wiki:Hicdep_1.70/TableLabResLvl2

tblLAB_RES_LVL_2 - Mutations

holds mutations and positions of PRO and RT sequences.

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

GENE

character:

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

Type of sequence/gene (PRO, RT, GP41, GP120)

AA_POS

numeric

Position of the mutation in the sequence

AA_POS_SUB

character:

  • a = first
  • b = second
  • etc.

Subposition used to code insertions

AA_FOUND_1

character. empty = Amino acid has been deleted.

Mutation (Amino acid) found in the sequence

AA_FOUND_2

character. empty = Amino acid has been deleted.

Mutation (Amino acid) found in the sequence (if more than 1)

AA_FOUND_3

character. empty = Amino acid has been deleted.

Mutation (Amino acid) found in the sequence (if more than 2)

AA_FOUND_4

character. empty = Amino acid has been deleted.

Mutation (Amino acid) found in the sequence (if more than 3)

AA_FOUND_# could be extended if mixtures with more than 4 amino acids are found.

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_2WithinTableL2W001AA_FOUND_x but nothing in AA_FOUND(x-1)YES
tblLAB_RES_LVL_2WithinTableL2W002Duplicate records per TEST_ID, GENE, AA_POS and AA_POS_SUBYES
tblLAB_RES_LVL_2WithinTableL2W003Missing TEST_IDYES
tblLAB_RES_LVL_2WithinTableL2W004Missing GENEYES
tblLAB_RES_LVL_2WithinTableL2W005Missing AA_POSYES
tblLAB_RES_LVL_2WithinTableL2W006Missing AA_POS_SUBYES
tblLAB_RES_LVL_2WithinTableL2W007Missing AA_FOUND_1YES
tblLAB_RES_LVL_2CrossTableL2C001TEST_ID not in tblLAB_RES.TEST_IDYES
Last modified 5 years ago Last modified on 11/16/12 15:08:17