Whole Genomic Sequencing
About
- Rapid sequencing of SARS-CoV-2 samples and bioinformatic analysis of genome data. This supports the identification of variants and mutants of concern and the detection and investigation of COVID-19 outbreaks and incidents.
- Positive test from PCR test are sent for genomic sequencing to identify the genetic structure of the virus
Useful Links
WGS_latest.md
Information
| value | |
|---|---|
| size | 10279575 |
| mtime | 2022-08-15 08:45:32 |
| ctime | 2022-08-15 08:45:32 |
| file | WGS_latest.rds |
| nrows | 352158 |
Columns
| name | type | label | examples | description |
|---|---|---|---|---|
| UniqID | chr | |||
| SubLab | chr | Sub lab | NHS:COV, GLA:REV, EDI:RVL, LAN:LAW, DEE:UNI | Sub lab ID |
| query | chr | |||
| SequenceID | chr | Sequence ID Number | Sequence ID number | |
| Collection_Date | date | Collection date | 2022-03-07, 2022-03-14, 2022-03-02, 2022-03-09, 2022-02-15 | Date sample collected |
| Sequencing_Date | chr | Sequencing date | 05/03/2022, 10/03/2022, 29/03/2022, 26/02/2022 | Date sample sequenced |
| Alignment_Date | chr | Alignment date | 01/03/2022, 15/03/2022, 28/02/2022, 22/03/2022, 09/03/2022 | The date the sequence is first available to PHS for analysis (used for sample tracking and calculating turn around times) |
| adm2 | chr | County of patient | GLASGOW, EDINBURGH, NORTH LANARKSHIRE, FIFE, SOUTH LANARKSHIRE | County level based on patient's outer postcode |
| HealthBoard | chr | NHS Health Board | GC, LO, LN, GR, TY | Name abbreviation of NHS Health Boards |
| VariantofInterest | chr | Variant of interest | VOC-22JAN-01, V-21APR-02, VOC-21NOV-01, V-20DEC-01, Not assigned VOC/VUI | whether VOC/VOI or not |
| VariantShorthand | chr | Variance shorthand | BA.2, B.1.617.2, BA.1, VOC1, NA | seems incomplete? - better to use lineage |
| VariantCalling | chr | Variant calling | Confirmed, Probable, NA, Probable; Secondary change | Based on the PHE VUI/VOC genomic definition, there are thresholds within number of mutation / deletions present within your sequence that match the profile. HR-LQG is high risk low quality. |
| ref_count | chr | Counts of reference bases | 0, NA, 1 | Counts of reference bases (not mutations) |
| alt_count | chr | Counts of mutations | 3, 11, 9, 13, NA | Counts of mutations (given that the mutation is an expected one within the VUI/VOC genomic profile) |
| other_count | chr | Other counts | 0, 1, NA, 3, 2 | Counts of bases that are not reference or expected mutations |
| Ambiguous | chr | Counts of ambiguous bases | 0, 1, NA, 3, 2 | Counts of bases which are ambiguous (typically due to low sequencing quality) |
| MOI_List | chr | K417N, L452R;A2529V, L452R, L452R;A222V;Y145H;A2529V | ||
| aa:S:E484K | chr | A, wt, amb | ||
| aa:S:G446V | chr | wt, S, amb, V | ||
| aa:S:N439k | chr | wt, amb, K | ||
| aa:S:K417N | chr | N, wt, amb, T | ||
| aa:S:E484Q | chr | A, wt, amb | ||
| aa:S:P251L | chr | wt, amb, L | ||
| aa:S:L452R | chr | wt, R, amb, Q | ||
| aa:S:A222V | chr | wt, V, amb | ||
| aa:S:Y145H | chr | wt, amb, H | ||
| aa:orf1ab:A2529V | chr | wt, V, amb | ||
| aa:S:L452W | chr | wt, R, amb, Q | ||
| aa:S:L452Q | chr | wt, R, amb, Q | ||
| aa:S:L452M | chr | wt, R, amb, Q | ||
| aa:orf10:L37F | chr | wt, -, F | ||
| aa:orf1ab:N4060S | chr | wt, amb | ||
| aa:orf1ab:S1221L | chr | wt, amb | ||
| lineage | chr | AY.4, BA.2, BA.1.1, B.1.1.7, BA.1 | ||
| pangolin_version | chr | 4.1.2 | ||
| ISO_Week | dbl | 9, 10, 12, 7, 8 | ||
| validchi | chr | Valid CHI | ||
| EAVE_LINKNO | chr | EAVE Study Identifier | EAVE-II Identifier, pseudoynmised CHI numbers are used to create randomly assigned study index numbers. |
Last update:
August 25, 2022
Created: August 25, 2022
Created: August 25, 2022