Well Ann, that was certainly informative information. It lead me to look up the ICW tool to review again, which led me to the article by Roberta Estes, Increasing “In Common With” (ICW) Functionality at Family Tree DNA where I learned that I have not been using this tool to it's full advantage. Thank you John and Ann for posting. CB On Sun, Oct 22, 2017 at 8:26 AM, Ann Turner <[email protected]> wrote: > I'm not sure if this fits your situation, but the ICW tool is just checking > at the person level, not the segment level. ICW simply means your cousin > (on your match list) appears on the other person's match list. It doesn't > actually look at where you match on a chromosome, nor does it examine > surnames/location. > > Ann Turner > > On Sun, Oct 22, 2017 at 4:19 AM, John Fletcher <[email protected]> > wrote: > > > Yesterday, I selected the 'in common with" tool on ftdna, and to my > > surprise it gave me a cousin already-known who is not matched by dna but > is > > matched by listed surnames/location. Is this normal? Never had it before! > > John Fletcher > > > > ------------------------------- > > To unsubscribe from the list, please send an email to > > [email protected] 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 > [email protected] with the word 'unsubscribe' without > the quotes in the subject and the body of the message >

I'm not sure if this fits your situation, but the ICW tool is just checking at the person level, not the segment level. ICW simply means your cousin (on your match list) appears on the other person's match list. It doesn't actually look at where you match on a chromosome, nor does it examine surnames/location. Ann Turner On Sun, Oct 22, 2017 at 4:19 AM, John Fletcher <[email protected]> wrote: > Yesterday, I selected the 'in common with" tool on ftdna, and to my > surprise it gave me a cousin already-known who is not matched by dna but is > matched by listed surnames/location. Is this normal? Never had it before! > John Fletcher > > ------------------------------- > To unsubscribe from the list, please send an email to > [email protected] with the word 'unsubscribe' without > the quotes in the subject and the body of the message >

Yesterday, I selected the 'in common with" tool on ftdna, and to my surprise it gave me a cousin already-known who is not matched by dna but is matched by listed surnames/location. Is this normal? Never had it before! John Fletcher

Yesterday my project got zero additional results. Today, one. At this rate I calculate it will be done in August. Doug McDonald -----Original Message----- FTDNA is revising and recalculating BigY results, a process estimated to take a week or more. If you look at the match's BigY and it says "Awaiting Results" then just hang in there. Ann Turner

I got that message. It said "We’re giving you the ability to view your SNP data from Big Y. This will allow you to personally assess all SNP call positions that are being evaluated for matching purposes. This data will be continuously updated." I don't have mine yet, but somebody sent me their bed/vcf files. Odd. I find positions that are clearly ancestral both by phylogeny and what the vcf file says, but the browser (the thing that shows reads like BAM browser) shows that ALL reads are derived. The vcf file says some reads have map quality zero, others are >10 map quality. Also there are three other positions in the reads that are phylogenetically wrong on the reads. The vcf file has some but not all of these. One has a wrong "name" listed! Yes, the bed has these positions listed. Oh yes, one more thing ... this is in the middle of the (former) 22,200,000 region, now 20,060,000 area. But if you look at only reads with map quality >10 in Build 37, its completely reliable. Also, the whole browser is sort of useless for matching as far as I can tell today, since I can't seem to get the thing to work with a matching person's read. I sure seemed to remember doing that a couple of days ago. If you could check the reads for both you and every match, at every position, and there were no gotchas (see above) then maybe the bam and maybe even the bed/vcf would be unneeded (except for things they don't list at all), so long as its a RARE need, not for admins with lots of BigYs. Why does my Outlook spell checker say bam is not a word? Did they never ask Emeril Lagasse?

We've known that my family's subgroup was I-L1275 since July 2012 when L1275 was discovered in WTY. Earlier this year FTDNA listed my cousin as A5338 (above L1275 and discovered in his Big-Y and two others); some time later, his subgroup was changed to A5339 (just below A5338). Since by this time we knew that he and one other member of the subgroup were A8177, I requested a correction which was made within a week.; however, when I checked a few minutes ago to see whether our Big-Y results had been updated, I was surprised to find that my cousin is now listed as L1275 and his closest match (the second A8177) is listed only as M253 unconfirmed. What is going on here? Lindsey

FTDNA is revising and recalculating BigY results, a process estimated to take a week or more. If you look at the match's BigY and it says "Awaiting Results" then just hang in there. Ann Turner On Wed, Oct 18, 2017 at 10:48 AM, Lindsey Britton <[email protected]> wrote: > > > We've known that my family's subgroup was I-L1275 since July 2012 when > L1275 was discovered in WTY. Earlier this year FTDNA listed my cousin as > A5338 (above L1275 and discovered in his Big-Y and two others); some time > later, his subgroup was changed to A5339 (just below A5338). Since by this > time we knew that he and one other member of the subgroup were A8177, I > requested a correction which was made within a week.; however, when I > checked a few minutes ago to see whether our Big-Y results had been > updated, I was surprised to find that my cousin is now listed as L1275 and > his closest match (the second A8177) is listed only as M253 unconfirmed. > What is going on here? > > Lindsey > > > ------------------------------- > To unsubscribe from the list, please send an email to > [email protected] with the word 'unsubscribe' without > the quotes in the subject and the body of the message >

Hi Lindsey, If I recall correctly, I am told that my M253 results should be reported in the next two to four weeks. According to the FTDNA Admin FB page, they appear to be working on nothing else at the moment (such as Y-STR's, etc.). So, tell me, should I be expecting a longer wait time?  - Dave Hamm RE: On 10/18/2017 3:00 AM, [email protected] wrote: > Not so odd--numbers matter, and there are probably more R1bs than R1as in FTDNA's database. My family belongs to a small subgroup of M253--who knows when we will get our results? > > Lindsey > > ********************************* > > > There is an interesting "feature" to the new Build 38 BigYs that my project (Clan Donald) > has received word of. > > Out of exactly 225 total BigY participants the ratio of R1b to R1a is 3:1. > So far I fave received zero OLD R1a results converted to Build 38 and only one NEW R1a result, > compared to lots of R1b. Its now well beyond statistical fluctuation. > > Another oddity: the R1bs I've got seem to be clustering around Build 610 (excluding > the "new" ones at Build 760+). > > Odd. > > Doug McDonald > >

There is an interesting "feature" to the new Build 38 BigYs that my project (Clan Donald) has received word of. Out of exactly 225 total BigY participants the ratio of R1b to R1a is 3:1. So far I fave received zero OLD R1a results converted to Build 38 and only one NEW R1a result, compared to lots of R1b. Its now well beyond statistical fluctuation. Another oddity: the R1bs I've got seem to be clustering around Build 610 (excluding the "new" ones at Build 760+). Odd. Doug McDonald

List A lot of people will be interested to see this paper - a free download at: http://www.cell.com/current-biology/fulltext/S0960-9822(17)31091-6 "Genetic Discontinuity between the Maritime Archaic and Beothuk Populations in Newfoundland, Canada" Ana T. Duggan, et al. This group of researchers has produced a set of 26 complete mtDNA sequences: from Haplogroups A, B, C, D & X; and about 50 other partial mtDNA sequences. The Summary of the paper is given below., together with an analysis of the complete genomes. The details of all the sequences is to be found on the EXCEL spreadsheet which is part of the supplementary material accompanying the paper. As usual I have added the complete sequences to my 'Checker' program to ensure accuracy of transcription. Ian www.ianlogan.co.uk -------------------------- Summary Situated at the furthest northeastern edge of Canada, the island of Newfoundland (approximately 110,000 km2) and Labrador (approximately 295,000 km2) today constitute a province characterized by abundant natural resources but low population density. Both landmasses were covered by the Laurentide ice sheet during the Last Glacial Maximum (18,000 years before present [YBP]); after the glacier retreated, ice patches remained on the island until ca. 9,000 calibrated (cal) YBP [1]. Nevertheless, indigenous peoples, whose ancestors had trekked some 5,000 km from the west coast, arrived approximately 10,000 cal YBP in Labrador and ca. 6,000 cal YBP in Newfoundland [2, 3]. Differential features in material culture indicate at least three settlement episodes by distinct cultural groups, including the Maritime Archaic, Palaeoeskimo, and Beothuk. Newfoundland has remained home to indigenous peoples until present day with only one apparent hiatus (3,400–2,800 YBP). This record suggests abandonment, severe constriction, or local extinction followed by subsequent immigrations from single or multiple source populations, but the specific dynamics and the cultural and biological relationships, if any, among these successive peoples remain enigmatic [4]. By examining the mitochondrial genome diversity and isotopic ratios of 74 ancient remains in conjunction with the archaeological record, we have provided definitive evidence for the genetic discontinuity between the maternal lineages of these populations. This northeastern margin of North America appears to have been populated multiple times by distinct groups that did not share a recent common ancestry, but rather one much deeper in time at the entry point into the continent. -------------------------- MF588810(Canada-ancient-BTK141) Duggan Haplogroup C1b 12-OCT-2017 A73G T236C A248G A263G A290- A291- T489C A493G C522- A523- A750G A1438G A2706G T3552A A4715G A4769G T4967C C7028T C7196A G8584A A8701G A8860G T9540C A9545G T10031C A10398G C10400T T10873C G11719A G11914A C12705T A13263G T14318C C14766T T14783C G15043A A15061G G15301A A15326G A15487T C16223T T16298C T16325C C16327T T16519C MF588811(Canada-ancient-BTK142) Duggan Haplogroup A2 12-OCT-2017 C64T A73G T146C A153G A235G A263G 309.1C 315.1C C522- A523- A663G A750G A1438G G1719A A1736G A2706G T4248C A4769G A4824G C7028T G8027A C8794T A8860G C11665T G11719A G12007A C12705T C14766T A15326G T16086C C16111T C16223T C16290T G16319A T16356C T16362C MF588812(Canada-ancient-BTK144) Duggan Haplogroup C1b 12-OCT-2017 A73G A263G A290- A291- T489C A493G C522- A523- A750G A1438G A2706G T3552A A4715G A4769G C7028T C7196A G8584A A8701G A8860G T9540C A9545G T10031C A10398G C10400T T10873C G11719A G11914A C12705T A13263G T14318C C14766T T14783C G15043A G15301A A15326G A15487T C16223T C16266T A16293C T16298C T16325C C16327T T16519C MF588813(Canada-ancient-BTK146) Duggan Haplogroup C1b 12-OCT-2017 A73G T236C A263G A290- A291- T489C A493G C522- A523- A750G A1438G A2706G T3552A A4715G A4769G T4967C C7028T C7196A G8584A A8701G A8860G T9540C A9545G T10031C A10398G C10400T T10873C G11719A G11914A C12705T A13263G T14318C C14766T T14783C G15043A A15061G G15301A A15326G A15487T C16223T T16298C T16325C C16327T T16519C MF588814(Canada-ancient-BTK147) Duggan Haplogroup A2 12-OCT-2017 C64T A73G T146C A153G T195C A235G A263G 309.1C 315.1C C522- A523- A663G A750G A1438G G1719A A1736G A2706G T4248C A4769G A4824G C7028T G8027A C8794T A8860G G11719A G12007A C12705T C14766T A15326G C16223T C16290T G16319A T16362C MF588815(Canada-ancient-BTK-150) Duggan Haplogroup C4c1 12-OCT-2017 A73G G143A A263G 309.1C 315.1C T489C A750G T1243C A1438G 2232.1A A2706G T3552A A4715G A4769G G6026A C7028T C7043T T7064C C7196A G8584A A8701G A8860G T9540C A9545G A10398G C10400T T10873C G11719A G11914A G11969A C12705T A13263G T14318C C14433T C14766T T14783C G15043A G15148A T15204C G15301A A15326G A15487T C16223T T16298C C16327T T16519C MF588816(Canada-ancient-BTK151) Duggan Haplogroup C1c 12-OCT-2017 A73G A263G A290- A291- 309.1C 315.1C T489C A750G A1438G G1888A A2706G T3552A A4715G A4769G T5201C C7028T C7196A G8584A A8701G A8860G T9540C A9545G A10398G C10400T T10873C T11087C G11719A G11914A C12705T A13263G T14318C C14766T T14783C G15043A G15301A A15326G A15487T G15930A C16223T T16298C T16325C C16327T MF588817(Canada-ancient-BTK153) Duggan Haplogroup B2c 12-OCT-2017 A73G A263G 309.1C 309.2C 315.1C G499A 523.1C 523.2A 523.3C 523.4A A750G A827G A1438G A2706G A3547G A4769G G4820A T4977C C6473T C7028T A7241G C8281- C8282- C8283- C8284- C8285- T8286- C8287- T8288- A8289- A8860G T9950C C11177T G11719A A11930G G13590A C14766T A15326G C15535T A16182- A16183- T16189C 16193.1C 16193.2C T16217C T16519C MF588823(Canada-ancient-BTk166) Duggan Haplogroup B2c 12-OCT-2017 A73G A263G 309.1C 309.2C 315.1C G499A 523.1C 523.2A 523.3C 523.4A A750G A827G A1438G A2706G A3547G A4769G G4820A T4977C C6473T C7028T A7241G C8281- C8282- C8283- C8284- C8285- T8286- C8287- T8288- A8289- A8860G T9950C C11177T G11719A A11930G G13590A C14766T A15326G C15535T A16182- A16183- T16189C 16193.1C 16193.2C T16217C T16519C MF588826(Canada-ancient-BTK178) Duggan Haplogroup X2a1 12-OCT-2017 A73G G143A A153G T195C A200G A263G 315.1C A750G A1438G G1719A A2706G T3552C A4769G T6221C C6371T C7028T A8860G A8913G G11719A A12397G C12705T A13966G T14470C T14502C C14766T A15326G T16093C A16183- T16189C 16193.1C G16213A C16223T C16278T T16519C MF588829(Canada-ancient-BTK189) Duggan Haplogroup X2a1b 12-OCT-2017 A73G G143A A153G T195C A200G A263G 309.1C 315.1C A750G A1438G G1719A A2706G T3552C A4769G T6221C C6371T C7028T A8422G A8860G A8913G G11719A C11932T A12397G C12705T A13966G T14470C T14502C C14766T T15001C A15326G T16093C A16183- T16189C 16193.1C G16213A C16223T C16278T T16519C MF588830(Canada-ancient-BTK190) Duggan Haplogroup C1c 12-OCT-2017 A73G C150T T152C A263G A290- A291- 315.1C T489C A750G A1438G G1888A A2706G T3552A A4702G A4715G A4769G C7028T C7196A G8584A A8701G A8860G T9540C A9545G A10398G C10400T T10873C G11719A G11914A C12705T A13263G T14318C C14766T T14783C C15007T G15043A G15301A A15326G A15487T G15930A C16223T T16298C T16325C C16327T MF588833(Canada-ancient-BTK36) Duggan Haplogroup X2a1 12-OCT-2017 A73G G143A A153G T195C A200G A263G 315.1C A750G A1438G G1719A A2706G T3552C A4769G T6221C C6371T C7028T A8860G A8913G G11719A A12397G C12705T A13966G T14470C T14502C C14766T A15326G A16183- T16189C 16193.1C G16213A C16223T C16278T T16519C MF588834(Canada-ancient-BTK37) Duggan Haplogroup D1 12-OCT-2017 A73G A263G C285T 315.1C T489C A750G A1438G C2092T A2706G G3010A A3805G A4769G C4883T C5178A C7028T C7747T T8022C C8414T A8701G A8860G T9540C A10398G C10400T T10873C G11719A A11959G C12705T C14668T C14766T T14783C G15043A G15301A A15326G C15760T C16223T T16325C T16362C MF588838(Canada-ancient-BTK41) Duggan Haplogroup C1b 12-OCT-2017 A73G A248N A263G A290- A291- T489C A493G C522- A523- A750G A1438G A2706G T3552A A4715G A4769G C7028T C7196A T7334C G8584A A8701G A8860G T9540C A9545G T10031C A10398G C10400T T10873C G11719A G11914A C12705T A13263G T14318C C14766T T14783C G15043A G15301A A15326G A15487T C16223T T16298C T16325C C16327T MF588840(Canada-ancient-BTK45) Duggan Haplogroup A2 12-OCT-2017 C64T A73G T146C A153G T195C A235G A263G 309.1C 315.1C C522- A523- A663G A750G A1438G G1719A A1736G A2706G T4248C A4769G A4824G C7028T G8027A C8794T A8860G G11719A G12007A C12705T C14766T A15326G T16086C C16111T C16223T C16290T G16319A T16362C MF588841(Canada-ancient-BTK-46) Duggan Haplogroup D1 12-OCT-2017 A73G A263G C285T 315.1C T489C 745.1T A750G A1438G C2092T A2706G G3010A A4769G C4883T C5178A C7028T C7747T T8022C C8414T A8701G A8860G T9540C A10398G C10400T T10873C G11719A A11959G C12705T C14668T C14766T T14783C G15043A G15301A A15326G C15760T C16223T T16325C T16342C T16362C MF588846(Canada-ancient-BTK53) Duggan Haplogroup C4c1 12-OCT-2017 A73G G143A A263G 309.1C 315.1C T489C A750G T1243C A1438G 2232.1A A2706G T3552A A4715G A4769G G6026A C7028T C7043T T7064C C7196A G8584A A8701G A8860G T9540C A9545G A10398G C10400T T10873C G11719A G11914A G11969A C12705T A13263G T14318C C14433T C14766T T14783C G15043A G15148A T15204C G15301A A15326G A15487T C16223T T16298C C16327T T16519C MF588847(Canada-ancient-BTK54) Duggan Haplogroup D1 12-OCT-2017 A73G T213C A240G A263G 315.1C T489C A750G A1438G C2092T A2706G G3010A A4769G C4883T C5178A C6395T C7028T C7747T C8414T A8701G A8860G T9540C A10398G C10400T T10873C G11719A C12705T G14249A C14668T C14766T T14783C G15043A G15301A A15326G C16223T T16325C T16362C MF588850(Canada-ancient-BTK62) Duggan Haplogroup X2a1b 12-OCT-2017 A73G G143A A153G T195C A200G A263G 309.1C 315.1C A750G A1438G G1719A A2706G T3552C A4769G T6221C C6371T C7028T A8422G A8860G A8913G G11719A C11932T A12397G C12705T A13966G T14470C T14502C C14766T T15001C A15326G T16093C A16183- T16189C 16193.1C G16213A C16223T C16278T T16519C MF588851(Canada-ancient- BTK63) Duggan Haplogroup X2a1b 12-OCT-2017 A73G G143A A153G T195C A200G A263G 309.1C 315.1C A750G A1438G G1719A A2706G T3552C A4769G T6221C C6371T C7028T A8422G A8860G A8913G G11719A C11932T A12397G C12705T A13966G T14470C T14502C C14766T T15001C A15326G T16093C A16183- T16189C 16193.1C G16213A C16223T C16278T T16519C MF588857(Canada-ancient-BTK75) Duggan Haplogroup D2a1 12-OCT-2017 A73G T152C A263G 315.1C T489C C525T A750G A1438G A2706G G3010A G3316A A4769G C4883T C5178A C7028T A7424G C7493T C8414T A8701G C8703T A8860G C9536T T9540C A9667G A10398G C10400T T10873C G11176A C11215T G11719A A11959G C12705T C14668T C14766T T14783C G15043A G15301A A15326G T16092C G16129A C16223T T16362C MF588858(Canada-ancient-BTK76) Duggan Haplogroup C1b 12-OCT-2017 A73G A259G A263G A290- A291- 309.1C 315.1C T489C A493G C522- A523- A750G A1438G A2706G T3552A A4225G A4769G T5981C C7028T C7196A G8584A A8701G A8860G G9055A T9540C A9545G C10094T A10398G C10400T T10873C G11719A G11914A C12705T A13263G T14318C C14766T T14783C G15043A G15301A A15326G A15487T T16126C C16223T T16298C T16325C C16327T T16519C MF588860(Canada-ancient-BTK80) Duggan Haplogroup C4c1b 12-OCT-2017 A73G A263G 309.1C 315.1C T489C G513A A750G G1007A T1243C A1438G 2232.1A A2706G T3552A A4715G A4769G G6026A C7028T C7196A G8584A A8701G A8860G T9540C A9545G A10398G C10400T T10873C G11719A G11914A G11969A C12705T A13263G T14318C C14433T C14766T T14783C G15043A G15148A T15204C G15301A A15326G A15487T T16189C C16223T T16298C C16327T T16519C MF588862(Canada-ancient-BTK84) Duggan Haplogroup A2 12-OCT-2017 A73G T146C A153G A235G A263G 309.1C 315.1C C522- A523- A663G A750G A1438G A1736G A2706G C3330T T4248C A4769G A4824G C7028T C7633T G8027A C8794T A8860G G11719A G12007A C12705T C14766T A15326G C16111T C16192T C16223T C16290T G16319A T16362C MF588863(Canada-ancient-BTK88) Duggan Haplogroup D1 12-OCT-2017 A73G A263G C285T 315.1C T489C A750G A1438G C2092T A2706G G3010A A4769G C4883T C5178A C7028T C7747T T8022C C8414T A8701G A8860G T9540C A10398G C10400T T10873C G11719A A11959G C12705T C14668T C14766T T14783C G15043A G15301A A15326G C15760T C16223T T16325C T16362C

Not so odd--numbers matter, and there are probably more R1bs than R1as in FTDNA's database. My family belongs to a small subgroup of M253--who knows when we will get our results? Lindsey ********************************* There is an interesting "feature" to the new Build 38 BigYs that my project (Clan Donald) has received word of. Out of exactly 225 total BigY participants the ratio of R1b to R1a is 3:1. So far I fave received zero OLD R1a results converted to Build 38 and only one NEW R1a result, compared to lots of R1b. Its now well beyond statistical fluctuation. Another oddity: the R1bs I've got seem to be clustering around Build 610 (excluding the "new" ones at Build 760+). Odd. Doug McDonald

I wanted to add two thoughts: 1. Generally the larger the shared segment is, the closer the relationship (not pushing back farther) 2. An X-match with no shared atDNA, is roughly equivalent to a Chr 5 match with no other shared atDNA - it happens all the time. I also note that the different tools at GEDmatch have different algorithms. The best advice I've heard is to rely on the one-to-one data. Jim Bartlett [email protected] -----Original Message----- From: Ann Turner <[email protected]> To: Wesley Johnston <[email protected]>; DNA Genealogy Mailing List <[email protected]> Sent: Sun, Oct 8, 2017 10:29 pm Subject: Re: [DNA] Working with high largest X-matches on GEDmatch I'm wondering if there's some sort of database error here. I'd suggest sending your findings to [email protected] Ann Turner On Sun, Oct 8, 2017 at 5:54 AM, Wesley Johnston <[email protected]> wrote: > I am looking to see just what a high X-match that has no shared atDNA can > tell us about shared ancestral lines. Clearly this is pushing back very far > in time. I am using a female kit that is of pure Czech ancestry as far back > as we know (roughly in the late 1600's and early 1700's). On her 6-gen > X-inheritance chart, we know at least the name of 9 of the 13 X-ancestors > and know the spouse's surname in all 13. So the challenge of finding a > matching line is narrowed to Czech or Slavic lines. > > But that is not the problem that I am running into on GEDmatch. The > problem is that different GEDmatch tools are presenting conflicting > results. The kits come from different test companies, so that I am not sure > if this is a factor. > > To allow anyone wanting to repeat this to do so, I am going to include kit > numbers. The kit of the focus person is T685302. > > Here are the steps that I have done. > 1 - Identify X-DNA matches, sorted by largest X-DNA cM. > I used the free one-to-many and then sort descending on largest X-DNA cM. > Setting aside immediate family members, the top 10 matches range from 16 to > 21 largest X-DNA cMs, and all but the top one show zero total atDNA cMs > (the top one M052745 has 5.1). > 2 - Do a one-to-one X-DNA comparison of some of the top 10. > Clicking on the X in the X-DNA Details column, you would expect to see the > same information shown in the one-to-one comparison as in the sorted > one-to-many. And in some cases, the X 1:1 does show about the same (an 18.8 > largest X-DNA A916434 on the 1:many shows as 18.7 on the X 1:1). But in > some cases, the X-DNA 1:1 shows zero shared X-DNA (an 18.3 largest X-DNA > M131017 on the 1:many shows as no match at all on the X 1:1). > So I tried dropping the SNP threshold with M131017 on the X 1:1 to 100 > SNPs and the minimum cMs to 1 (which should not be necessary if there is > indeed a largest X shared 18.3 cM as the 1:many list shows). And this does > generate a list of shared ranges on the X, the largest of which is 5.4 cM > (162 SNPs) by cMs or by SNPs 3.5 cM (295 SNPs). So clearly this is a > radical difference from what the 1:many list is showing when it reports a > largest shared X of 18.3 cM). > 3 - Create a Tag Group for the highest matches. > I used the Tier1 1 1:many tool to create the group, setting the option to > filter by X (instead of autosomal) with offset 0, limit 500 (the minimum > allowed) and cM size 3 (the minimum allowed. This gives a completely > different (from step 1) top 10 list. Where the free 1:many had largest cMs > of 16 or more for the top 10, the Tier1 1:many showed no one (other than > close family) with a largest cM of more than 11.2. > > So I then tried the Tier1 1:1 on autosomal and setting to the minima and > sorting on the largest X (trying to re-create the list in step 1. But since > the Tier1 1:1 does not include atDNA matches of zero, neither one of these > methods was able to find the same high largest X but low atDNA matches that > the free 1:1 tool found. > Nevertheless, I created a tag group of those X-matches (from the atDNA > version of the Tier1 1:1) who had the highest total X cMS (20.0 and above, > minus immediate family). This tag group has 20 members. > 4 - Run the X-DNA Matrix Comparison for this tag group. > This was a real shock. Since the tag group had been specifically created > from a 1:many list of the X-DNA matches of T685302 who had 20.0 or more > total cMs, you would expect to see a number in every cell of T685302's > row/column. But 8 of the 19 cells are empty. Going back to the Tier1 1:1 > list used to create this tag group, one of these empty cells is the second > highest total cMs (40.8), but the largest for this match is just 6.4 and > thus under the threshold of 7 cM for the matrix, which explains the empty > cell. > > > The bottom line seems to me to be implicit and explicit threshold > differences among the tools. I really would like to work with the top 10 > from the free 1:many, but even the free X 1:1 conflicts with some of the > ones shown in that list. And the Tier1 1:many does not even discover these > matches (apparently because the Tier1, even when choosing the X option) > still has some implicit atDNA threshold). > Choosing these low-autosomal / high largest X matches as a target is a > challenge in the first place. But the GEDmatch tools make it extremely more > challenging when they do not allow exploration of those matches. > Clearly having more ability to twist the knobs on GEDmatch would help. But > the fact that (step 1 and step 2) there are very significant conflicts > between one GEDmatch tool showing 18.3 cM of a largest shared X and > another showing nothing more than 5.4 cM for the same two people seems to > be more than just finding the right settings of the knobs.

Its speeding up! I've got 4 so far today. This brings the expected finish time down from 75 days to perhaps 65 days. Doug McDonald -----Original Message----- I see 6 of 80 so far in the R-L226 branch Dennis Wright // On 15/10/2017 1:43 AM, McDonald, J Douglas wrote: > So far I have 5 of the 225 older BigYs in my project have received new Build 38 web pages at FTDNA, > plus several ones that just completed the actual sequencing. >

I see 6 of 80 so far in the R-L226 branch Dennis Wright // On 15/10/2017 1:43 AM, McDonald, J Douglas wrote: > So far I have 5 of the 225 older BigYs in my project have received new Build 38 web pages at FTDNA, > plus several ones that just completed the actual sequencing. > > So far all of these have been in oddball areas of the project, and for none of them of I > previously received VCF and BED files, let alone BAMs. > > > Is this the rate that other project admins are getting them? > > The number of "compared" SNPs listed grows with time. But so far, I have not seen > growth in the numbers of "known" SNPs in the R1a-CTS4179 problem area. > > Doug McDonald > > > ------------------------------- > To unsubscribe from the list, please send an email to [email protected] with the word 'unsubscribe' without the quotes in the subject and the body of the message >

So far I have 5 of the 225 older BigYs in my project have received new Build 38 web pages at FTDNA, plus several ones that just completed the actual sequencing. So far all of these have been in oddball areas of the project, and for none of them of I previously received VCF and BED files, let alone BAMs. Is this the rate that other project admins are getting them? The number of "compared" SNPs listed grows with time. But so far, I have not seen growth in the numbers of "known" SNPs in the R1a-CTS4179 problem area. Doug McDonald

This is a second cousin's paternal line and I am looking for more information on it. Thanks, Steven -- Steven C. Perkins [email protected] http://stevencperkins.com/ Indigenous Peoples' Rights http://intelligent-internet.info/law/ipr2.html Indigenous & Ethnic Minority Legal News http://iemlnews.blogspot.com/ Online Journal of Genetics and Genealogy http://jgg-online.blogspot.com/ S.C. Perkins' Genealogy Page http://stevencperkins.com/genealogy.html S.C. Perkins' Genealogy Blog http://scpgen.blogspot.com/

Doug, I take you point, however, the new tools, by colour density, attempt to advise, High, Medium or Low quality.  As you say, lets see the actual revised BAM files. Cheers *Dennis Wright* // On 14/10/2017 10:23 AM, McDonald, J Douglas wrote: > Yes, and what fraction of those will turn out to be wrong or useless? > > Look where they are. When the BAMs arrive, look at their mapping quality! > > Doug McDonald > ________________________________________ > From: GENEALOGY-DNA [[email protected]] on behalf of Dennis Wright [[email protected]] > Sent: Friday, October 13, 2017 5:14 PM > To: R1b-L21 Yahoo Groups; Rootsweb Genealogy DNA > Subject: [DNA] HG38 Results are revealing additional SNPs > > It appears that in the new Big-Y result pages that are slowly coming > through, the 'unnamed variants' are indeed new, and not recognised in > the earlier hg19 VCF/BAM files. > > The new tools are very workable, and perhaps there is less need for our > detailed analysis ... time will tell. > > -- > *Dennis Wright* > > > ------------------------------- > To unsubscribe from the list, please send an email to [email protected] 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 [email protected] with the word 'unsubscribe' without the quotes in the subject and the body of the message >

It appears that in the new Big-Y result pages that are slowly coming through, the 'unnamed variants' are indeed new, and not recognised in the earlier hg19 VCF/BAM files. The new tools are very workable, and perhaps there is less need for our detailed analysis ...  time will tell. -- *Dennis Wright*

I think they mean high BASE call quality. That's meaningless if the reads are in the wrong place and your base is correct at the correct spot. This has long been a terrible problem ________________________________________ From: GENEALOGY-DNA [[email protected]] on behalf of Dennis Wright [[email protected]] Sent: Friday, October 13, 2017 6:37 PM To: [email protected] Subject: Re: [DNA] HG38 Results are revealing additional SNPs Doug, I take you point, however, the new tools, by colour density, attempt to advise, High, Medium or Low quality. As you say, lets see the actual revised BAM files. Cheers *Dennis Wright* // On 14/10/2017 10:23 AM, McDonald, J Douglas wrote: > Yes, and what fraction of those will turn out to be wrong or useless? > > Look where they are. When the BAMs arrive, look at their mapping quality! > > Doug McDonald > ________________________________________ > From: GENEALOGY-DNA [[email protected]] on behalf of Dennis Wright [[email protected]] > Sent: Friday, October 13, 2017 5:14 PM > To: R1b-L21 Yahoo Groups; Rootsweb Genealogy DNA > Subject: [DNA] HG38 Results are revealing additional SNPs > > It appears that in the new Big-Y result pages that are slowly coming > through, the 'unnamed variants' are indeed new, and not recognised in > the earlier hg19 VCF/BAM files. > > The new tools are very workable, and perhaps there is less need for our > detailed analysis ... time will tell. > > -- > *Dennis Wright* > > > ------------------------------- > To unsubscribe from the list, please send an email to [email protected] 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 [email protected] 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 [email protected] with the word 'unsubscribe' without the quotes in the subject and the body of the message

Yes, and what fraction of those will turn out to be wrong or useless? Look where they are. When the BAMs arrive, look at their mapping quality! Doug McDonald ________________________________________ From: GENEALOGY-DNA [[email protected]] on behalf of Dennis Wright [[email protected]] Sent: Friday, October 13, 2017 5:14 PM To: R1b-L21 Yahoo Groups; Rootsweb Genealogy DNA Subject: [DNA] HG38 Results are revealing additional SNPs It appears that in the new Big-Y result pages that are slowly coming through, the 'unnamed variants' are indeed new, and not recognised in the earlier hg19 VCF/BAM files. The new tools are very workable, and perhaps there is less need for our detailed analysis ... time will tell. -- *Dennis Wright* ------------------------------- To unsubscribe from the list, please send an email to [email protected] with the word 'unsubscribe' without the quotes in the subject and the body of the message