GENEALOGY-DNA-L Archives

Archiver > GENEALOGY-DNA > 2010-02 > 1265289509


From: William Hurst <>
Subject: Re: [DNA] FTDNA admits to errors in many mtDNA sequences
Date: Thu, 4 Feb 2010 08:18:29 -0500


Hi Ann and Ian and all,

(Pardon me if this is a duplicate. Didn't appear to go the first time.)

When I started working with mtDNA, FTDNA was reporting most of the insertions as 524.1C, 524.2A, etc. However, some were shown as 524.1A, 524.2C, etc. At some point they standardized on the former. As Ian listed, many sequences were submitted to GenBank by Linda Jonas and then Ian, using 524.1C, etc., not from FASTA files, which most customers did not know they had, but from typed or cut-and-paste mutation lists. If this introduced an error in the sequence, the main result is that if someone downloaded the FASTA file from GenBank, ran it through a program such as Gen-Snip, the sequences were reported as, in some cases at least, 525.1A, 525.2C, etc. (Actually, they are reported as 525insA, 525insC, etc.) Ian would report them to the list as 524.C, 524.A, etc. If the same person tested with SMGF, they would probably report them as 524.1A, 524.2C, etc., which I believe is the method suggested in the Wilson, et al., FBI paper. As of last October, FTDNA now has them reported as 523.1C, 523.2A, etc.

Confused? Any mtDNA specialist would know that all these various methods of reporting these insertions mean exactly the same thing. The specialist would simply convert them to the format he or she uses and not worry about it.

I'm not discouraging anyone from taking up Ian's kind offer to assist in making the minor change to their GenBank entry. But we are not talking about some type of fatal flaw in what's there now. Insertions and deletions and heteroplasmies tend to make mtDNA sequences rather messy.

Now I'm going to have coffee, then later get in my Toyota-made car and go to the grocery store before the blizzard comes tomorrow. I don't need groceries, but there's a federal law that you have to go to the grocery store the day before a storm. Isn't there?

Bill Hurst



Ann wrote:

> The link to the FASTA file was recently removed from the customer's results
> page, so there will be no way to check unless people saved a FASTA file.
>
> I thought I understood from Eileen Krause that last fall's nomenclature
> update at FTDNA would bring it into alignment with SMGF, which in turn is based
> on recommendations from the FBI. This would be 524.1A 524.2C (adding an AC
> repeat to the right-hand end) or 523d 524d (removing the last AC repeat).
> FTDNA has reported it in different ways over the years, and apparently it
> still differs from the FBI recommendation (AFAIK, the only organization that has
> published a paper). MITOMAP has quite an ugly list of nomenclature
> variations that have been used in the literature, and Bill Hurst might have covered
> even more in his JoGG article.
>
> http://mitomap.org/bin/view/MITOMAP/PolymorphismsControl
>
> http://www.jogg.info/32/hurst.pdf
>
> As Thomas noted, the raw sequence data would be the same, regardless of how
> the mutation list was presented. However, Ian's point is that working from
> the mutation list to create a FASTA file for GenBank submissions (as he
> often/always does) may generate an error in the FASTA file there.
>
> Ann Turner
>
>
>
> In a message dated 2/4/2010 3:11:16 AM Pacific Standard Time,
> writes:
>
> > Dr. Krahn appears to be claiming that the FASTA file is actually the
> > 'master', and is correct; and that only the mutation list is nonstandard.
> > Can someone confirm this?
>
> -------------------------------
> To unsubscribe from the list, please send an email to with the word 'unsubscribe' without the quotes in the subject and the body of the message



This thread: