GENEALOGY-DNA-L Archives

Archiver > GENEALOGY-DNA > 2012-08 > 1345318929


From: "G. Magoon" <>
Subject: Re: [DNA] mtDNA from 1000 Genomes Project
Date: Sat, 18 Aug 2012 15:42:09 -0400
References: <CADz9sbpDYGm2Ud3DxmV3G0=_n-Nw4SM5zd4tZR-XE_7bN9=SQQ@mail.gmail.com><BAY160-W2011E77599549E4A2362F1F1BB0@phx.gbl>
In-Reply-To: <BAY160-W2011E77599549E4A2362F1F1BB0@phx.gbl>


Thanks William,
I've posted an unzipped (6 MB) version of their mtDNA file at
https://www.box.com/s/90bc49c49833a93a2fd4 for those who might have issues
with the decompression.

I'm a little skeptical of the way they are reporting the calls; as I think
Bonnie mentioned in the other thread, they seem to be only posting the
results as 1 or 0, which is OK if there is full coverage of all the sites
and no ambiguous results, but typically there are some sites that just
don't have any mapped reads and it is essentially a no-call...presumably
these would be reported as 0; I don't know how they would report
heteroplasmies. In principle I could look at the actual mapped data or run
my own variant call runs (as I've been doing with chrY), but that is deeper
than I want to delve into this at present.

I took a quick look at my maternal haplogroup, H3. For what it's worth, I
found 17 samples with the defining T6776C mutation (8 British samples (~8%
of all the GBR samples), 2 Finish, 1 Spanish, 4 Utah, and 2 Tuscan)

Greg

On Sat, Aug 18, 2012 at 3:08 PM, William Hurst <> wrote:

>
>
> Hi Greg and all,
>
> This came up last year when a Chinese group successfully obtained mtDNA
> sequences from Chinese and Japanese 1KGP files. See
> http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0025835 One sequence, NA18539, is now a reference sequence for the new K3
> subclade. I would certainly like to see sequences from populations a little
> more likely to have K and U8 examples. If you can squeeze out some of those
> from the files, I would be happy to look at them to see if they are usable.
>
> Yes, the rCRS is still the reference sequence we use.
>
> I tried to open one of the files below using Winzip and got error messages.
>
> Bill Hurst
>
> > Has anyone looked at the newest mtDNA variant calls in the Phase 1 folder
> > below? I seem to recall someone (maybe Ann?) had looked at the 1000
> Genomes
> > Project mitochondrial data about a year ago and mentioned something to
> the
> > effect that the data weren't particularly clean. Though maybe they have
> > they improved their mapping/variant calling since that time...
> >
> > I may take a quick look if no-one else has. Is the revised Cambridge
> > Reference sequence still the sequence used by the reference human genome?
> >
> > Greg
> >
> > On Sat, Aug 18, 2012 at 1:43 PM, Dienekes Pontikos <
> > > wrote:
> >
> > > working:
> > >
> http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20111123_chrY_snps/
> > > phase1<
> http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20111123_chrY_snps/phase1
> >:
> > >
> > >
> http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/integrated_call_sets/
>
>
>
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