/** * See the NOTICE file distributed with this work for additional information * regarding copyright ownership. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ import { SpeciesSidebarPayload } from 'src/content/app/species/state/sidebar/speciesSidebarSlice'; import { SpeciesStatsSection } from 'src/content/app/species/state/general/speciesGeneralHelper'; type RawSpeciesStats = { [genomeId: string]: { [key in SpeciesStatsSection]?: { [key: string]: string | number | null; }; }; }; export const sampleData: RawSpeciesStats = { homo_sapiens_GCA_000001405_28: { assembly_stats: { contig_n50: 56413054, total_genome_length: 3272116950, total_coding_sequence_length: 34378305, total_gap_length: 161368351, spanned_gaps: 661, chromosomes: 25, toplevel_sequences: 640, component_sequences: 36734, gc_percentage: 38.87 }, coding_stats: { coding_genes: 20424, average_genomic_span: 67123.2, average_sequence_length: 3538.93, average_cds_length: 1160.33, shortest_gene_length: 8, longest_gene_length: 2473539, total_transcripts: 162478, coding_transcripts: 106190, transcripts_per_gene: 7.96, coding_transcripts_per_gene: 5.2, total_exons: 1268315, total_coding_exons: 825666, average_exon_length: 246.94, average_coding_exon_length: 149.22, average_exons_per_transcript: 7.81, average_coding_exons_per_coding_transcript: 7.78, total_introns: 1105837, average_intron_length: 6237.5 }, non_coding_stats: { non_coding_genes: 23967, small_non_coding_genes: 4863, long_non_coding_genes: 16884, misc_non_coding_genes: 2220, average_genomic_span: 23077.19, average_sequence_length: 940.34, shortest_gene_length: 41, longest_gene_length: 1375317, total_transcripts: 54748, transcripts_per_gene: 2.28, total_exons: 184477, average_exon_length: 347.04, average_exons_per_transcript: 3.37, total_introns: 129729, average_intron_length: 15993.77 }, pseudogene_stats: { pseudogenes: 15217, average_genomic_span: 4218.48, average_sequence_length: 726.42, shortest_gene_length: 23, longest_gene_length: 909387, total_transcripts: 18617, transcripts_per_gene: 1.22, total_exons: 44532, average_exon_length: 353.34, average_exons_per_transcript: 2.39, total_introns: 25915, average_intron_length: 4372.89 }, homology_stats: { coverage: 86 }, variation_stats: { short_variants: 713749788, structural_variants: 32170052, short_variants_with_phenotype_assertions: 13365325, short_variants_with_publications: 429376, short_variants_frequency_studies: 8, structural_variants_with_phenotype_assertions: 320417 }, regulation_stats: { enhancers: 132592, promoters: 35191 } }, homo_sapiens_GCA_000001405_14: { assembly_stats: { contig_n50: 38440852, total_genome_length: 3234834689, total_coding_sequence_length: 33914472, total_gap_length: 243146473, spanned_gaps: 242, chromosomes: 25, toplevel_sequences: 297, component_sequences: null, gc_percentage: 37.81 }, coding_stats: { coding_genes: 20787, average_genomic_span: 63989.1, average_sequence_length: 3136.38, average_cds_length: 1141.09, shortest_gene_length: 8, longest_gene_length: 2304638, total_transcripts: 146152, coding_transcripts: 95346, transcripts_per_gene: 7.03, coding_transcripts_per_gene: 4.59, total_exons: 1072753, total_coding_exons: 724218, average_exon_length: 231.84, average_coding_exon_length: 150.21, average_exons_per_transcript: 7.34, average_coding_exons_per_coding_transcript: 7.6, total_introns: 926601, average_intron_length: 6220.21 }, non_coding_stats: { non_coding_genes: 22948, small_non_coding_genes: 7050, long_non_coding_genes: 13860, misc_non_coding_genes: 2038, average_genomic_span: 15206.48, average_sequence_length: 712.2, shortest_gene_length: 35, longest_gene_length: 1536213, total_transcripts: 32971, transcripts_per_gene: 1.44, total_exons: 82828, average_exon_length: 289.17, average_exons_per_transcript: 2.51, total_introns: 49857, average_intron_length: 12156.05 }, pseudogene_stats: { pseudogenes: 14170, average_genomic_span: 3525.6, average_sequence_length: 809.46, shortest_gene_length: 23, longest_gene_length: 586570, total_transcripts: 17378, transcripts_per_gene: 1.23, total_exons: 40183, average_exon_length: 362.52, average_exons_per_transcript: 2.31, total_introns: 22805, average_intron_length: 3049.46 }, homology_stats: { coverage: 0 }, variation_stats: { structural_variants: 36348512, short_variants_with_phenotype_assertions: 10233814, short_variants_with_publications: 328161, short_variants_frequency_studies: 8, structural_variants_with_phenotype_assertions: 1682589 }, regulation_stats: { enhancers: 92264, promoters: 21822 } }, escherichia_coli_str_k_12_substr_mg1655_gca_000005845_GCA_000005845_2: { assembly_stats: { contig_n50: null, total_genome_length: 4641652, total_coding_sequence_length: 3977025, total_gap_length: 0, spanned_gaps: 0, chromosomes: 1, toplevel_sequences: 1, component_sequences: 1, gc_percentage: 50.79 }, coding_stats: { coding_genes: 4240, average_genomic_span: 939.92, average_sequence_length: 939.92, average_cds_length: 938.55, shortest_gene_length: 42, longest_gene_length: 7077, total_transcripts: 4242, coding_transcripts: 4239, transcripts_per_gene: 1.0, coding_transcripts_per_gene: 1.0, total_exons: 4245, total_coding_exons: 4242, average_exon_length: 939.17, average_coding_exon_length: 937.89, average_exons_per_transcript: 1.0, average_coding_exons_per_coding_transcript: 1.0, total_introns: 3, average_intron_length: 1.67 }, non_coding_stats: { non_coding_genes: 179, small_non_coding_genes: 179, long_non_coding_genes: 0, misc_non_coding_genes: 0, average_genomic_span: 269.83, average_sequence_length: 269.83, shortest_gene_length: 53, longest_gene_length: 2905, total_transcripts: 179, transcripts_per_gene: 1.0, total_exons: 179, average_exon_length: 269.83, average_exons_per_transcript: 1.0, total_introns: 0, average_intron_length: null }, pseudogene_stats: { pseudogenes: 115, average_genomic_span: 1103.18, average_sequence_length: 913.03, shortest_gene_length: 51, longest_gene_length: 8622, total_transcripts: 115, transcripts_per_gene: 1.0, total_exons: 134, average_exon_length: 783.57, average_exons_per_transcript: 1.17, total_introns: 19, average_intron_length: 1150.95 }, homology_stats: { coverage: 93.1 } }, caenorhabditis_elegans_GCA_000002985_3: { assembly_stats: { contig_n50: null, total_genome_length: 100272607, total_coding_sequence_length: 24880113, total_gap_length: 0, spanned_gaps: 0, chromosomes: 6, toplevel_sequences: 6, component_sequences: 3267, gc_percentage: 35.44 }, coding_stats: { coding_genes: 20191, average_genomic_span: 3149.75, average_sequence_length: 1402.22, average_cds_length: 1425.34, shortest_gene_length: 30, longest_gene_length: 102626, total_transcripts: 34214, coding_transcripts: 33552, transcripts_per_gene: 1.69, coding_transcripts_per_gene: 1.66, total_exons: 240193, total_coding_exons: 225661, average_exon_length: 236.95, average_coding_exon_length: 211.92, average_exons_per_transcript: 7.02, average_coding_exons_per_coding_transcript: 6.73, total_introns: 205969, average_intron_length: 398.96 }, non_coding_stats: { non_coding_genes: 24791, small_non_coding_genes: 24515, long_non_coding_genes: 276, misc_non_coding_genes: 0, average_genomic_span: 81.87, average_sequence_length: 74.6, shortest_gene_length: 17, longest_gene_length: 14770, total_transcripts: 25279, transcripts_per_gene: 1.02, total_exons: 25763, average_exon_length: 72.63, average_exons_per_transcript: 1.02, total_introns: 484, average_intron_length: 401.85 }, pseudogene_stats: { pseudogenes: 1922, average_genomic_span: 1474.68, average_sequence_length: 899.83, shortest_gene_length: 63, longest_gene_length: 17899, total_transcripts: 1958, transcripts_per_gene: 1.02, total_exons: 7695, average_exon_length: 230.92, average_exons_per_transcript: 3.93, total_introns: 5737, average_intron_length: 203.57 }, homology_stats: { coverage: 87.3 } }, plasmodium_falciparum_GCA_000002765_2: { assembly_stats: { contig_n50: null, total_genome_length: 23292622, total_coding_sequence_length: 12309897, total_gap_length: 0, spanned_gaps: 0, chromosomes: 14, toplevel_sequences: 0, component_sequences: 14, gc_percentage: 19.34 }, coding_stats: { coding_genes: 5362, average_genomic_span: 2569.88, average_sequence_length: 2296.23, average_cds_length: 2297.48, shortest_gene_length: 90, longest_gene_length: 30864, total_transcripts: 5362, coding_transcripts: 5358, transcripts_per_gene: 1.0, coding_transcripts_per_gene: 1.0, total_exons: 14146, total_coding_exons: 14139, average_exon_length: 870.38, average_coding_exon_length: 870.63, average_exons_per_transcript: 2.64, average_coding_exons_per_coding_transcript: 2.64, total_introns: 8784, average_intron_length: 167.04 }, non_coding_stats: { non_coding_genes: 252, small_non_coding_genes: 252, long_non_coding_genes: 0, misc_non_coding_genes: 0, average_genomic_span: 553.68, average_sequence_length: 553.68, shortest_gene_length: 68, longest_gene_length: 6175, total_transcripts: 252, transcripts_per_gene: 1.0, total_exons: 252, average_exon_length: 553.68, average_exons_per_transcript: 1.0, total_introns: 0, average_intron_length: null }, pseudogene_stats: { pseudogenes: 153, average_genomic_span: 1665.66, average_sequence_length: 1568.01, shortest_gene_length: 72, longest_gene_length: 11291, total_transcripts: 153, transcripts_per_gene: 1.0, total_exons: 461, average_exon_length: 520.4, average_exons_per_transcript: 3.01, total_introns: 308, average_intron_length: 48.51 }, homology_stats: { coverage: 43.3 } }, saccharomyces_cerevisiae_GCA_000146045_2: { assembly_stats: { contig_n50: null, total_genome_length: 12071326, total_coding_sequence_length: 8762001, total_gap_length: 0, spanned_gaps: 0, chromosomes: 16, toplevel_sequences: 16, component_sequences: 16, gc_percentage: 38.15 }, coding_stats: { coding_genes: 6600, average_genomic_span: 1344.37, average_sequence_length: 1327.58, average_cds_length: 1327.58, shortest_gene_length: 51, longest_gene_length: 14733, total_transcripts: 6600, coding_transcripts: 6600, transcripts_per_gene: 1.0, coding_transcripts_per_gene: 1.0, total_exons: 6913, total_coding_exons: 6913, average_exon_length: 1267.47, average_coding_exon_length: 1267.47, average_exons_per_transcript: 1.05, average_coding_exons_per_coding_transcript: 1.05, total_introns: 313, average_intron_length: 348.08 }, non_coding_stats: { non_coding_genes: 424, small_non_coding_genes: 424, long_non_coding_genes: 0, misc_non_coding_genes: 0, average_genomic_span: 208.59, average_sequence_length: 198.77, shortest_gene_length: 58, longest_gene_length: 5947, total_transcripts: 424, transcripts_per_gene: 1.0, total_exons: 491, average_exon_length: 171.64, average_exons_per_transcript: 1.16, total_introns: 67, average_intron_length: 62.18 }, pseudogene_stats: { pseudogenes: 12, average_genomic_span: 863.25, average_sequence_length: 863.25, shortest_gene_length: 228, longest_gene_length: 3147, total_transcripts: 12, transcripts_per_gene: 1.0, total_exons: 12, average_exon_length: 863.25, average_exons_per_transcript: 1.0, total_introns: 0, average_intron_length: null }, variation_stats: { short_variants: 263537, structural_variants: 0, short_variants_with_phenotype_assertions: 0, short_variants_with_publications: 0, short_variants_frequency_studies: 0, structural_variants_with_phenotype_assertions: 0 }, homology_stats: { coverage: 57.7 } }, triticum_aestivum_GCA_900519105_1: { assembly_stats: { contig_n50: 51842, total_genome_length: 14547261565, total_coding_sequence_length: 133312441, total_gap_length: 275682619, spanned_gaps: 692976, chromosomes: 22, toplevel_sequences: 22, component_sequences: 22, gc_percentage: 45.18 }, coding_stats: { coding_genes: 107891, average_genomic_span: 3488.91, average_sequence_length: 1570.98, average_cds_length: 1332.42, shortest_gene_length: 54, longest_gene_length: 124945, total_transcripts: 133744, coding_transcripts: 133346, transcripts_per_gene: 1.24, coding_transcripts_per_gene: 1.24, total_exons: 749233, total_coding_exons: 712204, average_exon_length: 303.33, average_coding_exon_length: 249.47, average_exons_per_transcript: 5.6, average_coding_exons_per_coding_transcript: 5.34, total_introns: 615489, average_intron_length: 491.21 }, non_coding_stats: { non_coding_genes: 12853, small_non_coding_genes: 12491, long_non_coding_genes: 362, misc_non_coding_genes: 0, average_genomic_span: 149.42, average_sequence_length: 149.42, shortest_gene_length: 42, longest_gene_length: 5792, total_transcripts: 12853, transcripts_per_gene: 1.0, total_exons: 12853, average_exon_length: 149.42, average_exons_per_transcript: 1.0, total_introns: 0, average_intron_length: null }, pseudogene_stats: { pseudogenes: 0, average_genomic_span: null, average_sequence_length: null, shortest_gene_length: null, longest_gene_length: null, total_transcripts: null, transcripts_per_gene: null, total_exons: null, average_exon_length: null, average_exons_per_transcript: null, total_introns: null, average_intron_length: null }, variation_stats: { short_variants: 18093911, structural_variants: 0, short_variants_frequency_studies: 1, short_variants_with_phenotype_assertions: 0, short_variants_with_publications: 0, structural_variants_with_phenotype_assertions: 0 }, homology_stats: { coverage: 98.8 } }, actinobacillus: { assembly_stats: { contig_n50: null, total_genome_length: 2274482, total_coding_sequence_length: 1964559, total_gap_length: 0, spanned_gaps: 0, chromosomes: 1, toplevel_sequences: 1, component_sequences: 1, gc_percentage: 41.3 }, coding_stats: { coding_genes: 2012, average_genomic_span: 976.42, average_sequence_length: 976.42, average_cds_length: 976.42, shortest_gene_length: 114, longest_gene_length: 10044, total_transcripts: 2012, coding_transcripts: 2012, transcripts_per_gene: 1.0, coding_transcripts_per_gene: 1.0, total_exons: 2012, total_coding_exons: 2012, average_exon_length: 976.42, average_coding_exon_length: 976.42, average_exons_per_transcript: 1.0, average_coding_exons_per_coding_transcript: 1.0, total_introns: 0, average_intron_length: null }, non_coding_stats: { non_coding_genes: 80, small_non_coding_genes: 80, long_non_coding_genes: 0, misc_non_coding_genes: 0, average_genomic_span: 412.6, average_sequence_length: 412.6, shortest_gene_length: 74, longest_gene_length: 2896, total_transcripts: 80, transcripts_per_gene: 1.0, total_exons: 80, average_exon_length: 412.6, average_exons_per_transcript: 1.0, total_introns: 0, average_intron_length: null }, pseudogene_stats: { pseudogenes: 0, average_genomic_span: null, average_sequence_length: null, shortest_gene_length: null, longest_gene_length: null, total_transcripts: null, transcripts_per_gene: null, total_exons: null, average_exon_length: null, average_exons_per_transcript: null, total_introns: null, average_intron_length: null } } }; type SpeciesSidebarData = { [genomeId: string]: SpeciesSidebarPayload; }; export const sidebarData: SpeciesSidebarData = { homo_sapiens_GCA_000001405_28: { id: 'GCA_000001405.28', taxonomy_id: '9606', strain: null, database_version: '104.38', common_name: 'Human', scientific_name: 'Homo sapiens', gencode_version: 'GENCODE 34', assembly_name: 'GRCh38.p13', assembly_provider: { name: 'INSDC assembly', url: '' }, annotation_provider: { name: 'Ensembl', url: 'http://www.ensembl.org' }, assembly_level: 'complete genome', annotation_method: 'full genebuild', assembly_date: '2019-02-01', notes: [ { heading: 'Pseudoautosomal regions', body: 'The Y chromosome in this assembly contains two psuedoautosomal regions (PARs) that were taken from the corresponding X chromosoles and are exact duplicates:\nchrX:10,000-2,781,479 = chrY:10,000-2,781,479\nchrX:155,701,382-156,030,895 = chrY:56,887,02-57,217,415' } ] }, homo_sapiens_GCA_000001405_14: { id: 'GCA_000001405.14', taxonomy_id: '9606', strain: null, database_version: '104.37', common_name: 'Human', scientific_name: 'Homo sapiens', gencode_version: 'GENCODE 19', assembly_name: 'GRCh37.p13', assembly_provider: { name: 'INSDC assembly', url: '' }, annotation_provider: { name: 'Ensembl', url: '' }, assembly_level: 'complete genome', annotation_method: 'full genebuild', assembly_date: '2013-06-01', notes: [] }, escherichia_coli_str_k_12_substr_mg1655_gca_000005845_GCA_000005845_2: { id: 'GCA_000005845.2', taxonomy_id: '511145', strain: null, database_version: '104.1', common_name: null, scientific_name: 'Escherichia coli str. K-12 substr. MG1655', gencode_version: null, assembly_name: 'ASM584v2', assembly_provider: { name: 'INSDC assembly', url: '' }, annotation_provider: { name: 'European Nucleotide Archive', url: 'http://www.ensembl.org' }, assembly_level: 'complete genome', annotation_method: 'Generated from ENA annotation', assembly_date: '2013-09-01', notes: [] }, caenorhabditis_elegans_GCA_000002985_3: { id: 'GCA_000002985.3', taxonomy_id: '6239', strain: { type: 'Strain', value: 'N2' }, database_version: '104.269', common_name: null, scientific_name: 'Caenorhabditis elegans', gencode_version: null, assembly_name: 'WBcel235', assembly_provider: { name: 'WormBase', url: 'http://www.wormbase.org' }, annotation_provider: { name: 'WormBase', url: 'http://www.wormbase.org' }, assembly_level: 'complete genome', annotation_method: 'Import', assembly_date: '2013-02-01', notes: [] }, plasmodium_falciparum_GCA_000002765_2: { id: 'GCA_000002765.2', taxonomy_id: '36329', strain: null, database_version: '104.1', common_name: null, scientific_name: 'Plasmodium falciparum 3D7', gencode_version: null, assembly_name: 'ASM276v2', assembly_provider: { name: 'Naval Medical Research Institute', url: 'http://www.ensembl.org' }, annotation_provider: { name: '', url: '' }, assembly_level: 'complete genome', annotation_method: 'Import', assembly_date: '2016-04-01', notes: [] }, saccharomyces_cerevisiae_GCA_000146045_2: { id: 'GCA_000146045.2', taxonomy_id: '4932', strain: { type: 'Strain', value: 'S288C' }, database_version: '104.4', common_name: 'Brewers yeast', scientific_name: 'Saccharomyces cerevisiae', gencode_version: null, assembly_name: 'R64', assembly_provider: { name: 'Saccharomyces Genome Database', url: '' }, annotation_provider: { name: 'Saccharomyces Genome Database', url: 'http://www.yeastgenome.org' }, assembly_level: 'complete genome', annotation_method: 'Import', assembly_date: '2014-12-01', notes: [] }, triticum_aestivum_GCA_900519105_1: { id: 'GCA_900519105.1', taxonomy_id: '4565', strain: { type: 'Cultivar', value: 'Chinese spring' }, database_version: '104.4', common_name: 'Wheat', scientific_name: 'Triticum aestivum', gencode_version: null, assembly_name: 'IWGSC', assembly_provider: { name: 'International Wheat Genome Sequencing Consortium', url: 'https://www.ebi.ac.uk/ena/data/view/GCA_900519105.1' }, annotation_provider: { name: 'International Wheat Genome Sequencing Consortium', url: 'https://www.ebi.ac.uk/ena/data/view/GCA_900519105.1' }, assembly_level: 'complete genome', annotation_method: 'Import', assembly_date: '2018-08-01', notes: [] } };