Good catch, Iain. You are correct, the .bam files must be reviewed for verification. In this case I think the odds are very high that there is an A223* for Milligan, while there is still the subclade for A224, A225 to go with parent A223. The reason I speculate on this is what you can see in Milligan's .bed regions file. A225 is 19305653G>A There is no "rejected" or low Quality call for A225+ in Milligan's .vcf file but the following is listed as a gold region in his .bed file. It looks like Big Y read this region and A225 is safely in the middle of it. The implication is A225 is negative/ancestral. chrY 19305555 19308322 The same goes for A224. A224 is 15826998 T>C chrY 15824037 15828540 Since Thomas Krahn named A223, A224 and A225 he must think these are SNPs that are stable and can be reliably tested. Again, the .bam file needs to be checked, though. I agree. Mike On Fri, Jun 27, 2014 at 10:37 AM, Iain Kennedy <ikennedy_msdn2@hotmail.com> wrote: > There have been two tree updates recently > > June 25th > Brenden Davitt #251441 FGC8739 > Alan Milliken #23702 A223 > > June 27th > Jacob McKee #88883 DF97 > Daniel Herring #85553 DF97 (only just spotted so might be an old result) > > Of these, Alan's result is the most significant as it potentially changes > the tree structure by splitting A223 from A224 and A225. I haven't changed > the raw tree (the one without names on) yet but will do so when the BAM > file becomes available and we can confirm Alan is negative for the other > two. > > If anyone is working their way through the sub-branches of S660/S659 they > should now bear in mind that it may suffice to test A223 without A224 and > A225. > > http://www.kennedydna.com/M222.pdf > > Iain > > > > > > ------------------------------- > To unsubscribe from the list, please send an email to > DNA-R1B1C7-request@rootsweb.com with the word 'unsubscribe' without the > quotes in the subject and the body of the message >

Yes BED file examination is of course part of what my analysis involves. Iain > Date: Fri, 27 Jun 2014 12:03:21 -0500 > From: mwwdna@gmail.com > To: R1b-M222-Project@yahoogroups.com; dna-r1b1c7@rootsweb.com > Subject: Re: [R-M222] Tree updates you may have missed > > Good catch, Iain. > > You are correct, the .bam files must be reviewed for verification. In this > case I think the odds are very high that there is an A223* for Milligan, > while there is still the subclade for A224, A225 to go with parent A223. > > The reason I speculate on this is what you can see in Milligan's .bed > regions file. > > A225 is 19305653G>A > > There is no "rejected" or low Quality call for A225+ in Milligan's .vcf > file but the following is listed as a gold region in his .bed file. It > looks like Big Y read this region and A225 is safely in the middle of it. > The implication is A225 is negative/ancestral. > > chrY 19305555 19308322 > > The same goes for A224. > > A224 is 15826998 T>C > > chrY 15824037 15828540 > > Since Thomas Krahn named A223, A224 and A225 he must think these are SNPs > that are stable and can be reliably tested. > > Again, the .bam file needs to be checked, though. I agree. > > Mike > > > On Fri, Jun 27, 2014 at 10:37 AM, Iain Kennedy <ikennedy_msdn2@hotmail.com> > wrote: > > > There have been two tree updates recently > > > > June 25th > > Brenden Davitt #251441 FGC8739 > > Alan Milliken #23702 A223 > > > > June 27th > > Jacob McKee #88883 DF97 > > Daniel Herring #85553 DF97 (only just spotted so might be an old result) > > > > Of these, Alan's result is the most significant as it potentially changes > > the tree structure by splitting A223 from A224 and A225. I haven't changed > > the raw tree (the one without names on) yet but will do so when the BAM > > file becomes available and we can confirm Alan is negative for the other > > two. > > > > If anyone is working their way through the sub-branches of S660/S659 they > > should now bear in mind that it may suffice to test A223 without A224 and > > A225. > > > > http://www.kennedydna.com/M222.pdf > > > > Iain > > > > > > > > > > > > ------------------------------- > > To unsubscribe from the list, please send an email to > > DNA-R1B1C7-request@rootsweb.com with the word 'unsubscribe' without the > > quotes in the subject and the body of the message > > > > ------------------------------- > To unsubscribe from the list, please send an email to DNA-R1B1C7-request@rootsweb.com with the word 'unsubscribe' without the quotes in the subject and the body of the message