wiki:Hicdep_1.80/TableLabResLvl1

Version 1 (modified by admin, 4 years ago) (diff)

Copy from Hicdep 1.70

tblLAB_RES_LVL_1 - Nucleotide sequences (PRO, RT, GP41, GP120)

holds nucleoside sequence for the PRO and RT sequences. No entry is made if the test was a phenotype test.

Note: This table is tightly linked to tblLAB_RES.

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:

  • PRO = PRO sequence
  • RT = RT sequence
  • GP41 = GP41 sequence
  • GP120 = GP120 sequence

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 HICDEP?
AllTablesCrossTableATC001any date in database after DEATH_D in tblLTFUYES
AllTablesCrossTableATC002any date in database after DROP_D in tblLTFUYES
AllTablesCrossTableATC003any date in database before BIRTH_D in tblBASYES
AllTablesCrossTableATC004any date in database in the futureYES
AllTablesCrossTableATC005patients submitted previously who have been missed outYES
AllTablesCrossTableATC006Any fields not coded as coding lists on table definitionYES
tblLAB_RES_LVL_1WithinTableL1W001Duplicate records per TEST_ID and SEQTYPEYES
tblLAB_RES_LVL_1WithinTableL1W002SEQ_START > SEQ_STOPYES
tblLAB_RES_LVL_1WithinTableL1W003SEQ_NUC contains invalid IUPAC characterYES
tblLAB_RES_LVL_1WithinTableL1W004Missing TEST_IDYES
tblLAB_RES_LVL_1WithinTableL1W005Missing SEQ_STARTYES
tblLAB_RES_LVL_1WithinTableL1W006Missing SEQ_STOPYES
tblLAB_RES_LVL_1WithinTableL1W007Missing SEQ_NUCYES
tblLAB_RES_LVL_1CrossTableL1C001TEST_ID not in tblLAB_RES.TEST_IDYES