| Atomic Warehouse Model Data Model |
| Description | An association between a sequence variation and a genotype experiment which can be used to identify the data recorded for a specific sequence variation in the context of a given genotype experiment. |
| Relationship | |
 Genotype Experiment / Sequence Variation Detail_Genotype Experiment / Sequence Variation_FK |
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| Primary Key | |
 Genotype Experiment / Sequence Variation Detail PK |
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| Dependencies | |
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| Reverse Dependencies | |
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| Attribute Details |
Alleles in Called Genotypes Cnt
| Description | Total number of alleles in called genotypes. |
| Data Type | Standards - Data Domains.ddm/Data Domains/Count [INTEGER] |
| Is Part Of PrimaryKey | false |
| Is Required | false |
| Is Derived | false |
| Is Surrogate Key | false |
Ancestral Allele
| Description | Specifies the ancestral allele. |
| Data Type | Standards - Data Domains.ddm/Data Domains/Alphanumeric [VARCHAR(80)] |
| Is Part Of PrimaryKey | false |
| Is Required | false |
| Is Derived | false |
| Is Surrogate Key | false |
Depth Num
| Description | Combined depth across samples. |
| Data Type | Standards - Data Domains.ddm/Data Domains/Number Integer [INTEGER] |
| Is Part Of PrimaryKey | false |
| Is Required | false |
| Is Derived | false |
| Is Surrogate Key | false |
Effective From Dt
| Description | Establishes a period where a set of attributes are true according to the business. |
| Data Type | Standards - Data Domains.ddm/Data Domains/Date [DATE] |
| Is Part Of PrimaryKey | false |
| Is Required | false |
| Is Derived | false |
| Is Surrogate Key | false |
Effective To Dt
| Description | Ends a period of effectivity. |
| Data Type | Standards - Data Domains.ddm/Data Domains/Date [DATE] |
| Is Part Of PrimaryKey | false |
| Is Required | false |
| Is Derived | false |
| Is Surrogate Key | false |
Filter
| Description | "PASS" if this position has passed all filters, i.e. a call is made at this position. Otherwise, if the site has not passed all filters, a semicolon-separated list of codes for filters that fail. For example "q10;s50" might indicate that at this site the quality is below 10 and the number of samples with data is below 50% of the total number of samples. "0" is reserved and should not be used as a filter String. If filters have not been applied, then this field should be set to the missing value. |
| Data Type | Standards - Data Domains.ddm/Data Domains/Alphanumeric [VARCHAR(80)] |
| Is Part Of PrimaryKey | false |
| Is Required | false |
| Is Derived | false |
| Is Surrogate Key | false |
Genotype Experiment / Sequence Variation Sk
| Description | The surrogate key for link Genotype Experiment / Sequence Variation. |
| Data Type | Standards - Data Domains.ddm/Data Domains/Surrogate Key Large [LONG] |
| Is Part Of PrimaryKey | true |
| Is Required | true |
| Is Derived | false |
| Is Surrogate Key | false |
Load Info Sk
| Description | The surrogate key of the load information entry describing the details regarding the loading of the row. |
| Data Type | Standards - Data Domains.ddm/Data Domains/Surrogate Key Large [LONG] |
| Is Part Of PrimaryKey | false |
| Is Required | false |
| Is Derived | false |
| Is Surrogate Key | false |
Mapping Quality Num
| Description | The mapping quality (RMS - Root Mean Square) of the sequence variation within the given genotype experiment. For example: 52 |
| Data Type | Standards - Data Domains.ddm/Data Domains/Number Integer [INTEGER] |
| Is Part Of PrimaryKey | false |
| Is Required | false |
| Is Derived | false |
| Is Surrogate Key | false |
Quality Score Num
| Description | Phred-scaled quality score for the assertion made in "Variation Sequence Txt" attribute of "Sequence Variation" entity. i.e. -10log_10 prob(call in "Variation Sequence Txt" attribute is wrong). If "Variation Sequence Txt" is ”.” (no variant) then this is -10log_10 p(variant), and if "Variation Sequence Txt" is not ”.” this is -10log_10 p(no variant). High scores indicate high confidence calls. This attribute is permitted to be a floating point to enable higher resolution for low confidence calls if desired. If unknown, the missing value should be specified. |
| Data Type | Standards - Data Domains.ddm/Data Domains/Number Float [FLOAT(5)] |
| Is Part Of PrimaryKey | false |
| Is Required | false |
| Is Derived | false |
| Is Surrogate Key | false |
Samples With Data Cnt
| Description | Number of samples with data. |
| Data Type | Standards - Data Domains.ddm/Data Domains/Count [INTEGER] |
| Is Part Of PrimaryKey | false |
| Is Required | false |
| Is Derived | false |
| Is Surrogate Key | false |
Source Code Sk
| Description | The origin of the data identifying the actual load source, vendor, manual key entry, or context of the data in a specific row in the database. |
| Data Type | Standards - Data Domains.ddm/Data Domains/Surrogate Key [INTEGER] |
| Is Part Of PrimaryKey | false |
| Is Required | false |
| Is Derived | false |
| Is Surrogate Key | false |
Tenant Sk
| Description | The surrogate key of the entry identifying the legal owner of the data. |
| Data Type | Standards - Data Domains.ddm/Data Domains/Surrogate Key [INTEGER] |
| Is Part Of PrimaryKey | false |
| Is Required | false |
| Is Derived | false |
| Is Surrogate Key | false |
Valid From Ts
| Description | Establishes a period where a set of attributes are true in the source system. This would be populated with the transaction timestamp and would be used for the snapshot date. |
| Data Type | Standards - Data Domains.ddm/Data Domains/Timestamp [TIMESTAMP] |
| Is Part Of PrimaryKey | true |
| Is Required | true |
| Is Derived | false |
| Is Surrogate Key | false |
Valid To Ts
| Description | Ends a period of validity. |
| Data Type | Standards - Data Domains.ddm/Data Domains/Timestamp [TIMESTAMP] |
| Is Part Of PrimaryKey | false |
| Is Required | false |
| Is Derived | false |
| Is Surrogate Key | false |
Zero MAPQ Reads Cnt
| Description | Number of MAPQ reads equal to 0 covering this record. |
| Data Type | Standards - Data Domains.ddm/Data Domains/Count [INTEGER] |
| Is Part Of PrimaryKey | false |
| Is Required | false |
| Is Derived | false |
| Is Surrogate Key | false |
| Relationship Details |
Genotype Experiment / Sequence Variation Detail_Genotype Experiment / Sequence Variation_FK
| Is Identifying Relationship | true |
| Child Table | Genotype Experiment / Sequence Variation Detail |
| Child Multiplicity | ZERO_TO_MANY |
| Child Referential Integrity: On Delete | NONE |
| Child Referential Integrity: On Insert | NONE |
| Child Referential Integrity: On Update | NONE |
| Parent Table | Genotype Experiment / Sequence Variation |
| Parent Multiplicity | ONE |
| Parent Referential Integrity: On Delete | NONE |
| Parent Referential Integrity: On Insert | NONE |
| Parent Referential Integrity: On Update | NONE |
| Primary Key Details |
Genotype Experiment / Sequence Variation Detail PK
| Key Attribute | Genotype Experiment / Sequence Variation Sk |
| Key Attribute | Valid From Ts |
| Atomic Warehouse Model Data Model |