wiki:Hicdep_1.50/TableLabResLvl1

Version 1 (modified by trac, 8 years ago) (diff)

copy from version 1.30

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.

  • SAMP_ID: The assigned sample ID
  • SEQTYPE: Type of nucleotide sequence if available
  • SEQ_START: Start position for the sequence
  • SEQ_STOP: Stop position for the sequence
  • SEQ_NUC: 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:

  • SEQ_AA: 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.