Unverified Commit 53b1dbc2 authored by Manoj Pandian Sakthivel's avatar Manoj Pandian Sakthivel Committed by GitHub
Browse files

Update species stats data to 104 (#546)

parent b7b3099d
Pipeline #182394 passed with stages
in 6 minutes and 26 seconds
......@@ -31,7 +31,7 @@ export const sampleData: RawSpeciesStats = {
assembly_stats: {
contig_n50: 56413054,
total_genome_length: 3272116950,
total_coding_sequence_length: 34317174,
total_coding_sequence_length: 34378305,
total_gap_length: 161368351,
spanned_gaps: 661,
chromosomes: 25,
......@@ -40,66 +40,66 @@ export const sampleData: RawSpeciesStats = {
gc_percentage: 38.87
},
coding_stats: {
coding_genes: 20420,
average_genomic_span: 66885.16,
average_sequence_length: 3443.15,
average_cds_length: 1139.02,
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: 153909,
coding_transcripts: 100607,
transcripts_per_gene: 7.54,
coding_transcripts_per_gene: 4.93,
total_exons: 1150521,
total_coding_exons: 764520,
average_exon_length: 243.09,
average_coding_exon_length: 149.87,
average_exons_per_transcript: 7.48,
average_coding_exons_per_coding_transcript: 7.6,
total_introns: 996612,
average_intron_length: 6367.19
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: 23985,
small_non_coding_genes: 4870,
long_non_coding_genes: 16895,
non_coding_genes: 23967,
small_non_coding_genes: 4863,
long_non_coding_genes: 16884,
misc_non_coding_genes: 2220,
average_genomic_span: 22904.09,
average_sequence_length: 1084.17,
average_genomic_span: 23077.19,
average_sequence_length: 940.34,
shortest_gene_length: 41,
longest_gene_length: 1375317,
total_transcripts: 54482,
transcripts_per_gene: 2.27,
total_exons: 183012,
average_exon_length: 347.07,
average_exons_per_transcript: 3.36,
total_introns: 128530,
average_intron_length: 15929.64
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: 4124.33,
average_sequence_length: 802.62,
average_genomic_span: 4218.48,
average_sequence_length: 726.42,
shortest_gene_length: 23,
longest_gene_length: 909387,
total_transcripts: 18474,
transcripts_per_gene: 1.21,
total_exons: 43639,
average_exon_length: 356.59,
average_exons_per_transcript: 2.36,
total_introns: 25165,
average_intron_length: 4336.85
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: 98.8
coverage: 86
},
variation_stats: {
short_variants: 713730678,
structural_variants: 32132047,
short_variants_with_phenotype_assertions: 13336864,
short_variants_with_publications: 303288,
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: 1921150
structural_variants_with_phenotype_assertions: 320417
},
regulation_stats: {
enhancers: 132592,
......@@ -122,7 +122,7 @@ export const sampleData: RawSpeciesStats = {
coding_genes: 20787,
average_genomic_span: 63989.1,
average_sequence_length: 3136.38,
average_CDS_length: 1141.09,
average_cds_length: 1141.09,
shortest_gene_length: 8,
longest_gene_length: 2304638,
total_transcripts: 146152,
......@@ -157,7 +157,7 @@ export const sampleData: RawSpeciesStats = {
},
pseudogene_stats: {
pseudogenes: 14170,
average_genomic_span: 3525.3,
average_genomic_span: 3525.6,
average_sequence_length: 809.46,
shortest_gene_length: 23,
longest_gene_length: 586570,
......@@ -169,11 +169,11 @@ export const sampleData: RawSpeciesStats = {
total_introns: 22805,
average_intron_length: 3049.46
},
homology_stats: {
coverage: 0
},
variation_stats: {
short_variants: 677181182,
structural_variants: 36348512,
short_variants_with_phenotype_assertions: 10233814,
short_variants_with_publications: 328161,
......@@ -201,19 +201,19 @@ export const sampleData: RawSpeciesStats = {
coding_genes: 4240,
average_genomic_span: 939.92,
average_sequence_length: 939.92,
average_CDS_length: 938.55,
average_cds_length: 938.55,
shortest_gene_length: 42,
longest_gene_length: 7077,
total_transcripts: 4242,
coding_transcripts: 4239,
transcripts_per_gene: 1,
coding_transcripts_per_gene: 1,
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,
average_coding_exons_per_coding_transcript: 1,
average_exons_per_transcript: 1.0,
average_coding_exons_per_coding_transcript: 1.0,
total_introns: 3,
average_intron_length: 1.67
},
......@@ -227,10 +227,10 @@ export const sampleData: RawSpeciesStats = {
shortest_gene_length: 53,
longest_gene_length: 2905,
total_transcripts: 179,
transcripts_per_gene: 1,
transcripts_per_gene: 1.0,
total_exons: 179,
average_exon_length: 269.83,
average_exons_per_transcript: 1,
average_exons_per_transcript: 1.0,
total_introns: 0,
average_intron_length: null
},
......@@ -241,7 +241,7 @@ export const sampleData: RawSpeciesStats = {
shortest_gene_length: 51,
longest_gene_length: 8622,
total_transcripts: 115,
transcripts_per_gene: 1,
transcripts_per_gene: 1.0,
total_exons: 134,
average_exon_length: 783.57,
average_exons_per_transcript: 1.17,
......@@ -268,14 +268,14 @@ export const sampleData: RawSpeciesStats = {
coding_genes: 20191,
average_genomic_span: 3149.75,
average_sequence_length: 1402.22,
average_CDS_length: 1425.34,
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: 240183,
total_exons: 240193,
total_coding_exons: 225661,
average_exon_length: 236.95,
average_coding_exon_length: 211.92,
......@@ -316,7 +316,7 @@ export const sampleData: RawSpeciesStats = {
average_intron_length: 203.57
},
homology_stats: {
coverage: 51.8
coverage: 87.3
}
},
plasmodium_falciparum_GCA_000002765_2: {
......@@ -327,7 +327,7 @@ export const sampleData: RawSpeciesStats = {
total_gap_length: 0,
spanned_gaps: 0,
chromosomes: 14,
toplevel_sequences: 14,
toplevel_sequences: 0,
component_sequences: 14,
gc_percentage: 19.34
},
......@@ -335,13 +335,13 @@ export const sampleData: RawSpeciesStats = {
coding_genes: 5362,
average_genomic_span: 2569.88,
average_sequence_length: 2296.23,
average_CDS_length: 2297.48,
average_cds_length: 2297.48,
shortest_gene_length: 90,
longest_gene_length: 30864,
total_transcripts: 5362,
coding_transcripts: 5358,
transcripts_per_gene: 1,
coding_transcripts_per_gene: 1,
transcripts_per_gene: 1.0,
coding_transcripts_per_gene: 1.0,
total_exons: 14146,
total_coding_exons: 14139,
average_exon_length: 870.38,
......@@ -361,10 +361,10 @@ export const sampleData: RawSpeciesStats = {
shortest_gene_length: 68,
longest_gene_length: 6175,
total_transcripts: 252,
transcripts_per_gene: 1,
transcripts_per_gene: 1.0,
total_exons: 252,
average_exon_length: 553.68,
average_exons_per_transcript: 1,
average_exons_per_transcript: 1.0,
total_introns: 0,
average_intron_length: null
},
......@@ -375,7 +375,7 @@ export const sampleData: RawSpeciesStats = {
shortest_gene_length: 72,
longest_gene_length: 11291,
total_transcripts: 153,
transcripts_per_gene: 1,
transcripts_per_gene: 1.0,
total_exons: 461,
average_exon_length: 520.4,
average_exons_per_transcript: 3.01,
......@@ -402,13 +402,13 @@ export const sampleData: RawSpeciesStats = {
coding_genes: 6600,
average_genomic_span: 1344.37,
average_sequence_length: 1327.58,
average_CDS_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,
coding_transcripts_per_gene: 1,
transcripts_per_gene: 1.0,
coding_transcripts_per_gene: 1.0,
total_exons: 6913,
total_coding_exons: 6913,
average_exon_length: 1267.47,
......@@ -416,7 +416,7 @@ export const sampleData: RawSpeciesStats = {
average_exons_per_transcript: 1.05,
average_coding_exons_per_coding_transcript: 1.05,
total_introns: 313,
average_intron_length: 354.08
average_intron_length: 348.08
},
non_coding_stats: {
non_coding_genes: 424,
......@@ -428,7 +428,7 @@ export const sampleData: RawSpeciesStats = {
shortest_gene_length: 58,
longest_gene_length: 5947,
total_transcripts: 424,
transcripts_per_gene: 1,
transcripts_per_gene: 1.0,
total_exons: 491,
average_exon_length: 171.64,
average_exons_per_transcript: 1.16,
......@@ -442,20 +442,20 @@ export const sampleData: RawSpeciesStats = {
shortest_gene_length: 228,
longest_gene_length: 3147,
total_transcripts: 12,
transcripts_per_gene: 1,
transcripts_per_gene: 1.0,
total_exons: 12,
average_exon_length: 863.25,
average_exons_per_transcript: 1,
average_exons_per_transcript: 1.0,
total_introns: 0,
average_intron_length: null
},
variation_stats: {
short_variants: 263537,
structural_variants: null,
short_variants_with_phenotype_assertions: null,
short_variants_with_publications: null,
short_variants_frequency_studies: null,
structural_variants_with_phenotype_assertions: null
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
......@@ -477,7 +477,7 @@ export const sampleData: RawSpeciesStats = {
coding_genes: 107891,
average_genomic_span: 3488.91,
average_sequence_length: 1570.98,
average_CDS_length: 1332.42,
average_cds_length: 1332.42,
shortest_gene_length: 54,
longest_gene_length: 124945,
total_transcripts: 133744,
......@@ -503,10 +503,10 @@ export const sampleData: RawSpeciesStats = {
shortest_gene_length: 42,
longest_gene_length: 5792,
total_transcripts: 12853,
transcripts_per_gene: 1,
transcripts_per_gene: 1.0,
total_exons: 12853,
average_exon_length: 149.42,
average_exons_per_transcript: 1,
average_exons_per_transcript: 1.0,
total_introns: 0,
average_intron_length: null
},
......@@ -526,14 +526,14 @@ export const sampleData: RawSpeciesStats = {
},
variation_stats: {
short_variants: 18093911,
structural_variants: null,
short_variants_with_phenotype_assertions: null,
short_variants_with_publications: null,
structural_variants: 0,
short_variants_frequency_studies: 1,
structural_variants_with_phenotype_assertions: null
short_variants_with_phenotype_assertions: 0,
short_variants_with_publications: 0,
structural_variants_with_phenotype_assertions: 0
},
homology_stats: {
coverage: 98.7
coverage: 98.8
}
},
actinobacillus: {
......@@ -552,19 +552,19 @@ export const sampleData: RawSpeciesStats = {
coding_genes: 2012,
average_genomic_span: 976.42,
average_sequence_length: 976.42,
average_CDS_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,
coding_transcripts_per_gene: 1,
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,
average_coding_exons_per_coding_transcript: 1,
average_exons_per_transcript: 1.0,
average_coding_exons_per_coding_transcript: 1.0,
total_introns: 0,
average_intron_length: null
},
......@@ -578,10 +578,10 @@ export const sampleData: RawSpeciesStats = {
shortest_gene_length: 74,
longest_gene_length: 2896,
total_transcripts: 80,
transcripts_per_gene: 1,
transcripts_per_gene: 1.0,
total_exons: 80,
average_exon_length: 412.6,
average_exons_per_transcript: 1,
average_exons_per_transcript: 1.0,
total_introns: 0,
average_intron_length: null
},
......@@ -630,8 +630,7 @@ export const sidebarData: SpeciesSidebarData = {
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'
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'
}
]
},
......
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