Alleles in Called Genotypes CntAncestral AlleleDepth NumFilterMapping Quality NumQuality Score NumSamples With Data CntZero MAPQ Reads Cnt
| Business Data 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. |
| Attributes | |
| Alleles in Called Genotypes Cnt |
|
| Ancestral Allele |
|
| Depth Num |
|
| Filter |
|
| Mapping Quality Num |
|
| Quality Score Num |
|
| Samples With Data Cnt |
|
| Zero MAPQ Reads Cnt |
|
| Relationship | |
 Assay / Sequence Variation_Sequence Variation_FK |
|
| Genotype Experiment / Sequence Variation_Genotype Experiment_FK |
|
| Dependencies | |
 NONE |
|
| Reverse Dependencies | |
| |
|
| 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 |
Filter
| Description | The filter value is PASS if this position has passed all filters (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 is generated. For example: "q10;s50" can 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 must not be used as a filter string. If filters have not been applied, this field must 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 |
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 | The phred-scaled quality score for the assertion made in the Variation Sequence Txt attribute of the Sequence Variation entity, namely -10log_10 prob(call in "Variation Sequence Txt" attribute is incorrect). 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 required. If unknown, the missing value must 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 |
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 |
Assay / Sequence Variation_Sequence Variation_FK
| Is Identifying Relationship | false |
| Child Table | Genotype Experiment / Sequence Variation |
| 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 | Sequence Variation |
| Parent Multiplicity | ZERO_TO_ONE |
| Parent Referential Integrity: On Delete | NONE |
| Parent Referential Integrity: On Insert | NONE |
| Parent Referential Integrity: On Update | NONE |
Genotype Experiment / Sequence Variation_Genotype Experiment_FK
| Is Identifying Relationship | false |
| Child Table | Genotype Experiment / Sequence Variation |
| 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 |
| Parent Multiplicity | ONE |
| Parent Referential Integrity: On Delete | NONE |
| Parent Referential Integrity: On Insert | NONE |
| Parent Referential Integrity: On Update | NONE |
| Business Data Model Data Model |