Plant Pathogen, Genomics, Illumina Shortread, Sample ID 394527
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Data and Resources
This data is made available openly under a Creative Commons Attribution license.
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Data Policy
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Additional Info Show Blank Fields
| Field | Value |
|---|---|
| Resource Permissions | organization_member_after_embargo:date_of_transfer_to_archive:365:pp-prj007 |
| Access Control Date | 2024-02-01 |
| Access Control Mode | date |
| Sequence Data Type | illumina-shortread |
| analysis_software | MiSeq Control Software (MCS) v3.1.0.13, Real Time Analysis (RTA) v1.18.54.4, DRAGEN BCL Convert 07.021.624.3.10.8 |
| base_url | https://downloads-qcif.bioplatforms.com/bpa/pp_staging/illumina-shortread/BPAOPS-1357/20230201_PP_AGRF_KTMDN/ |
| bioplatforms_dataset_id | 102.100.100/399013 |
| bioplatforms_library_id | 102.100.100/396777 |
| bioplatforms_project | Plant Pathogen Initiative |
| bioplatforms_project_code | PP007_JGMV |
| bioplatforms_sample_id | 102.100.100/394527 |
| ccg_jira_ticket | BPAOPS-1357 |
| class | Stelpaviricetes |
| collection_date | 2022-02-23 |
| collector | Sharman, M. |
| common_name | Johnsongrass mosaic virus |
| coord_uncertainty_metres | 10.0 |
| country | Australia |
| data_context | Genomics |
| data_type | Illumina short read |
| date_data_published | 15/02/2023 |
| date_of_transfer | 2023-02-01 |
| date_of_transfer_to_archive | 2023-02-01 |
| decimal_latitude_public | -25.67166 |
| decimal_longitude_public | 151.84374 |
| description | Illmina short read |
| download | https://data.bioplatforms.com/dataset?ext_search_by=&q=ticket%3ABPAOPS-1357 |
| facility | AGRF |
| facility_project_code | CAGRF221012335 |
| facility_sample_id | 13370-15 |
| family | Potyviridae |
| flowcell_id | KTMDN |
| flowcell_type | V2-300 |
| folder_name | 20230201_PP_AGRF_KTMDN |
| genus | Potyvirus |
| host_common_name | Johnson grass |
| host_family | Poaceae |
| host_organ | Leaf |
| host_scientific_name | Sorghum halepense |
| host_status | Wild growth |
| host_symptom | Chlorotic Mosaic |
| insert_size_range | 250 bp |
| library_construction_protocol | TruSeq Stranded Total RNA with Ribo-Zero Plant |
| library_id | 396777 |
| library_index_id_dual | UDI0067-F & UDI0067-R |
| library_index_seq_dual | TTCCTGTT-AGTATCTT |
| library_layout | Paired-End |
| library_location | AGRF Melbourne |
| library_ng_ul | 4.1579062577 |
| library_pcr_cycles | 13 |
| library_prep_date | 2023-01-16 |
| library_prepared_by | Vanessa Bromley |
| library_selection | Stranded RNA with rRNA Depletion |
| library_source | Purified RNA Virus |
| library_strategy | Whole Genome Sequencing |
| library_type | Illumina-shortread |
| location_text | Isis HWY, 3.2km from Burnett HWY, Ban Ban Springs |
| material_conc_ng_ul | 336.0 |
| material_extracted_by | Peter Vukovic |DAFQ |
| material_extraction_date | 2022-04-28 |
| material_extraction_method | CTAB |
| material_extraction_type | Total Nucleic acid |
| metadata_revision_date | 2024-01-16 |
| metadata_revision_filename | 2024-01-16_Combined_Plant_Pathogen_sample_metadata_forQCIF_removelatlong_v2.xlsx |
| order | Patatavirales |
| phylum | Pisuviricota |
| project_lead | Murray Sharman | DAFQ |
| sample_collection_type | Domestic Isolate |
| sample_custodian | Murray Sharman | DAFQ |
| sample_type | Freeze Dried |
| scientific_name | Johnsongrass mosaic virus |
| sequencing_facility | AGRF |
| sequencing_kit_chemistry_version | V2 |
| sequencing_platform | MiSeq |
| species | Johnsongrass mosaic virus |
| specimen_custodian | DAFQ Domestic Isolate Collection |
| specimen_id | 5872 |
| specimen_id_description | DAFQ Domestic Isolate Collection |
| state_or_region | Queensland |
| taxon_id | 31742 |
| taxonomic_group | Virus |
| ticket | BPAOPS-1357 |
| tissue | Leaf |
| tissue_preservation | Fresh tissue, Freeze dried |
| tissue_preservation_temperature | -20°C |
| wild_captive | Wild |
| work_order | 20001 |