Login
[x]
Log in using an account from:
Fedora Account System
Red Hat Associate
Red Hat Customer
Or login using a Red Hat Bugzilla account
Forgot Password
Login:
Hide Forgot
Create an Account
Red Hat Bugzilla – Attachment 318022 Details for
Bug 464460
Review Request: pypop - Python for Population Genomics
[?]
New
Simple Search
Advanced Search
My Links
Browse
Requests
Reports
Current State
Search
Tabular reports
Graphical reports
Duplicates
Other Reports
User Changes
Plotly Reports
Bug Status
Bug Severity
Non-Defaults
|
Product Dashboard
Help
Page Help!
Bug Writing Guidelines
What's new
Browser Support Policy
5.0.4.rh83 Release notes
FAQ
Guides index
User guide
Web Services
Contact
Legal
This site requires JavaScript to be enabled to function correctly, please enable it.
sample-out.txt (output file that should be generated)
sample-out.txt (text/plain), 29.26 KB, created by
Alex Lancaster
on 2008-09-29 22:57:35 UTC
(
hide
)
Description:
sample-out.txt (output file that should be generated)
Filename:
MIME Type:
Creator:
Alex Lancaster
Created:
2008-09-29 22:57:35 UTC
Size:
29.26 KB
patch
obsolete
>Results of data analysis >Performed on the 'sample.pop' file at: 2008-09-29-15-53-31 > > >Population Summary >================== > >Population Totals >_________________ >Sample Size (n): 47 >Allele Count (2n): 94 >Total loci in file: 9 [A, C, B, DRA, DRB1, DQA1, DQB1, DPA1, DPB1] >Total loci with data: 8 [A, C, B, DRB1, DQA1, DQB1, DPA1, DPB1] > > >Legend for all analyses >_______________________ > > * = significant at the 5% level > ** = significant at the 1% level > *** = significant at the 0.1% level > **** = significant at the 0.01% level >***** = significant at the 0.001% level > > >I. Single Locus Analyses >======================== > >1. Locus: A >___________ > >1.1. Allele Counts [A] >---------------------- >Untyped individuals: 2.0 >Sample Size (n): 45.0 >Allele Count (2n): 90 >Distinct alleles (k): 10 > >Counts ordered by frequency | Counts ordered by name >Name Frequency (Count) | Name Frequency (Count) >0201 0.21111 19 | 0101 0.13333 12 >03012 0.15556 14 | 0201 0.21111 19 >0101 0.13333 12 | 0210 0.10000 9 >2501 0.12222 11 | 0218 0.10000 9 >0210 0.10000 9 | 03012 0.15556 14 >0218 0.10000 9 | 2501 0.12222 11 >3204 0.08889 8 | 3204 0.08889 8 >6901 0.04444 4 | 6814 0.03333 3 >6814 0.03333 3 | 6901 0.04444 4 >7403 0.01111 1 | 7403 0.01111 1 >Total 1.00000 90 | Total 1.00000 90 > > >1.2. HardyWeinberg [A] >---------------------- >Table of genotypes, format of each cell is: observed/expected. > > 0101 0/0.8 > 0201 2/2.5 6/2.0 > 0210 1/1.2 0/1.9 1/0.5 > 0218 4/1.2 0/1.9 0/0.9 1/0.5 >03012 0/1.9 0/3.0 4/1.4 0/1.4 3/1.1 > 2501 3/1.5 2/2.3 0/1.1 1/1.1 2/1.7 0/0.7 > 3204 1/1.1 1/1.7 1/0.8 0/0.8 1/1.2 3/1.0 0/0.4 > 6814 0/0.4 1/0.6 0/0.3 1/0.3 0/0.5 0/0.4 1/0.3 0/0.1 > 6901 1/0.5 0/0.8 1/0.4 1/0.4 1/0.6 0/0.5 0/0.4 0/0.1 0/0.1 > 7403 0/0.1 1/0.2 0/0.1 0/0.1 0/0.2 0/0.1 0/0.1 0/0.0 0/0.0 0/0.0 > 0101 0201 0210 0218 03012 2501 3204 6814 6901 7403 > [Cols: 1 to 10] > > Observed Expected Chi-square DoF p-value >------------------------------------------------------------------------------ > Common No commmon genotypes; chi-square cannot be calculated > >------------------------------------------------------------------------------ > Lumped genotypes Value not calculated. > >------------------------------------------------------------------------------ > Common + lumped Value not calculated. > >------------------------------------------------------------------------------ > All homozygotes 11 5.97 4.25 1 0.0393* >------------------------------------------------------------------------------ > All heterozygotes 34 39.03 0.65 1 0.4205 >------------------------------------------------------------------------------ >Common heterozygotes by allele > 0101 12 10.40 0.25 0.6198 > 0201 7 14.99 4.26 0.0391* > 0210 7 8.10 0.15 0.6991 > 0218 7 8.10 0.15 0.6991 > 03012 8 11.82 1.24 0.2663 > 2501 11 9.66 0.19 0.6653 > 3204 8 7.29 0.07 0.7922 > >------------------------------------------------------------------------------ >Common genotypes > Total 0 0.00 >------------------------------------------------------------------------------ > > >1.3. Slatkin's implementation of EW homozygosity test of neutrality [A] >----------------------------------------------------------------------- >Observed F: 0.1326, Expected F: 0.2654, Variance in F: 0.0083 >Normalized deviate of F (Fnd): -1.4603, p-value of F: 0.0029** > > >2. Locus: C >___________ > >2.1. Allele Counts [C] >---------------------- >Untyped individuals: 0.0 >Sample Size (n): 47.0 >Allele Count (2n): 94 >Distinct alleles (k): 15 > >Counts ordered by frequency | Counts ordered by name >Name Frequency (Count) | Name Frequency (Count) >0307 0.29787 28 | 0102 0.23404 22 >0102 0.23404 22 | 02025 0.03191 3 >0605 0.14894 14 | 03021 0.02128 2 >1202 0.08511 8 | 0307 0.29787 28 >0712 0.05319 5 | 0403 0.01064 1 >1507 0.05319 5 | 0408 0.01064 1 >02025 0.03191 3 | 0501 0.01064 1 >03021 0.02128 2 | 0605 0.14894 14 >0403 0.01064 1 | 0712 0.05319 5 >0408 0.01064 1 | 0804 0.01064 1 >0501 0.01064 1 | 1202 0.08511 8 >0804 0.01064 1 | 1208 0.01064 1 >1208 0.01064 1 | 1301 0.01064 1 >1301 0.01064 1 | 1507 0.05319 5 >1801 0.01064 1 | 1801 0.01064 1 >Total 1.00000 94 | Total 1.00000 94 > > >2.2. HardyWeinberg [C] >---------------------- >Table of genotypes, format of each cell is: observed/expected. > > 0102 6/2.6 >02025 2/0.7 0/0.0 >03021 0/0.5 0/0.1 0/0.0 > 0307 3/6.6 0/0.9 0/0.6 7/4.2 > 0403 0/0.2 0/0.0 0/0.0 1/0.3 0/0.0 > 0408 0/0.2 0/0.0 0/0.0 0/0.3 0/0.0 0/0.0 > 0501 0/0.2 0/0.0 0/0.0 0/0.3 0/0.0 1/0.0 0/0.0 > 0605 1/3.3 0/0.4 1/0.3 5/4.2 0/0.1 0/0.1 0/0.1 2/1.0 > 0712 3/1.2 0/0.2 1/0.1 1/1.5 0/0.1 0/0.1 0/0.1 0/0.7 0/0.1 > 0804 0/0.2 0/0.0 0/0.0 0/0.3 0/0.0 0/0.0 0/0.0 0/0.1 0/0.1 0/0.0 > 1202 0/1.9 1/0.3 0/0.2 0/2.4 0/0.1 0/0.1 0/0.1 2/1.2 0/0.4 1/0.1 1/0.3 > 1208 0/0.2 0/0.0 0/0.0 1/0.3 0/0.0 0/0.0 0/0.0 0/0.1 0/0.1 0/0.0 0/0.1 0/0.0 > 1301 0/0.2 0/0.0 0/0.0 1/0.3 0/0.0 0/0.0 0/0.0 0/0.1 0/0.1 0/0.0 0/0.1 0/0.0 > 1507 0/1.2 0/0.2 0/0.1 2/1.5 0/0.1 0/0.1 0/0.1 1/0.7 0/0.3 0/0.1 2/0.4 0/0.1 > 1801 1/0.2 0/0.0 0/0.0 0/0.3 0/0.0 0/0.0 0/0.0 0/0.1 0/0.1 0/0.0 0/0.1 0/0.0 > 0102 02025 03021 0307 0403 0408 0501 0605 0712 0804 1202 1208 > [Cols: 1 to 12] > 1301 0/0.0 > 1507 0/0.1 0/0.1 > 1801 0/0.0 0/0.1 0/0.0 > 1301 1507 1801 > [Cols: 13 to 15] > > Observed Expected Chi-square DoF p-value >------------------------------------------------------------------------------ > Common Too many parameters for chi-square test. > >------------------------------------------------------------------------------ > Lumped genotypes Value not calculated. > >------------------------------------------------------------------------------ > Common + lumped Value not calculated. > >------------------------------------------------------------------------------ > All homozygotes 16 8.50 6.62 1 0.0101* >------------------------------------------------------------------------------ > All heterozygotes 31 38.50 1.46 1 0.2268 >------------------------------------------------------------------------------ >Common heterozygotes by allele > 0102 10 16.85 2.79 0.0951 > 0307 14 19.66 1.63 0.2018 > 0605 10 11.91 0.31 0.5791 > 1202 6 7.32 0.24 0.6258 > >------------------------------------------------------------------------------ >Common genotypes > 0102:0307 3 6.55 1.93 0.1651 > Total 3 6.55 >------------------------------------------------------------------------------ > > >2.3. Slatkin's implementation of EW homozygosity test of neutrality [C] >----------------------------------------------------------------------- >Observed F: 0.1809, Expected F: 0.1732, Variance in F: 0.0031 >Normalized deviate of F (Fnd): 0.1365, p-value of F: 0.6659 > > >3. Locus: B >___________ > >3.1. Allele Counts [B] >---------------------- >Untyped individuals: 0.0 >Sample Size (n): 47.0 >Allele Count (2n): 94 >Distinct alleles (k): 12 > >Counts ordered by frequency | Counts ordered by name >Name Frequency (Count) | Name Frequency (Count) >1401 0.29787 28 | 1301 0.19149 18 >1301 0.19149 18 | 1401 0.29787 28 >39021 0.12766 12 | 1520 0.07447 7 >4005 0.09574 9 | 18012 0.03191 3 >1520 0.07447 7 | 35091 0.02128 2 >51013 0.06383 6 | 39021 0.12766 12 >18012 0.03191 3 | 4005 0.09574 9 >5703 0.03191 3 | 51013 0.06383 6 >35091 0.02128 2 | 5703 0.03191 3 >67011 0.02128 2 | 67011 0.02128 2 >78021 0.02128 2 | 78021 0.02128 2 >8101 0.02128 2 | 8101 0.02128 2 >Total 1.00000 94 | Total 1.00000 94 > > >3.2. HardyWeinberg [B] >---------------------- >Table of genotypes, format of each cell is: observed/expected. > > 1301 6/1.7 > 1401 1/5.4 6/4.2 > 1520 3/1.3 2/2.1 0/0.3 >18012 1/0.6 0/0.9 1/0.2 0/0.0 >35091 0/0.4 0/0.6 0/0.1 0/0.1 0/0.0 >39021 0/2.3 6/3.6 0/0.9 0/0.4 1/0.3 1/0.8 > 4005 0/1.7 1/2.7 0/0.7 1/0.3 1/0.2 2/1.1 1/0.4 >51013 0/1.1 2/1.8 0/0.4 0/0.2 0/0.1 1/0.8 2/0.6 0/0.2 > 5703 0/0.6 2/0.9 1/0.2 0/0.1 0/0.1 0/0.4 0/0.3 0/0.2 0/0.0 >67011 0/0.4 0/0.6 0/0.1 0/0.1 0/0.0 0/0.3 0/0.2 1/0.1 0/0.1 0/0.0 >78021 1/0.4 1/0.6 0/0.1 0/0.1 0/0.0 0/0.3 0/0.2 0/0.1 0/0.1 0/0.0 0/0.0 > 8101 0/0.4 1/0.6 0/0.1 0/0.1 0/0.0 0/0.3 0/0.2 0/0.1 0/0.1 1/0.0 0/0.0 0/0.0 > 1301 1401 1520 18012 35091 39021 4005 51013 5703 67011 78021 8101 > [Cols: 1 to 12] > > Observed Expected Chi-square DoF p-value >------------------------------------------------------------------------------ > Common Too many parameters for chi-square test. > >------------------------------------------------------------------------------ > Lumped genotypes Value not calculated. > >------------------------------------------------------------------------------ > Common + lumped Value not calculated. > >------------------------------------------------------------------------------ > All homozygotes 14 7.72 5.10 1 0.0239* >------------------------------------------------------------------------------ > All heterozygotes 33 39.28 1.00 1 0.3166 >------------------------------------------------------------------------------ >Common heterozygotes by allele > 1301 6 14.55 5.03 0.0250* > 1401 16 19.66 0.68 0.4092 > 1520 7 6.48 0.04 0.8377 > 39021 10 10.47 0.02 0.8850 > 4005 7 8.14 0.16 0.6899 > 51013 6 5.62 0.03 0.8716 > >------------------------------------------------------------------------------ >Common genotypes > 1301:1401 1 5.36 3.55 0.0596 > Total 1 5.36 >------------------------------------------------------------------------------ > > >3.3. Slatkin's implementation of EW homozygosity test of neutrality [B] >----------------------------------------------------------------------- >Observed F: 0.1643, Expected F: 0.2216, Variance in F: 0.0057 >Normalized deviate of F (Fnd): -0.7610, p-value of F: 0.2180 > > >4. Locus: DRA >_____________ > No data for this locus! > >5. Locus: DRB1 >______________ > >5.1. Allele Counts [DRB1] >------------------------- >Untyped individuals: 0.0 >Sample Size (n): 47.0 >Allele Count (2n): 94 >Distinct alleles (k): 7 > >Counts ordered by frequency | Counts ordered by name >Name Frequency (Count) | Name Frequency (Count) >0802 0.29787 28 | 0402 0.22340 21 >0402 0.22340 21 | 0404 0.09574 9 >0407 0.11702 11 | 0407 0.11702 11 >1602 0.11702 11 | 0802 0.29787 28 >0404 0.09574 9 | 0901 0.08511 8 >0901 0.08511 8 | 1101 0.06383 6 >1101 0.06383 6 | 1602 0.11702 11 >Total 1.00000 94 | Total 1.00000 94 > > >5.2. HardyWeinberg [DRB1] >------------------------- >Table of genotypes, format of each cell is: observed/expected. > >0402 5/2.3 >0404 2/2.0 1/0.4 >0407 3/2.5 2/1.1 0/0.6 >0802 3/6.3 1/2.7 3/3.3 7/4.2 >0901 0/1.8 1/0.8 0/0.9 1/2.4 2/0.3 >1101 2/1.3 0/0.6 1/0.7 1/1.8 1/0.5 0/0.2 >1602 1/2.5 1/1.1 2/1.3 5/3.3 1/0.9 1/0.7 0/0.6 > 0402 0404 0407 0802 0901 1101 1602 > [Cols: 1 to 7] > > Observed Expected Chi-square DoF p-value >------------------------------------------------------------------------------ > Common Too many parameters for chi-square test. > >------------------------------------------------------------------------------ > Lumped genotypes Value not calculated. > >------------------------------------------------------------------------------ > Common + lumped Value not calculated. > >------------------------------------------------------------------------------ > All homozygotes 15 8.77 4.43 1 0.0352* >------------------------------------------------------------------------------ > All heterozygotes 32 38.23 1.02 1 0.3134 >------------------------------------------------------------------------------ >Common heterozygotes by allele > 0402 11 16.31 1.73 0.1887 > 0404 7 8.14 0.16 0.6899 > 0407 11 9.71 0.17 0.6796 > 0802 14 19.66 1.63 0.2018 > 0901 4 7.32 1.51 0.2199 > 1101 6 5.62 0.03 0.8716 > 1602 11 9.71 0.17 0.6796 > >------------------------------------------------------------------------------ >Common genotypes > 0402:0802 3 6.26 1.69 0.1931 > Total 3 6.26 >------------------------------------------------------------------------------ > > >5.3. Slatkin's implementation of EW homozygosity test of neutrality [DRB1] >-------------------------------------------------------------------------- >Observed F: 0.1865, Expected F: 0.3740, Variance in F: 0.0167 >Normalized deviate of F (Fnd): -1.4526, p-value of F: 0.0081* > > >6. Locus: DQA1 >______________ > >6.1. Allele Counts [DQA1] >------------------------- >Untyped individuals: 0.0 >Sample Size (n): 47.0 >Allele Count (2n): 94 >Distinct alleles (k): 5 > >Counts ordered by frequency | Counts ordered by name >Name Frequency (Count) | Name Frequency (Count) >0201 0.32979 31 | 0201 0.32979 31 >0401 0.22340 21 | 03011 0.12766 12 >05012 0.21277 20 | 0401 0.22340 21 >03011 0.12766 12 | 0501 0.10638 10 >0501 0.10638 10 | 05012 0.21277 20 >Total 1.00000 94 | Total 1.00000 94 > > >6.2. HardyWeinberg [DQA1] >------------------------- >Table of genotypes, format of each cell is: observed/expected. > > 0201 8/5.1 >03011 4/4.0 1/0.8 > 0401 3/6.9 1/2.7 6/2.3 > 0501 4/3.3 2/1.3 1/2.2 0/0.5 >05012 4/6.6 3/2.6 4/4.5 3/2.1 3/2.1 > 0201 03011 0401 0501 05012 > [Cols: 1 to 5] > > Observed Expected Chi-square DoF p-value >------------------------------------------------------------------------------ > Common Too many parameters for chi-square test. > >------------------------------------------------------------------------------ > Lumped genotypes Value not calculated. > >------------------------------------------------------------------------------ > Common + lumped Value not calculated. > >------------------------------------------------------------------------------ > All homozygotes 18 10.88 4.65 1 0.0310* >------------------------------------------------------------------------------ > All heterozygotes 29 36.12 1.40 1 0.2363 >------------------------------------------------------------------------------ >Common heterozygotes by allele > 0201 15 20.78 1.61 0.2050 > 03011 10 10.47 0.02 0.8850 > 0401 9 16.31 3.28 0.0703 > 0501 10 8.94 0.13 0.7219 > 05012 14 15.74 0.19 0.6602 > >------------------------------------------------------------------------------ >Common genotypes > 0201:0201 8 5.11 1.63 0.2014 > 0201:0401 3 6.93 2.23 0.1358 > 0201:05012 4 6.60 1.02 0.3122 > Total 15 18.63 >------------------------------------------------------------------------------ > > >6.3. Slatkin's implementation of EW homozygosity test of neutrality [DQA1] >-------------------------------------------------------------------------- >Observed F: 0.2316, Expected F: 0.4865, Variance in F: 0.0249 >Normalized deviate of F (Fnd): -1.6149, p-value of F: 0.0036** > > >7. Locus: DQB1 >______________ > >7.1. Allele Counts [DQB1] >------------------------- >Untyped individuals: 0.0 >Sample Size (n): 47.0 >Allele Count (2n): 94 >Distinct alleles (k): 6 > >Counts ordered by frequency | Counts ordered by name >Name Frequency (Count) | Name Frequency (Count) >03032 0.29787 28 | 0202 0.21277 20 >06011 0.22340 21 | 0301 0.11702 11 >0202 0.21277 20 | 03032 0.29787 28 >0301 0.11702 11 | 0304 0.08511 8 >0304 0.08511 8 | 05031 0.06383 6 >05031 0.06383 6 | 06011 0.22340 21 >Total 1.00000 94 | Total 1.00000 94 > > >7.2. HardyWeinberg [DQB1] >------------------------- >Table of genotypes, format of each cell is: observed/expected. > > 0202 3/2.1 > 0301 3/2.3 0/0.6 >03032 4/6.0 5/3.3 7/4.2 > 0304 1/1.7 1/0.9 1/2.4 2/0.3 >05031 1/1.3 1/0.7 1/1.8 1/0.5 0/0.2 >06011 5/4.5 1/2.5 3/6.3 0/1.8 2/1.3 5/2.3 > 0202 0301 03032 0304 05031 06011 > [Cols: 1 to 6] > > Observed Expected Chi-square DoF p-value >------------------------------------------------------------------------------ > Common Too many parameters for chi-square test. > >------------------------------------------------------------------------------ > Lumped genotypes Value not calculated. > >------------------------------------------------------------------------------ > Common + lumped Value not calculated. > >------------------------------------------------------------------------------ > All homozygotes 17 9.82 5.25 1 0.0219* >------------------------------------------------------------------------------ > All heterozygotes 30 37.18 1.39 1 0.2389 >------------------------------------------------------------------------------ >Common heterozygotes by allele > 0202 14 15.74 0.19 0.6602 > 0301 11 9.71 0.17 0.6796 > 03032 14 19.66 1.63 0.2018 > 0304 4 7.32 1.51 0.2199 > 05031 6 5.62 0.03 0.8716 > 06011 11 16.31 1.73 0.1887 > >------------------------------------------------------------------------------ >Common genotypes > 0202:03032 4 5.96 0.64 0.4226 > 03032:06011 3 6.26 1.69 0.1931 > Total 7 12.21 >------------------------------------------------------------------------------ > > >7.3. Slatkin's implementation of EW homozygosity test of neutrality [DQB1] >-------------------------------------------------------------------------- >Observed F: 0.2089, Expected F: 0.4232, Variance in F: 0.0199 >Normalized deviate of F (Fnd): -1.5173, p-value of F: 0.0053* > > >8. Locus: DPA1 >______________ > >8.1. Allele Counts [DPA1] >------------------------- >Untyped individuals: 1.0 >Sample Size (n): 46.0 >Allele Count (2n): 92 >Distinct alleles (k): 3 > >Counts ordered by frequency | Counts ordered by name >Name Frequency (Count) | Name Frequency (Count) >0103 0.59783 55 | 0103 0.59783 55 >02011 0.22826 21 | 02011 0.22826 21 >02013 0.17391 16 | 02013 0.17391 16 >Total 1.00000 92 | Total 1.00000 92 > > >8.2. HardyWeinberg [DPA1] >------------------------- >Table of genotypes, format of each cell is: observed/expected. > > 0103 17/16.4 >02011 11/12.6 2/2.4 >02013 10/9.6 6/3.7 0/1.4 > 0103 02011 02013 > [Cols: 1 to 3] > > Observed Expected Chi-square DoF p-value >------------------------------------------------------------------------------ > Common N/A N/A 0.23 1 0.6306 >------------------------------------------------------------------------------ > Lumped genotypes N/A N/A 0.04 1 0.8374 >------------------------------------------------------------------------------ > Common + lumped N/A N/A 0.27 1 0.6011 >------------------------------------------------------------------------------ > All homozygotes 19 20.23 0.07 1 0.7848 >------------------------------------------------------------------------------ > All heterozygotes 27 25.77 0.06 1 0.8088 >------------------------------------------------------------------------------ >Common heterozygotes by allele > 0103 21 22.12 0.06 0.8118 > 02011 17 16.21 0.04 0.8437 > 02013 16 13.22 0.59 0.4440 > >------------------------------------------------------------------------------ >Common genotypes > 0103:0103 17 16.44 0.02 0.8902 > 0103:02011 11 12.55 0.19 0.6609 > 0103:02013 10 9.57 0.02 0.8882 > Total 38 38.56 >------------------------------------------------------------------------------ > > >8.3. Slatkin's implementation of EW homozygosity test of neutrality [DPA1] >-------------------------------------------------------------------------- >Observed F: 0.4397, Expected F: 0.6683, Variance in F: 0.0326 >Normalized deviate of F (Fnd): -1.2664, p-value of F: 0.0993 > > >9. Locus: DPB1 >______________ > >9.1. Allele Counts [DPB1] >------------------------- >Untyped individuals: 3.0 >Sample Size (n): 44.0 >Allele Count (2n): 88 >Distinct alleles (k): 7 > >Counts ordered by frequency | Counts ordered by name >Name Frequency (Count) | Name Frequency (Count) >0403 0.37500 33 | 0202 0.02273 2 >1401 0.32955 29 | 0403 0.37500 33 >5801 0.13636 12 | 1401 0.32955 29 >3901 0.06818 6 | 1901 0.03409 3 >1901 0.03409 3 | 3901 0.06818 6 >4901 0.03409 3 | 4901 0.03409 3 >0202 0.02273 2 | 5801 0.13636 12 >Total 1.00000 88 | Total 1.00000 88 > > >9.2. HardyWeinberg [DPB1] >------------------------- >Table of genotypes, format of each cell is: observed/expected. > >0202 0/0.0 >0403 0/0.8 5/6.2 >1401 0/0.7 12/10.9 7/4.8 >1901 1/0.1 0/1.1 0/1.0 0/0.1 >3901 1/0.1 2/2.3 1/2.0 1/0.2 0/0.2 >4901 0/0.1 1/1.1 0/1.0 1/0.1 1/0.2 0/0.1 >5801 0/0.3 8/4.5 2/4.0 0/0.4 0/0.8 0/0.4 1/0.8 > 0202 0403 1401 1901 3901 4901 5801 > [Cols: 1 to 7] > > Observed Expected Chi-square DoF p-value >------------------------------------------------------------------------------ > Common Too many parameters for chi-square test. > >------------------------------------------------------------------------------ > Lumped genotypes Value not calculated. > >------------------------------------------------------------------------------ > Common + lumped Value not calculated. > >------------------------------------------------------------------------------ > All homozygotes 13 12.11 0.06 1 0.7990 >------------------------------------------------------------------------------ > All heterozygotes 31 31.89 0.02 1 0.8753 >------------------------------------------------------------------------------ >Common heterozygotes by allele > 0403 23 20.63 0.27 0.6010 > 1401 15 19.44 1.02 0.3136 > 3901 6 5.59 0.03 0.8626 > 5801 10 10.36 0.01 0.9101 > >------------------------------------------------------------------------------ >Common genotypes > 0403:0403 5 6.19 0.23 0.6331 > 0403:1401 12 10.88 0.12 0.7330 > Total 17 17.06 >------------------------------------------------------------------------------ > > >9.3. Slatkin's implementation of EW homozygosity test of neutrality [DPB1] >-------------------------------------------------------------------------- >Observed F: 0.2753, Expected F: 0.3693, Variance in F: 0.0161 >Normalized deviate of F (Fnd): -0.7415, p-value of F: 0.2536 > > > >II. Multi-locus Analyses >======================== > >Haplotype / linkage disequilibrium (LD) statistics >__________________________________________________ > >Pairwise LD estimates >--------------------- >Locus pair D D' Wn ln(L_1) ln(L_0) S # permu p-value >A:C 0.01465 0.49229 0.39472 -289.09 -326.81 75.44 - - >A:B 0.01503 0.51142 0.40001 -293.47 -330.84 74.73 - - >A:DRB1 0.01395 0.44396 0.37769 -282.00 -309.16 54.32 - - >A:DQA1 0.01219 0.33413 0.36466 -269.57 -286.08 33.02 - - >A:DQB1 0.01356 0.39266 0.37495 -275.58 -297.62 44.07 - - >A:DPA1 0.01682 0.32399 0.36667 -219.78 -226.97 14.38 - - >A:DPB1 0.01362 0.42240 0.40404 -237.85 -262.06 48.42 - - >C:B 0.04135 0.89434 0.84992 -210.37 -342.68 264.63 - - >C:DRB1 0.01698 0.48046 0.47513 -280.34 -317.66 74.62 - - >C:DQA1 0.02072 0.47797 0.49368 -263.23 -293.74 61.01 - - >C:DQB1 0.01766 0.45793 0.49879 -269.55 -305.28 71.46 - - >C:DPA1 0.02039 0.41030 0.46438 -224.72 -236.52 23.61 - - >C:DPB1 0.01898 0.46442 0.36990 -242.45 -268.46 52.01 - - >B:DRB1 0.01745 0.50109 0.41670 -286.79 -320.50 67.42 - - >B:DQA1 0.01847 0.44283 0.43422 -271.36 -296.59 50.45 - - >B:DQB1 0.01958 0.49040 0.43654 -277.30 -308.13 61.65 - - >B:DPA1 0.01875 0.37438 0.40118 -229.76 -239.16 18.80 - - >B:DPB1 0.01898 0.46082 0.38001 -247.84 -272.77 49.86 - - >DRB1:DQA1 0.06145 0.92556 0.91975 -164.06 -271.56 214.99 - - >DRB1:DQB1 0.06058 1.00000 1.00000 -147.74 -283.10 270.72 - - >DRB1:DPA1 0.02795 0.38642 0.39936 -202.51 -211.42 17.81 - - >DRB1:DPB1 0.01291 0.32216 0.32030 -231.03 -247.29 32.53 - - >DQA1:DQB1 0.06876 0.92556 0.92384 -152.52 -259.18 213.33 - - >DQA1:DPA1 0.02242 0.25405 0.27212 -185.25 -189.23 7.97 - - >DQA1:DPB1 0.01617 0.30441 0.34388 -210.93 -226.09 30.33 - - >DQB1:DPA1 0.02740 0.34112 0.36604 -193.17 -200.77 15.20 - - >DQB1:DPB1 0.01145 0.26607 0.30921 -222.73 -236.89 28.34 - - >DPA1:DPB1 0.02008 0.28507 0.35928 -165.96 -173.31 14.68 - - > > >
<b>You cannot view the attachment while viewing its details because your browser does not support IFRAMEs. <a href="attachment.cgi?id=318022">View the attachment on a separate page</a>.</b>
View Attachment As Raw
Actions:
View
Attachments on
bug 464460
:
318020
|
318021
| 318022