tblLAB_RES_LVL_1 - Nucleotide sequences (PRO, RT, GP41, GP120)
holds nucleoside sequence for the PRO and RT sequences
Core Fields
Note: Fields marked bold form the unique identifier for a record of the table.
| Field name | Format | Description |
|---|---|---|
| TEST_ID | character (or numeric if possible) | Identifier linking this record to tblLAB_RES |
| SEQTYPE | character:
|
Type of nucleotide sequence if available |
| SEQ_START | numeric | Start position for the sequence |
| SEQ_STOP | numeric | Stop position for the sequence |
| SEQ_NUC | character | Nucleotide sequence if available |
Additional Fields
In cases where the amino acid sequence is collected rather than the nucleotide sequence, the field SEQ_NUC might be replaced with SEQ_AA, which is the nucleotide sequence, expressed in an amino acid sequence:
| Field name | Format | Description |
|---|---|---|
| SEQ_AA | character | Amino acid sequence if available (empty if test was phenotype) |
However using the amino acid sequence does not give the same detail of data as the nucleoside sequence: wobbles in the nucleoside sequence can either complicate the reading and alignment of the amino acid sequence or the wobbles can be lost and silent mutations are lost.
QA Checks
| Table | Crosstable | Error Code | Description | Study specific | Is HICDEP |
|---|---|---|---|---|---|
| AllTables | CrossTable | ATC001 | any date in database after DEATH_D in tblLTFU | Yes | |
| AllTables | CrossTable | ATC002 | any date in database after DROP_D in tblLTFU | Yes | |
| AllTables | CrossTable | ATC003 | any date in database before BIRTH_D in tblBAS | Yes | |
| AllTables | CrossTable | ATC004 | any date in database in the future | Yes | |
| AllTables | CrossTable | ATC005 | patients submitted previously who have been missed out | Yes | |
| AllTables | CrossTable | ATC006 | Any fields not coded as coding lists on table definition | Yes | |
| tblLAB_RES_LVL_1 | WithinTable | L1W001 | Duplicate records per TEST_ID and SEQTYPE | Yes | |
| tblLAB_RES_LVL_1 | WithinTable | L1W002 | SEQ_START > SEQ_STOP | Yes | |
| tblLAB_RES_LVL_1 | WithinTable | L1W003 | SEQ_NUC contains invalid IUPAC character | Yes | |
| tblLAB_RES_LVL_1 | WithinTable | L1W004 | Missing TEST_ID | Yes | |
| tblLAB_RES_LVL_1 | WithinTable | L1W005 | Missing SEQ_START | Yes | |
| tblLAB_RES_LVL_1 | WithinTable | L1W006 | Missing SEQ_STOP | Yes | |
| tblLAB_RES_LVL_1 | WithinTable | L1W007 | Missing SEQ_NUC | Yes | |
| tblLAB_RES_LVL_1 | CrossTable | L1C001 | TEST_ID not in tblLAB_RES.TEST_ID | Yes |