1000G high coverage depth of sequencing?

A number of 1000G samples were sequenced to high coverage:

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20140502_sample_summary_info/20140502.high_coverage_pcr_bams

What is the sequencing depth of these samples?

sequencing 1000g coverage depth

• 4,469 views • link

updated 3.6 years ago by Ram

• written 11.2 years ago by Tommy Carstensen

1 answer

They're at least 30X, but can average a bit higher. See the link below (which can be quite slow) for an example.

http://bam.iobio.io/?bam=http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00096/high_coverage_alignment/HG00096.wgs.ILLUMINA.bwa.GBR.high_cov_pcr_free.20140203.bam&region=1

• 0 views • link

updated 3.6 years ago by Ram

• written 11.2 years ago by Adam

Very neat website that sub samples the reads instead of checking them all. It's a lot faster than running samtools flagstat across the entire bam file. Thanks.

• 0 views • link

updated 3.6 years ago by Ram

• written 11.2 years ago by Tommy Carstensen

Wow! nice website.

• 0 views • link

written 11.2 years ago by poisonAlien

More posts like this

hg38 vs GRCh38 chr prefix
written 1.0 years ago by DBScan •

Is there an official documentation about the differences between hg38 and GRCh38? To my understanding, there is no differences between them. However, in gnomAD, which …
1000 Genome Project Structural Variants for Illumina
written 5.9 years ago by Yasin Uzun •

I am trying to access 1000 Genome Project structural variants (SV). I specifically need the variants called on Illumina sequenced samples. In the read me …
1000 Human Genomes Project Population Alignment Data
written 6.9 years ago by AXR •

I found raw variant calls for individuals in high coverage data (30X) which I found right here: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20190425_NYGC_GATK/raw_calls/ Where could I find either the BAM/CRAM …
Where can I find the reference files for the 1000 Genome project VCF data?
written 7.6 years ago by caggtaagtat

Hello, I just started working with VCF files and would like to use the data of the 1000 Genome project. I found that the most …
News: 1000 Genomes data on GRCh38
written 10.8 years ago by fairley •

The low coverage 1000 Genomes sequence data has been realigned to GRCh38. Reads were aligned to the full assembly, including the GRC maintained alternate loci …
Does build 37 of the human reference genome contain 2.85Gbp?
written 11.5 years ago by Tommy Carstensen

When converting from base count to coverage in [this document][1] they divide by 2.85 billion nucleotides: ``` POP BASE COUNT COVERAGE ACB 3182037349066 1116.50433300561 ``` …
Looking For 1000 Genomes Samples With Sequence And Chips Data
written 13.2 years ago by carmayna •

Hi, we are defining new pipelines for processing our data. We are testing the pipelines using 1000 Genomes data. We are looking for samples with …
Iupac Bases In The Hg19 1000G Reference ?
written 13.5 years ago by Gabriel R.

If you download the reference from 1000g : <a href="ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz">ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz</a> Why is there a double "RR" in chr 3 ? <pre><code>zcat human_g1k_v37.fasta.gz.1 | grep -n …
Problems Accessing 1000G Data
written 14.5 years ago by Ahdf-Lell-Kocks •

I am just copy+pasting from the 1000g instructions here: <a href="http://www.1000genomes.org/faq/how-do-i-get-sub-section-bam-file">http://www.1000genomes.org/faq/how-do-i-get-sub-section-bam-file</a> <pre><code>samtools view -h ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/HG00154/alignment/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam 17:7512445-7513455 </code></pre> But I can't get it to work: …
Bam Files Of Exomes From 1000 Genomes Project
written 15.2 years ago by Jorjial

Hi everybody, I'm working with some exome sequencing data. I'd like to compare my results with data from 1000 genomes project. I have not found …