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 = { ...@@ -31,7 +31,7 @@ export const sampleData: RawSpeciesStats = {
assembly_stats: { assembly_stats: {
contig_n50: 56413054, contig_n50: 56413054,
total_genome_length: 3272116950, total_genome_length: 3272116950,
total_coding_sequence_length: 34317174, total_coding_sequence_length: 34378305,
total_gap_length: 161368351, total_gap_length: 161368351,
spanned_gaps: 661, spanned_gaps: 661,
chromosomes: 25, chromosomes: 25,
...@@ -40,66 +40,66 @@ export const sampleData: RawSpeciesStats = { ...@@ -40,66 +40,66 @@ export const sampleData: RawSpeciesStats = {
gc_percentage: 38.87 gc_percentage: 38.87
}, },
coding_stats: { coding_stats: {
coding_genes: 20420, coding_genes: 20424,
average_genomic_span: 66885.16, average_genomic_span: 67123.2,
average_sequence_length: 3443.15, average_sequence_length: 3538.93,
average_cds_length: 1139.02, average_cds_length: 1160.33,
shortest_gene_length: 8, shortest_gene_length: 8,
longest_gene_length: 2473539, longest_gene_length: 2473539,
total_transcripts: 153909, total_transcripts: 162478,
coding_transcripts: 100607, coding_transcripts: 106190,
transcripts_per_gene: 7.54, transcripts_per_gene: 7.96,
coding_transcripts_per_gene: 4.93, coding_transcripts_per_gene: 5.2,
total_exons: 1150521, total_exons: 1268315,
total_coding_exons: 764520, total_coding_exons: 825666,
average_exon_length: 243.09, average_exon_length: 246.94,
average_coding_exon_length: 149.87, average_coding_exon_length: 149.22,
average_exons_per_transcript: 7.48, average_exons_per_transcript: 7.81,
average_coding_exons_per_coding_transcript: 7.6, average_coding_exons_per_coding_transcript: 7.78,
total_introns: 996612, total_introns: 1105837,
average_intron_length: 6367.19 average_intron_length: 6237.5
}, },
non_coding_stats: { non_coding_stats: {
non_coding_genes: 23985, non_coding_genes: 23967,
small_non_coding_genes: 4870, small_non_coding_genes: 4863,
long_non_coding_genes: 16895, long_non_coding_genes: 16884,
misc_non_coding_genes: 2220, misc_non_coding_genes: 2220,
average_genomic_span: 22904.09, average_genomic_span: 23077.19,
average_sequence_length: 1084.17, average_sequence_length: 940.34,
shortest_gene_length: 41, shortest_gene_length: 41,
longest_gene_length: 1375317, longest_gene_length: 1375317,
total_transcripts: 54482, total_transcripts: 54748,
transcripts_per_gene: 2.27, transcripts_per_gene: 2.28,
total_exons: 183012, total_exons: 184477,
average_exon_length: 347.07, average_exon_length: 347.04,
average_exons_per_transcript: 3.36, average_exons_per_transcript: 3.37,
total_introns: 128530, total_introns: 129729,
average_intron_length: 15929.64 average_intron_length: 15993.77
}, },
pseudogene_stats: { pseudogene_stats: {
pseudogenes: 15217, pseudogenes: 15217,
average_genomic_span: 4124.33, average_genomic_span: 4218.48,
average_sequence_length: 802.62, average_sequence_length: 726.42,
shortest_gene_length: 23, shortest_gene_length: 23,
longest_gene_length: 909387, longest_gene_length: 909387,
total_transcripts: 18474, total_transcripts: 18617,
transcripts_per_gene: 1.21, transcripts_per_gene: 1.22,
total_exons: 43639, total_exons: 44532,
average_exon_length: 356.59, average_exon_length: 353.34,
average_exons_per_transcript: 2.36, average_exons_per_transcript: 2.39,
total_introns: 25165, total_introns: 25915,
average_intron_length: 4336.85 average_intron_length: 4372.89
}, },
homology_stats: { homology_stats: {
coverage: 98.8 coverage: 86
}, },
variation_stats: { variation_stats: {
short_variants: 713730678, short_variants: 713749788,
structural_variants: 32132047, structural_variants: 32170052,
short_variants_with_phenotype_assertions: 13336864, short_variants_with_phenotype_assertions: 13365325,
short_variants_with_publications: 303288, short_variants_with_publications: 429376,
short_variants_frequency_studies: 8, short_variants_frequency_studies: 8,
structural_variants_with_phenotype_assertions: 1921150 structural_variants_with_phenotype_assertions: 320417
}, },
regulation_stats: { regulation_stats: {
enhancers: 132592, enhancers: 132592,
...@@ -122,7 +122,7 @@ export const sampleData: RawSpeciesStats = { ...@@ -122,7 +122,7 @@ export const sampleData: RawSpeciesStats = {
coding_genes: 20787, coding_genes: 20787,
average_genomic_span: 63989.1, average_genomic_span: 63989.1,
average_sequence_length: 3136.38, average_sequence_length: 3136.38,
average_CDS_length: 1141.09, average_cds_length: 1141.09,
shortest_gene_length: 8, shortest_gene_length: 8,
longest_gene_length: 2304638, longest_gene_length: 2304638,
total_transcripts: 146152, total_transcripts: 146152,
...@@ -157,7 +157,7 @@ export const sampleData: RawSpeciesStats = { ...@@ -157,7 +157,7 @@ export const sampleData: RawSpeciesStats = {
}, },
pseudogene_stats: { pseudogene_stats: {
pseudogenes: 14170, pseudogenes: 14170,
average_genomic_span: 3525.3, average_genomic_span: 3525.6,
average_sequence_length: 809.46, average_sequence_length: 809.46,
shortest_gene_length: 23, shortest_gene_length: 23,
longest_gene_length: 586570, longest_gene_length: 586570,
...@@ -169,11 +169,11 @@ export const sampleData: RawSpeciesStats = { ...@@ -169,11 +169,11 @@ export const sampleData: RawSpeciesStats = {
total_introns: 22805, total_introns: 22805,
average_intron_length: 3049.46 average_intron_length: 3049.46
}, },
homology_stats: { homology_stats: {
coverage: 0 coverage: 0
}, },
variation_stats: { variation_stats: {
short_variants: 677181182,
structural_variants: 36348512, structural_variants: 36348512,
short_variants_with_phenotype_assertions: 10233814, short_variants_with_phenotype_assertions: 10233814,
short_variants_with_publications: 328161, short_variants_with_publications: 328161,
...@@ -201,19 +201,19 @@ export const sampleData: RawSpeciesStats = { ...@@ -201,19 +201,19 @@ export const sampleData: RawSpeciesStats = {
coding_genes: 4240, coding_genes: 4240,
average_genomic_span: 939.92, average_genomic_span: 939.92,
average_sequence_length: 939.92, average_sequence_length: 939.92,
average_CDS_length: 938.55, average_cds_length: 938.55,
shortest_gene_length: 42, shortest_gene_length: 42,
longest_gene_length: 7077, longest_gene_length: 7077,
total_transcripts: 4242, total_transcripts: 4242,
coding_transcripts: 4239, coding_transcripts: 4239,
transcripts_per_gene: 1, transcripts_per_gene: 1.0,
coding_transcripts_per_gene: 1, coding_transcripts_per_gene: 1.0,
total_exons: 4245, total_exons: 4245,
total_coding_exons: 4242, total_coding_exons: 4242,
average_exon_length: 939.17, average_exon_length: 939.17,
average_coding_exon_length: 937.89, average_coding_exon_length: 937.89,
average_exons_per_transcript: 1, average_exons_per_transcript: 1.0,
average_coding_exons_per_coding_transcript: 1, average_coding_exons_per_coding_transcript: 1.0,
total_introns: 3, total_introns: 3,
average_intron_length: 1.67 average_intron_length: 1.67
}, },
...@@ -227,10 +227,10 @@ export const sampleData: RawSpeciesStats = { ...@@ -227,10 +227,10 @@ export const sampleData: RawSpeciesStats = {
shortest_gene_length: 53, shortest_gene_length: 53,
longest_gene_length: 2905, longest_gene_length: 2905,
total_transcripts: 179, total_transcripts: 179,
transcripts_per_gene: 1, transcripts_per_gene: 1.0,
total_exons: 179, total_exons: 179,
average_exon_length: 269.83, average_exon_length: 269.83,
average_exons_per_transcript: 1, average_exons_per_transcript: 1.0,
total_introns: 0, total_introns: 0,
average_intron_length: null average_intron_length: null
}, },
...@@ -241,7 +241,7 @@ export const sampleData: RawSpeciesStats = { ...@@ -241,7 +241,7 @@ export const sampleData: RawSpeciesStats = {
shortest_gene_length: 51, shortest_gene_length: 51,
longest_gene_length: 8622, longest_gene_length: 8622,
total_transcripts: 115, total_transcripts: 115,
transcripts_per_gene: 1, transcripts_per_gene: 1.0,
total_exons: 134, total_exons: 134,
average_exon_length: 783.57, average_exon_length: 783.57,
average_exons_per_transcript: 1.17, average_exons_per_transcript: 1.17,
...@@ -268,14 +268,14 @@ export const sampleData: RawSpeciesStats = { ...@@ -268,14 +268,14 @@ export const sampleData: RawSpeciesStats = {
coding_genes: 20191, coding_genes: 20191,
average_genomic_span: 3149.75, average_genomic_span: 3149.75,
average_sequence_length: 1402.22, average_sequence_length: 1402.22,
average_CDS_length: 1425.34, average_cds_length: 1425.34,
shortest_gene_length: 30, shortest_gene_length: 30,
longest_gene_length: 102626, longest_gene_length: 102626,
total_transcripts: 34214, total_transcripts: 34214,
coding_transcripts: 33552, coding_transcripts: 33552,
transcripts_per_gene: 1.69, transcripts_per_gene: 1.69,
coding_transcripts_per_gene: 1.66, coding_transcripts_per_gene: 1.66,
total_exons: 240183, total_exons: 240193,
total_coding_exons: 225661, total_coding_exons: 225661,
average_exon_length: 236.95, average_exon_length: 236.95,
average_coding_exon_length: 211.92, average_coding_exon_length: 211.92,
...@@ -316,7 +316,7 @@ export const sampleData: RawSpeciesStats = { ...@@ -316,7 +316,7 @@ export const sampleData: RawSpeciesStats = {
average_intron_length: 203.57 average_intron_length: 203.57
}, },
homology_stats: { homology_stats: {
coverage: 51.8 coverage: 87.3
} }
}, },
plasmodium_falciparum_GCA_000002765_2: { plasmodium_falciparum_GCA_000002765_2: {
...@@ -327,7 +327,7 @@ export const sampleData: RawSpeciesStats = { ...@@ -327,7 +327,7 @@ export const sampleData: RawSpeciesStats = {
total_gap_length: 0, total_gap_length: 0,
spanned_gaps: 0, spanned_gaps: 0,
chromosomes: 14, chromosomes: 14,
toplevel_sequences: 14, toplevel_sequences: 0,
component_sequences: 14, component_sequences: 14,
gc_percentage: 19.34 gc_percentage: 19.34
}, },
...@@ -335,13 +335,13 @@ export const sampleData: RawSpeciesStats = { ...@@ -335,13 +335,13 @@ export const sampleData: RawSpeciesStats = {
coding_genes: 5362, coding_genes: 5362,
average_genomic_span: 2569.88, average_genomic_span: 2569.88,
average_sequence_length: 2296.23, average_sequence_length: 2296.23,
average_CDS_length: 2297.48, average_cds_length: 2297.48,
shortest_gene_length: 90, shortest_gene_length: 90,
longest_gene_length: 30864, longest_gene_length: 30864,
total_transcripts: 5362, total_transcripts: 5362,
coding_transcripts: 5358, coding_transcripts: 5358,
transcripts_per_gene: 1, transcripts_per_gene: 1.0,
coding_transcripts_per_gene: 1, coding_transcripts_per_gene: 1.0,
total_exons: 14146, total_exons: 14146,
total_coding_exons: 14139, total_coding_exons: 14139,
average_exon_length: 870.38, average_exon_length: 870.38,
...@@ -361,10 +361,10 @@ export const sampleData: RawSpeciesStats = { ...@@ -361,10 +361,10 @@ export const sampleData: RawSpeciesStats = {
shortest_gene_length: 68, shortest_gene_length: 68,
longest_gene_length: 6175, longest_gene_length: 6175,
total_transcripts: 252, total_transcripts: 252,
transcripts_per_gene: 1, transcripts_per_gene: 1.0,
total_exons: 252, total_exons: 252,
average_exon_length: 553.68, average_exon_length: 553.68,
average_exons_per_transcript: 1, average_exons_per_transcript: 1.0,
total_introns: 0, total_introns: 0,
average_intron_length: null average_intron_length: null
}, },
...@@ -375,7 +375,7 @@ export const sampleData: RawSpeciesStats = { ...@@ -375,7 +375,7 @@ export const sampleData: RawSpeciesStats = {
shortest_gene_length: 72, shortest_gene_length: 72,
longest_gene_length: 11291, longest_gene_length: 11291,
total_transcripts: 153, total_transcripts: 153,
transcripts_per_gene: 1, transcripts_per_gene: 1.0,
total_exons: 461, total_exons: 461,
average_exon_length: 520.4, average_exon_length: 520.4,
average_exons_per_transcript: 3.01, average_exons_per_transcript: 3.01,
...@@ -402,13 +402,13 @@ export const sampleData: RawSpeciesStats = { ...@@ -402,13 +402,13 @@ export const sampleData: RawSpeciesStats = {
coding_genes: 6600, coding_genes: 6600,
average_genomic_span: 1344.37, average_genomic_span: 1344.37,
average_sequence_length: 1327.58, average_sequence_length: 1327.58,
average_CDS_length: 1327.58, average_cds_length: 1327.58,
shortest_gene_length: 51, shortest_gene_length: 51,
longest_gene_length: 14733, longest_gene_length: 14733,
total_transcripts: 6600, total_transcripts: 6600,
coding_transcripts: 6600, coding_transcripts: 6600,
transcripts_per_gene: 1, transcripts_per_gene: 1.0,
coding_transcripts_per_gene: 1, coding_transcripts_per_gene: 1.0,
total_exons: 6913, total_exons: 6913,
total_coding_exons: 6913, total_coding_exons: 6913,
average_exon_length: 1267.47, average_exon_length: 1267.47,
...@@ -416,7 +416,7 @@ export const sampleData: RawSpeciesStats = { ...@@ -416,7 +416,7 @@ export const sampleData: RawSpeciesStats = {
average_exons_per_transcript: 1.05, average_exons_per_transcript: 1.05,
average_coding_exons_per_coding_transcript: 1.05, average_coding_exons_per_coding_transcript: 1.05,
total_introns: 313, total_introns: 313,
average_intron_length: 354.08 average_intron_length: 348.08
}, },
non_coding_stats: { non_coding_stats: {
non_coding_genes: 424, non_coding_genes: 424,
...@@ -428,7 +428,7 @@ export const sampleData: RawSpeciesStats = { ...@@ -428,7 +428,7 @@ export const sampleData: RawSpeciesStats = {
shortest_gene_length: 58, shortest_gene_length: 58,
longest_gene_length: 5947, longest_gene_length: 5947,
total_transcripts: 424, total_transcripts: 424,
transcripts_per_gene: 1, transcripts_per_gene: 1.0,
total_exons: 491, total_exons: 491,
average_exon_length: 171.64, average_exon_length: 171.64,
average_exons_per_transcript: 1.16, average_exons_per_transcript: 1.16,
...@@ -442,20 +442,20 @@ export const sampleData: RawSpeciesStats = { ...@@ -442,20 +442,20 @@ export const sampleData: RawSpeciesStats = {
shortest_gene_length: 228, shortest_gene_length: 228,
longest_gene_length: 3147, longest_gene_length: 3147,
total_transcripts: 12, total_transcripts: 12,
transcripts_per_gene: 1, transcripts_per_gene: 1.0,
total_exons: 12, total_exons: 12,
average_exon_length: 863.25, average_exon_length: 863.25,
average_exons_per_transcript: 1, average_exons_per_transcript: 1.0,
total_introns: 0, total_introns: 0,
average_intron_length: null average_intron_length: null
}, },
variation_stats: { variation_stats: {
short_variants: 263537, short_variants: 263537,
structural_variants: null, structural_variants: 0,
short_variants_with_phenotype_assertions: null, short_variants_with_phenotype_assertions: 0,
short_variants_with_publications: null, short_variants_with_publications: 0,
short_variants_frequency_studies: null, short_variants_frequency_studies: 0,
structural_variants_with_phenotype_assertions: null structural_variants_with_phenotype_assertions: 0
}, },
homology_stats: { homology_stats: {
coverage: 57.7 coverage: 57.7
...@@ -477,7 +477,7 @@ export const sampleData: RawSpeciesStats = { ...@@ -477,7 +477,7 @@ export const sampleData: RawSpeciesStats = {
coding_genes: 107891, coding_genes: 107891,
average_genomic_span: 3488.91, average_genomic_span: 3488.91,
average_sequence_length: 1570.98, average_sequence_length: 1570.98,
average_CDS_length: 1332.42, average_cds_length: 1332.42,
shortest_gene_length: 54, shortest_gene_length: 54,
longest_gene_length: 124945, longest_gene_length: 124945,
total_transcripts: 133744, total_transcripts: 133744,
...@@ -503,10 +503,10 @@ export const sampleData: RawSpeciesStats = { ...@@ -503,10 +503,10 @@ export const sampleData: RawSpeciesStats = {
shortest_gene_length: 42, shortest_gene_length: 42,
longest_gene_length: 5792, longest_gene_length: 5792,
total_transcripts: 12853, total_transcripts: 12853,
transcripts_per_gene: 1, transcripts_per_gene: 1.0,
total_exons: 12853, total_exons: 12853,
average_exon_length: 149.42, average_exon_length: 149.42,
average_exons_per_transcript: 1, average_exons_per_transcript: 1.0,
total_introns: 0, total_introns: 0,
average_intron_length: null average_intron_length: null
}, },
...@@ -526,14 +526,14 @@ export const sampleData: RawSpeciesStats = { ...@@ -526,14 +526,14 @@ export const sampleData: RawSpeciesStats = {
}, },
variation_stats: { variation_stats: {
short_variants: 18093911, short_variants: 18093911,
structural_variants: null, structural_variants: 0,
short_variants_with_phenotype_assertions: null,
short_variants_with_publications: null,
short_variants_frequency_studies: 1, 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: { homology_stats: {
coverage: 98.7 coverage: 98.8
} }
}, },
actinobacillus: { actinobacillus: {
...@@ -552,19 +552,19 @@ export const sampleData: RawSpeciesStats = { ...@@ -552,19 +552,19 @@ export const sampleData: RawSpeciesStats = {
coding_genes: 2012, coding_genes: 2012,
average_genomic_span: 976.42, average_genomic_span: 976.42,
average_sequence_length: 976.42, average_sequence_length: 976.42,
average_CDS_length: 976.42, average_cds_length: 976.42,
shortest_gene_length: 114, shortest_gene_length: 114,
longest_gene_length: 10044, longest_gene_length: 10044,
total_transcripts: 2012, total_transcripts: 2012,
coding_transcripts: 2012, coding_transcripts: 2012,
transcripts_per_gene: 1, transcripts_per_gene: 1.0,
coding_transcripts_per_gene: 1, coding_transcripts_per_gene: 1.0,
total_exons: 2012, total_exons: 2012,
total_coding_exons: 2012, total_coding_exons: 2012,
average_exon_length: 976.42, average_exon_length: 976.42,
average_coding_exon_length: 976.42, average_coding_exon_length: 976.42,
average_exons_per_transcript: 1, average_exons_per_transcript: 1.0,
average_coding_exons_per_coding_transcript: 1, average_coding_exons_per_coding_transcript: 1.0,
total_introns: 0, total_introns: 0,
average_intron_length: null average_intron_length: null
}, },
...@@ -578,10 +578,10 @@ export const sampleData: RawSpeciesStats = { ...@@ -578,10 +578,10 @@ export const sampleData: RawSpeciesStats = {
shortest_gene_length: 74, shortest_gene_length: 74,
longest_gene_length: 2896, longest_gene_length: 2896,
total_transcripts: 80, total_transcripts: 80,
transcripts_per_gene: 1, transcripts_per_gene: 1.0,
total_exons: 80, total_exons: 80,
average_exon_length: 412.6, average_exon_length: 412.6,
average_exons_per_transcript: 1, average_exons_per_transcript: 1.0,
total_introns: 0, total_introns: 0,
average_intron_length: null average_intron_length: null
}, },
...@@ -630,8 +630,7 @@ export const sidebarData: SpeciesSidebarData = { ...@@ -630,8 +630,7 @@ export const sidebarData: SpeciesSidebarData = {
notes: [ notes: [
{ {
heading: 'Pseudoautosomal regions', heading: 'Pseudoautosomal regions',
body: 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'
'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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