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Size: 2145
Comment:
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Size: 3387
Comment:
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| Deletions are marked like this. | Additions are marked like this. |
| Line 9: | Line 9: |
| ||<tablewidth="485px" tableheight="333px">'''Column ''' ||'''Name of Variable ''' ||'''Example ''' || | ||<tablewidth="800px">'''Column ''' ||'''Name of Variable ''' ||'''Example ''' || |
| Line 22: | Line 22: |
| ||<tablewidth="200px">751 ||BSW ||CHE ||pro ||BSWUSAM000000109152 ||-64.7036923 ||0.0000 || | ||<tablewidth="800px">751 ||BSW ||CHE ||pro ||BSWUSAM000000109152 ||-64.7036923 ||0.0000 || |
| Line 27: | Line 27: |
| ||<tablewidth="200px">752 ||BSW ||CHE ||pro ||BSWGRP0000000000000 ||7.9706095 ||0.0000 || | ||<tablewidth="800px">752 ||BSW ||CHE ||pro ||BSWGRP0000000000000 ||7.9706095 ||0.0000 || |
| Line 32: | Line 32: |
| ||<tablewidth="200px">753 ||BSW ||CHE ||pro ||BSWUSAM000000109152 ||-68.9313108 ||0.6500 || | ||<tablewidth="800px">753 ||BSW ||CHE ||pro ||BSWUSAM000000109152 ||-68.9313108 ||0.6500 || |
| Line 36: | Line 36: |
| <<BR>> | |
| Line 38: | Line 39: |
| ||<tablewidth="485px" tableheight="333px">'''Column ''' ||'''Name of Variable ''' ||'''Example ''' || ||1 ||Chromosome number || 1|| ||2 ||Position || 135098|| ||3 ||idx on IG reference map || 1|| ||4 ||Sample frequency || 0.3787|| ||5 ||SNP effect || -0.005343431|| ||6 ||SNP Name || Hapmap43437-BTA-101873|| ||6 ||Base population frequency || 0.4004|| |
||<tablewidth="800px">'''Column ''' ||'''Name of Variable ''' ||'''Example ''' || ||1 ||Chromosome number ||1 || ||2 ||Position ||135098 || ||3 ||idx on IG reference map ||1 || ||4 ||Sample frequency ||0.3787 || ||5 ||SNP effect ||-0.005343431 || ||6 ||SNP Name ||Hapmap43437-BTA-101873 || ||6 ||Base population frequency ||0.4004 || |
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| <<BR>> | |
| Line 49: | Line 51: |
| ||<tablewidth="485px" tableheight="333px">'''Column ''' ||'''Name of Variable ''' ||'''Example ''' || | ||<tablewidth="800px">'''Column ''' ||'''Name of Variable ''' ||'''Example ''' || |
| Line 51: | Line 53: |
| ||2 ||Contributor Name || VIT|| ||3 ||Publishable Status (Y/N)|| N|| |
||2 ||Contributor Name ||VIT || ||3 ||Publishable Status (Y/N) ||N || <<BR>> == Format for file pedigree_names.txt (semicolon delimited) == ||<tablewidth="800px">'''Column ''' ||'''Name of Variable ''' ||'''Example ''' || ||1 ||Animal international identification:<<BR>>- Breed of animal<<BR>>- Country of registration<<BR>>- Sex<<BR>>- ID number of animal||BSW840F003000210772 || ||2 ||Sire international identification ||BSWUSAM000068122123 || ||3 ||Dam international identification ||BSWUSAF000068123589 || ||4 ||Date of birth ||20130114 || ||5 ||Name ||BMG DD PRETTY LIL LIAR ET || ||6 ||Status^1^ ||U || 1. Pedigree Verification Status: A = auto-created; U = unverified; V = verified; X = invalid. Animals with pedigree changes due to pedigree pruning or parentage conflicts identified by genotypes have Pedigree Verification Status = U. <<BR>> == Format for file auxdata_$RUNID.csv (auxiliary information from GenoEx-GDE, semicolon delimited) == ||<tablewidth="800px">'''Column ''' ||'''Name of Variable ''' ||'''Example ''' || ||1 ||Country uploading the genotype ||USA || ||2 ||Animal international identification:<<BR>>- Breed of animal<<BR>>- Country of registration<<BR>>- Sex<<BR>>- ID number of animal||BSWUSAM000470210343 || ||3 ||SNPChip Array Code ||76999_a || ||4 ||UUID ||792b990c-67f0-4879-9d57-fa15b19a71c2 || |
Description of InterGenomics results files format
Contents
-
Description of InterGenomics results files format
- Format for DGVs, Polygenic effect and gEBVs result files
- Format for SNPs effects result files (tab delimited)
- Format for publishable status of Contributor's Holstein young bulls in A.I. (semicolon delimited)
- Format for file pedigree_names.txt (semicolon delimited)
- Format for file auxdata_$RUNID.csv (auxiliary information from GenoEx-GDE, semicolon delimited)
Format for DGVs, Polygenic effect and gEBVs result files
Column |
Name of Variable |
Example |
1-3 |
File Identifies |
751, 752, 753 |
4-6 |
Breed |
BSW |
7-9 |
Country |
USA |
11-13 |
Trait |
mil |
15-33 |
Animal ID |
BSWUSAM000000109152 |
35-49 |
Value |
DGV, polygenic effect, or gEBV |
52-57 |
Reliability (if applicable) |
0.6500 |
Examples:
DGVs
751 |
BSW |
CHE |
pro |
BSWUSAM000000109152 |
-64.7036923 |
0.0000 |
751 |
BSW |
CHE |
pro |
BSWDEUM000803611398 |
-46.9769316 |
0.0000 |
751 |
BSW |
CHE |
pro |
BSWUSAM000000118619 |
-23.1922227 |
0.0000 |
Polygenic effects
752 |
BSW |
CHE |
pro |
BSWGRP0000000000000 |
7.9706095 |
0.0000 |
752 |
BSW |
CHE |
pro |
BSWUSAF000000029496 |
7.3884218 |
0.0000 |
752 |
BSW |
CHE |
pro |
BSWUSAM000000021760 |
7.3884218 |
0.0000 |
gEBV
753 |
BSW |
CHE |
pro |
BSWUSAM000000109152 |
-68.9313108 |
0.6500 |
753 |
BSW |
CHE |
pro |
BSWDEUM000803611398 |
-52.4821532 |
0.6500 |
753 |
BSW |
CHE |
pro |
BSWUSAM000000118619 |
-27.5975303 |
0.6700 |
Format for SNPs effects result files (tab delimited)
Column |
Name of Variable |
Example |
1 |
Chromosome number |
1 |
2 |
Position |
135098 |
3 |
idx on IG reference map |
1 |
4 |
Sample frequency |
0.3787 |
5 |
SNP effect |
-0.005343431 |
6 |
SNP Name |
Hapmap43437-BTA-101873 |
6 |
Base population frequency |
0.4004 |
Format for publishable status of Contributor's Holstein young bulls in A.I. (semicolon delimited)
Column |
Name of Variable |
Example |
1 |
Young bulls in A.I. ID |
HOLDEUM000000109152 |
2 |
Contributor Name |
VIT |
3 |
Publishable Status (Y/N) |
N |
Format for file pedigree_names.txt (semicolon delimited)
Column |
Name of Variable |
Example |
1 |
Animal international identification: |
BSW840F003000210772 |
2 |
Sire international identification |
BSWUSAM000068122123 |
3 |
Dam international identification |
BSWUSAF000068123589 |
4 |
Date of birth |
20130114 |
5 |
Name |
BMG DD PRETTY LIL LIAR ET |
6 |
Status1 |
U |
1. Pedigree Verification Status: A = auto-created; U = unverified; V = verified; X = invalid. Animals with pedigree changes due to pedigree pruning or parentage conflicts identified by genotypes have Pedigree Verification Status = U.
Format for file auxdata_$RUNID.csv (auxiliary information from GenoEx-GDE, semicolon delimited)
Column |
Name of Variable |
Example |
1 |
Country uploading the genotype |
USA |
2 |
Animal international identification: |
BSWUSAM000470210343 |
3 |
SNPChip Array Code |
76999_a |
4 |
UUID |
792b990c-67f0-4879-9d57-fa15b19a71c2 |