------ Summary for ./data/seq/HsaE ------
Log file to ./data/seq/HsaE/xSummary.log
Verbose output
Sequence directory: ./data/seq/HsaE 24-Aug-2024 05:42
Homo_sapiens.GRCh38.dna_sm.toplevel.fa.gz
Annotation directory: ./data/seq/HsaE
Homo_sapiens.GRCh38.112.gff3
FASTA sequence file(s)
Example header lines:
Chr: >1 dna_sm:chromosome chromosome:GRCh38:1:1:248956422:1 REF
Mt: >MT dna_sm:chromosome chromosome:GRCh38:MT:1:16569:1 REF
Scaf: >HG76_PATCH dna_sm:scaffold scaffold:GRCh38:HG76_PATCH:1:6367528:1
Scaf: >HSCHR15_4_CTG8 dna_sm:scaffold scaffold:GRCh38:HSCHR15_4_CTG8:1:5161414:1
Scaf: >HSCHRX_1_CTG14 dna_sm:scaffold scaffold:GRCh38:HSCHRX_1_CTG14:1:619716:1
Scaf: >KI270728.1 dna_sm:scaffold scaffold:GRCh38:KI270728.1:1:1872759:1 REF
Scaf: >GL000225.1 dna_sm:scaffold scaffold:GRCh38:GL000225.1:1:211173:1 REF
Count Totals:
24 Chromosomes
681 Scaffolds
1 Mt/Pt
706 Total sequences
Count Prefixes:
342 HSCHR
163 HG
153 KI
24 Number, X, Y, Roman
16 GL
7 HSCHRX
1 MT
Counts of Length Ranges:
91<10k 97<100k 463<1M 31<10M 1<50M 7<100M 14<200M 2>=200M
3,291,585,349 Total length
Lengths of first 5 sequences:
1 248,956,422
2 242,193,529
3 198,295,559
4 190,214,555
5 181,538,259
Base counts:
A 427,892,127 a 493,309,384
T 428,411,414 t 495,585,932
C 295,725,867 c 345,462,265
G 296,048,044 g 347,815,722
N 150,910,698 n 10,423,896
GFF Annotation file(s)
Example lines:
1 ensembl_havana gene 65419 71585 . + . ID=gene:ENSG00000186092;Name=OR4F5;biotype=protein_coding;description=olfactory receptor family...
1 havana mRNA 65419 71585 . + . ID=transcript:ENST00000641515;Parent=gene:ENSG00000186092;Name=OR4F5-201;biotype=protein_coding;ccdsid=...
1 havana exon 65419 65433 . + . Parent=transcript:ENST00000641515;Name=ENSE00003812156;constitutive=1;ensembl_end_phase=-1;ensembl_phas...
Summary:
20,089 Genes from 21,571 (use protein_coding only)
20,089 mRNAs from 111,563 (20,089 has protein_id)
189,587 Exons from 1,668,828
Types: 26
900,301 CDS 29 C_gene_segment 42 D_gene_segment
97 J_gene_segment 252 V_gene_segment 182,818 biological_region
25 chromosome 1,668,828 exon 175,449 five_prime_UTR
21,571 gene 92,171 lnc_RNA 111,563 mRNA
1,879 miRNA 26,350 ncRNA_gene 10 processed_transcript
15,219 pseudogene 15,222 pseudogenic_transcript 55 rRNA
50 scRNA 169 scaffold 1,915 snRNA
942 snoRNA 22 tRNA 211,674 three_prime_UTR
28,741 transcript 1,139 unconfirmed_transcript
Gene Attributes biotype: 11
14 IG_C_gene 37 IG_D_gene 18 IG_J_gene
145 IG_V_gene 1,052 TEC 6 TR_C_gene
5 TR_D_gene 79 TR_J_gene 107 TR_V_gene
19 artifact 20,089 protein_coding
Gene Attribute: 7
20,089 ID 19,463 Name
20,089 biotype 20,067 description
20,089 gene_id 20,089 logic_name
20,089 version
Input type: Ensembl chr 'Number, X, Y, Roman'
Ensembl 'biotype' keyword; gene 'description' keyword
------ Finish summary for ./data/seq/HsaE/ ------