| Business Data Model Data Model |
| Description | An association between an array, 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 assay. |
| Relationship | |
 Assay / Sequence Variation_Genotype Experiment / Sequence Variation_FK |
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| Assay / Sequence Variation_Assay_FK |
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| Dependencies | |
 NONE |
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| Reverse Dependencies | |
| |
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| Attribute Details |
Expected Alternate Allele Counts Txt
| Description | Comma separated list of expected alternate allele counts for each alternate allele in the same order as listed in the "Variation Sequence Txt" attribute of "Sequence Variation" entity (typically used in association analyses). |
| Data Type | Standards - Data Domains.ddm/Data Domains/Text Very Large [VARCHAR(2048)] |
| Is Part Of PrimaryKey | false |
| Is Required | false |
| Is Derived | false |
| Is Surrogate Key | false |
Genotype Filter
| Description | Sample genotype filter indicating if this genotype was "called". Use PASS to indicate that all filters have been passed, a semi-colon separated list of codes for filters that fail, or "." to indicate that filters have not been applied. |
| 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 Likelihoods of Heterogeneous Ploidy Txt
| Description | Genotype likelihoods of heterogeneous ploidy, used in presence of uncertain copy number. For example: GLE=0:-75.22,1:-223.42,0/0:-323.03,1/0:-99.29,1/1:-802.53 |
| Data Type | Standards - Data Domains.ddm/Data Domains/Text Very Large [VARCHAR(2048)] |
| Is Part Of PrimaryKey | false |
| Is Required | false |
| Is Derived | false |
| Is Surrogate Key | false |
Genotype Likelihoods Txt
| Description | A text field that comprises comma-separated floating point log10-scaled likelihoods for all possible genotypes given the set of alleles defined in the Original Sequence Txt and the Variation Sequence Txt attributes of the Sequence Variation entity. In presence of the value in the Genotype attribute, the same ploidy is expected and the canonical order is used; without value in Genotype attribute, diploidy is assumed. If A is the allele in Original Sequence Txt and B,C and so on are the alleles as ordered in Variation Sequence Txt, the ordering of genotypes for the likelihoods is given by: F(j/k) = (k*(k+1)/2)+j. In other words, for biallelic sites the ordering is: AA,AB,BB; for triallelic sites the ordering is: AA,AB,BB,AC,BC,CC and so on. For example: GT:GL 0/1:-323.03,-99.29,-802.53 |
| Data Type | Standards - Data Domains.ddm/Data Domains/Text Very Large [VARCHAR(2048)] |
| Is Part Of PrimaryKey | false |
| Is Required | false |
| Is Derived | false |
| Is Surrogate Key | false |
Genotype Quality Txt
| Description | Conditional genotype quality, encoded as a phred quality -10log_10p. |
| Data Type | Standards - Data Domains.ddm/Data Domains/Text Very Large [VARCHAR(2048)] |
| Is Part Of PrimaryKey | false |
| Is Required | false |
| Is Derived | false |
| Is Surrogate Key | false |
Genotype Txt
| Description | Genotype, encoded as allele values separated by either of "/" or "|". The allele values are 0 for the reference allele (value stored in the "Original Sequence Txt" attribute of "Sequence Variation" entity), 1 for the first allele listed in in the "Variation Sequence Txt" attribute of "Sequence Variation" entity, 2 for the second allele list in in the "Variation Sequence Txt" attribute of "Sequence Variation" entity and so on. For diploid calls examples could be 0/1, 1|0, or 1/2, etc. For haploid calls, e.g. on Y, male non-pseudoautosomal X, or mitochondrion, only one allele value should be given; a triploid call might look like 0/0/1. If a call cannot be made for a sample at a given locus, "." should be specified for each missing allele in this attribute (for example "./." for a diploid genotype and "." for haploid genotype). The meanings of the separators are as follows (see the "Phase Set" attribute for more details on incorporating phasing information into the genotypes): / : genotype unphased | : genotype phase |
| Data Type | Standards - Data Domains.ddm/Data Domains/Text Very Large [VARCHAR(2048)] |
| Is Part Of PrimaryKey | false |
| Is Required | false |
| Is Derived | false |
| Is Surrogate Key | false |
Haplotype Qualities Txt
| Description | Haplotype qualities, two comma separated phred qualities. |
| Data Type | Standards - Data Domains.ddm/Data Domains/Text Very Large [VARCHAR(2048)] |
| 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 assay. 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 |
Phase Set Txt
| Description | A phase set is defined as a set of phased genotypes to which this genotype belongs. Phased genotypes for an individual that are on the same chromosome and have the same phase set value are in the same phased set. A phase set specifies multi-marker haplotypes for the phased genotypes in the set. All phased genotypes that do not contain a phase set subfield are assumed to belong to the same phased set. If the genotype is unphased, the corresponding phase set attribute is ignored. The recommended convention is to use the position of the first variant in the set as the phase set identifier (although this is not required). |
| Data Type | Standards - Data Domains.ddm/Data Domains/Text Very Large [VARCHAR(2048)] |
| Is Part Of PrimaryKey | false |
| Is Required | false |
| Is Derived | false |
| Is Surrogate Key | false |
Phasing Quality Txt
| Description | Phasing quality, the phred-scaled probability that alleles are ordered incorrectly in a heterozygote (against all other members in the phase set). |
| Data Type | Standards - Data Domains.ddm/Data Domains/Text Very Large [VARCHAR(2048)] |
| Is Part Of PrimaryKey | false |
| Is Required | false |
| Is Derived | false |
| Is Surrogate Key | false |
Phred-Scaled Genotype Likelihoods Txt
| Description | The phred-scaled genotype likelihoods rounded to the closest integer. |
| Data Type | Standards - Data Domains.ddm/Data Domains/Text Very Large [VARCHAR(2048)] |
| Is Part Of PrimaryKey | false |
| Is Required | false |
| Is Derived | false |
| Is Surrogate Key | false |
Phred-Scaled Genotype Posterior Probabilities Txt
| Description | The phred-scaled genotype posterior probabilities intended to store imputed genotype probabilities. |
| Data Type | Standards - Data Domains.ddm/Data Domains/Text Very Large [VARCHAR(2048)] |
| Is Part Of PrimaryKey | false |
| Is Required | false |
| Is Derived | false |
| Is Surrogate Key | false |
Read Depth Num
| Description | Read depth at this position for this sample. |
| 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 |
| Relationship Details |
Assay / Sequence Variation_Genotype Experiment / Sequence Variation_FK
| Is Identifying Relationship | false |
| Child Table | Assay / 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 / Sequence Variation |
| Parent Multiplicity | ONE |
| Parent Referential Integrity: On Delete | NONE |
| Parent Referential Integrity: On Insert | NONE |
| Parent Referential Integrity: On Update | NONE |
Assay / Sequence Variation_Assay_FK
| Is Identifying Relationship | false |
| Child Table | Assay / 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 | Assay |
| 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 |