------ Summary for ./data/seq/HsaN ------
Log file to ./data/seq/HsaN/xSummary.log
Verbose output
Sequence directory: ./data/seq/HsaN/ncbi_dataset/data/GCF_000001405.40 02-Aug-2024 12:22
GCF_000001405.40_GRCh38.p14_genomic.fna
Annotation directory: ./data/seq/HsaN/ncbi_dataset/data/GCF_000001405.40
genomic.gff
FASTA sequence file(s)
Chr: >NC_000001.11 Homo sapiens chromosome 1, GRCh38.p14 Primary Assembly
Scaf: >NT_187361.1 Homo sapiens chromosome 1 unlocalized genomic scaffold, GRCh38.p14 Primary Assembly HSCHR1_CTG1_UNLOCALIZED
Scaf: >NW_012132914.1 Homo sapiens chromosome 1 genomic patch of type FIX, GRCh38.p14 PATCHES HG1342_HG2282_PATCH
Mt: >NC_012920.1 Homo sapiens mitochondrion, complete genome
Count Totals:
24 Chromosomes
680 Scaffolds
1 Mt/Pt
705 Total sequences
Count Prefixes:
355 NT_
325 NW_
25 NC_
Counts of Length Ranges:
91<10k 96<100k 461<1M 33<10M 1<50M 7<100M 14<200M 2>=200M
3,298,430,636 Total length
Lengths of first 5 sequences:
NC_000001.11 248,956,422
NT_187361.1 175,055
NT_187362.1 32,032
NT_187363.1 127,682
NT_187364.1 66,860
Base counts:
A 558,619,211 a 364,497,992
T 559,373,567 t 366,543,471
C 413,530,454 c 229,022,463
G 413,917,617 g 231,314,379
N 161,611,379 n 0
B 2 K 8 M 8 R 29 S 5 W 15 Y 36
GFF Annotation file(s)
Example lines:
NC_000001.11 BestRefSeq gene 65419 71585 . + . ID=gene-OR4F5;Dbxref=GeneID:79501,HGNC:HGNC:14825;Name=OR4F5;description=olfactory receptor family 4 subfamily F member 5;gbkey=Gene;gene=OR4F5;gene_biotype=protein_coding
NC_000001.11 BestRefSeq mRNA 65419 71585 . + . ID=rna-NM_001005484.2;Parent=gene-OR4F5;Dbxref=Ensembl:ENST00000641515.2,GeneID:79501,GenBank:NM_001005484.2,HGNC:HGNC:14825;Name=NM_001005484.2;gbkey=mRNA;gene=OR4F5;product=olfactory...
NC_000001.11 BestRefSeq exon 65419 65433 . + . ID=exon-NM_001005484.2-1;Parent=rna-NM_001005484.2;Dbxref=Ensembl:ENST00000641515.2,GeneID:79501,GenBank:NM_001005484.2,HGNC:HGNC:14825;gbkey=mRNA;gene=OR4F5;product=olfactory receptor...
Summary:
23,314 Genes from 48,104 (use protein_coding only)
23,314 mRNAs from 144,481 (23,312 has protein_id)
233,893 Exons from 2,307,779
Types: 73
6 CAAT_signal 96 CAGE_cluster 1,838,180 CDS
44 C_gene_segment 177 DNaseI_hypersensitive_site 61 D_gene_segment
15 GC_rich_promoter_region 128 J_gene_segment 2 RNase_P_RNA
30 TATA_box 664 V_gene_segment 4 Y_RNA
39 antisense_RNA 137,091 biological_region 26,404 cDNA_match
24 centromere 14 chromosome_breakpoint 138 conserved_region
20 direct_repeat 5 dispersed_repeat 115,163 enhancer
59 enhancer_blocking_element 12 epigenetically_modified_region 2,307,779 exon
48,104 gene 2 imprinting_control_region 12 insulator
32,844 lnc_RNA 14 locus_control_region 144,481 mRNA
161,162 match 18 matrix_attachment_site 368 meiotic_recombination_region
3,218 miRNA 5 microsatellite 13 minisatellite
54 mitotic_recombination_region 204 mobile_genetic_element 54 ncRNA
514 non_allelic_homologous_recombination_region 4 nucleotide_cleavage_site 623 nucleotide_motif
87 origin_of_replication 2,139 primary_transcript 438 promoter
1,418 protein_binding_site 19,252 pseudogene 80 rRNA
632 recombination_feature 709 region 2 regulatory_region
62 repeat_instability_region 10 repeat_region 11 replication_regulatory_region
3 replication_start_site 20 response_element 4 scRNA
30 sequence_alteration 10 sequence_alteration_artifact 2 sequence_comparison
1,964 sequence_feature 14 sequence_secondary_structure 35,932 silencer
172 snRNA 1,300 snoRNA 691 tRNA
64 tandem_repeat 14,974 transcript 2,259 transcriptional_cis_regulatory_region
4 vault_RNA
Gene Attributes biotype: 21
33 C_region 61 D_segment 117 J_segment
2 RNase_P_RNA 365 V_segment 4 Y_RNA
20 antisense_RNA 19,645 lncRNA 2,139 miRNA
68 misc_RNA 54 ncRNA 29 other
23,314 protein_coding 80 rRNA 4 scRNA
172 snRNA 1,300 snoRNA 691 tRNA
4 vault_RNA
Gene Attribute: 12
23,314 Dbxref 23,314 ID
23,314 Name 23,301 description
195 end_range 18 exception
23,314 gbkey 23,314 gene
23,314 gene_biotype 19,894 gene_synonym
335 partial 141 start_range
mRNA Attribute:
23,301 product
Input type: NCBI chr NC_ prefix; NCBI GFF header
NCBI 'gene_biotype' keyword; NCBI mRNA 'product' keyword; gene 'description' keyword
------ Finish summary for ./data/seq/HsaN/ ------