Page 405: ...Appendix I Hot Key Descriptions GTYPE_manual book Page 397 Wednesday August 2 2006 11 31 AM...
Page 406: ...Appendix I GTYPE_manual book Page 398 Wednesday August 2 2006 11 31 AM...
Page 409: ...Index GTYPE_manual book Page 401 Wednesday August 2 2006 11 31 AM...
Page 410: ...GTYPE_manual book Page 402 Wednesday August 2 2006 11 31 AM...