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== Description of format for IG result files ==
||<tablewidth="485px" tableheight="333px">'''Column ''' ||'''Name of Variable ''' ||'''Example ''' ||		 = Description of InterGenomics results files format =
----
<<TableOfContents()>>

----

== Format for DGVs, Polygenic effect and gEBVs result files ==
||<tablewidth="800px">'''Column ''' ||'''Name of Variable ''' ||'''Example ''' ||
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||35-49 ||Value ||DGV, polygenic effect, or GEBV || ||35-49 ||Value ||DGV, polygenic effect, or gEBV ||
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Example: Examples:
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 . '''DGVs''' <<BR>>

||<tablewidth="200px">751 ||BSW ||CHE ||pro ||BSWUSAM000000109152 ||-64.7036923 ||0.0000 ||		 '''DGVs'''<<BR>>
||<tablewidth="800px">751 ||BSW ||CHE ||pro ||BSWUSAM000000109152 ||-64.7036923 ||0.0000 ||
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 . <<BR>>
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||<tablewidth="200px">752 ||BSW ||CHE ||pro ||BSWGRP0000000000000 ||7.9706095 ||0.0000 || ||<tablewidth="800px">752 ||BSW ||CHE ||pro ||BSWGRP0000000000000 ||7.9706095 ||0.0000 ||
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'''gEBV'''<<BR>>
||<tablewidth="800px">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 ||
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'''GEBV'''<<BR>>
||<tablewidth="200px">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) ==
||<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>>
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== Format for publishable status of Contributor's Holstein young bulls in A.I. (semicolon delimited) ==
||<tablewidth="800px">'''Column ''' ||'''Name of Variable ''' ||'''Example ''' ||
||1 ||Young bulls in A.I. ID ||HOLDEUM000000109152 ||
||2 ||Contributor Name ||VIT ||
||3 ||Publishable Status (Y/N) ||N ||
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<<BR>>
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 . == 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

  1. Description of InterGenomics results files format
    1. Format for DGVs, Polygenic effect and gEBVs result files
    2. Format for SNPs effects result files (tab delimited)
    3. Format for publishable status of Contributor's Holstein young bulls in A.I. (semicolon delimited)
    4. Format for file pedigree_names.txt (semicolon delimited)
    5. 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:
- Breed of animal
- Country of registration
- Sex
- 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

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:
- Breed of animal
- Country of registration
- Sex
- ID number of animal

BSWUSAM000470210343

3

SNPChip Array Code

76999_a

4

UUID

792b990c-67f0-4879-9d57-fa15b19a71c2

public/IG_results_file_format (last edited 2022-08-24 09:47:38 by Valentina)