Slot: assembly_qual
placeholder description; linter will ignore this
URI: MIXS:0000056
Applicable Classes
| Name | Description | Modifies Slot |
|---|---|---|
| Agriculture | placeholder description; linter will ignore this | yes |
| Checklist | placeholder description; linter will ignore this | yes |
| MigsBa | placeholder description; linter will ignore this | yes |
| MigsEu | placeholder description; linter will ignore this | yes |
| MigsOrg | placeholder description; linter will ignore this | yes |
| MigsPl | placeholder description; linter will ignore this | yes |
| MigsVi | placeholder description; linter will ignore this | yes |
| Mimag | placeholder description; linter will ignore this | yes |
| Mims | placeholder description; linter will ignore this | yes |
| Misag | placeholder description; linter will ignore this | yes |
| Miuvig | placeholder description; linter will ignore this | yes |
| MigsBaPlantAssociated | placeholder description; linter will ignore this | no |
| MigsBaSediment | placeholder description; linter will ignore this | no |
| MigsBaSoil | placeholder description; linter will ignore this | no |
| MigsBaWater | placeholder description; linter will ignore this | no |
| MimarksC | placeholder description; linter will ignore this | no |
| MimarksS | placeholder description; linter will ignore this | no |
| MimsPlantAssociated | placeholder description; linter will ignore this | no |
| MimsSediment | placeholder description; linter will ignore this | no |
| MimsSoil | placeholder description; linter will ignore this | no |
| MimsWater | placeholder description; linter will ignore this | no |
Properties
- Range: ASSEMBLYQUALENUM
Identifier and Mapping Information
Annotations
| property | value |
|---|---|
| global_raw_definition | The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling >= 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totaling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated |
Schema Source
- from schema: https://github.com/turbomam/mixs-subset-examples-first/tree/main/src/mixs_subset_examples_first
LinkML Source
name: assembly_qual
annotations:
global_raw_definition:
tag: global_raw_definition
value: 'The assembly quality category is based on sets of criteria outlined for
each assembly quality category. For MISAG/MIMAG; Finished: Single, validated,
contiguous sequence per replicon without gaps or ambiguities with a consensus
error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments
where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes
and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no
review of assembly other than reporting of standard assembly statistics. Low
Quality Draft:Many fragments with little to no review of assembly other than
reporting of standard assembly statistics. Assembly statistics include, but
are not limited to total assembly size, number of contigs, contig N50/L50, and
maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence
per replicon without gaps or ambiguities, with extensive manual review and editing
to annotate putative gene functions and transcriptional units. High-quality
draft genome: One or multiple fragments, totaling >= 90% of the expected genome
or replicon sequence or predicted complete. Genome fragment(s): One or multiple
fragments, totaling < 90% of the expected genome or replicon sequence, or for
which no genome size could be estimated'
global_value_syntax:
tag: global_value_syntax
value: '[Finished genome|High-quality draft genome|Medium-quality draft genome|Low-quality
draft genome|Genome fragment(s)]'
description: placeholder description; linter will ignore this
title: assembly quality
from_schema: https://github.com/turbomam/mixs-subset-examples-first/tree/main/src/mixs_subset_examples_first
rank: 1000
slot_uri: MIXS:0000056
alias: assembly_qual
domain_of:
- Agriculture
- Checklist
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: ASSEMBLY_QUAL_ENUM