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apophis99942
08-26-2012, 04:09 PM
Here's the link, in case anyone is interested in this tool: http://www.math.mun.ca/~dapike/FF23utils/roh.php

These were my results:


ROHs of length at least 400 will be reported.
No-Call runs of length at least 10 will be reported.
No-Calls will be treated as homozygous.
Heterozygous SNPs that are at least 150 SNPs away from the nearest heterozygous SNP will be treated as homozygous.
Chr 11 has a No-Call run of length 13 from position 55122337 to position 55163740 (41.40 Kb)
Chr Y has a No-Call run of length 20 from position 2980925 to position 3064873 (83.95 Kb)
Chr Y has a No-Call run of length 18 from position 3119025 to position 3187531 (68.51 Kb)
Chr Y has a No-Call run of length 17 from position 3199658 to position 3288828 (89.17 Kb)
Chr Y has a No-Call run of length 16 from position 3370270 to position 3461707 (91.44 Kb)
Chr Y has a No-Call run of length 25 from position 3496718 to position 3540985 (44.27 Kb)
Chr Y has a No-Call run of length 17 from position 3607060 to position 3687909 (80.85 Kb)
Chr Y has a No-Call run of length 17 from position 3700050 to position 3742867 (42.82 Kb)
Chr Y has a No-Call run of length 37 from position 3757126 to position 3824211 (67.08 Kb)
Chr Y has a No-Call run of length 45 from position 3850709 to position 4125381 (274.67 Kb)
Chr Y has a No-Call run of length 10 from position 4188793 to position 4259133 (70.34 Kb)
Chr Y has a No-Call run of length 16 from position 4268457 to position 4299428 (30.97 Kb)
Chr Y has a No-Call run of length 14 from position 4322761 to position 4369606 (46.84 Kb)
Chr Y has a No-Call run of length 56 from position 4372811 to position 4610107 (237.30 Kb)
Chr Y has a No-Call run of length 44 from position 4619101 to position 4783799 (164.70 Kb)
Chr Y has a No-Call run of length 18 from position 4809584 to position 4860467 (50.88 Kb)
Chr Y has a No-Call run of length 38 from position 4864521 to position 4931809 (67.29 Kb)
Chr Y has a No-Call run of length 24 from position 4942982 to position 4985084 (42.10 Kb)
Chr Y has a No-Call run of length 18 from position 4987998 to position 4999145 (11.15 Kb)
Chr Y has a No-Call run of length 41 from position 5017608 to position 5072099 (54.49 Kb)
Chr Y has a No-Call run of length 50 from position 5118273 to position 5247330 (129.06 Kb)
Chr Y has a No-Call run of length 38 from position 5263601 to position 5352479 (88.88 Kb)
Chr Y has a No-Call run of length 42 from position 5358470 to position 5426585 (68.11 Kb)
Chr Y has a No-Call run of length 85 from position 5445063 to position 5634967 (189.90 Kb)
Chr Y has a No-Call run of length 27 from position 5637743 to position 5732315 (94.57 Kb)
Chr Y has a No-Call run of length 20 from position 5740126 to position 5814102 (73.98 Kb)
Chr Y has a No-Call run of length 26 from position 5815943 to position 5957277 (141.33 Kb)
Chr Y has a No-Call run of length 14 from position 6009606 to position 6066768 (57.16 Kb)
Chr Y has a No-Call run of length 13 from position 6079917 to position 6133852 (53.94 Kb)
Chr Y has a No-Call run of length 12 from position 6142930 to position 6509519 (366.59 Kb)
Chr Y has a No-Call run of length 25 from position 6515097 to position 6796154 (281.06 Kb)
Chr Y has a No-Call run of length 11 from position 19612089 to position 19613242 ( 1.15 Kb)

Chr 6 has a ROH of length 654 from position 31669023 to position 32185146 ( 0.52 Mb)
Chr 16 has a ROH of length 448 from position 2047219 to position 2085788 ( 0.04 Mb)

Chr 1: 69.824 % (53699 of 76906 SNPs) are homozygous, 197 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 2: 68.351 % (52863 of 77341 SNPs) are homozygous, 207 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 3: 67.148 % (42492 of 63281 SNPs) are homozygous, 155 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 4: 67.122 % (36920 of 55004 SNPs) are homozygous, 151 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 5: 67.600 % (37869 of 56019 SNPs) are homozygous, 146 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 6: 68.938 % (43595 of 63238 SNPs) are homozygous, 171 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 7: 69.687 % (35557 of 51024 SNPs) are homozygous, 135 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 8: 68.673 % (33796 of 49213 SNPs) are homozygous, 129 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 9: 68.095 % (29259 of 42968 SNPs) are homozygous, 98 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 10: 68.119 % (34274 of 50315 SNPs) are homozygous, 146 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 11: 70.462 % (33781 of 47942 SNPs) are homozygous, 141 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 12: 68.151 % (32114 of 47122 SNPs) are homozygous, 130 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 13: 68.172 % (24593 of 36075 SNPs) are homozygous, 78 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 14: 68.337 % (21060 of 30818 SNPs) are homozygous, 88 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 15: 69.778 % (19817 of 28400 SNPs) are homozygous, 68 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 16: 69.427 % (20908 of 30115 SNPs) are homozygous, 85 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 17: 69.528 % (18580 of 26723 SNPs) are homozygous, 69 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 18: 68.614 % (19192 of 27971 SNPs) are homozygous, 62 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 19: 70.849 % (13129 of 18531 SNPs) are homozygous, 66 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 20: 67.081 % (15988 of 23834 SNPs) are homozygous, 57 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 21: 64.453 % ( 8638 of 13402 SNPs) are homozygous, 39 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 22: 67.064 % ( 9456 of 14100 SNPs) are homozygous, 49 No-Calls, 0 heterozygous SNPs treated as homozygous

Chr X: 1.531 % ( 398 of 26001 SNPs) are homozygous, 75 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr Y: 1764 SNPs, 1002 No-Calls, 0 heterozygous SNPs treated as homozygous
mtDNA : 2459 SNPs, 81 No-Calls, 0 heterozygous SNPs treated as homozygous

Total autosomal (Chr 1-22): 0.265 % ( 2467 of 930342 SNPs) are NoCalls
Total autosomal (Chr 1-22): 31.468 % (292762 of 930342 SNPs) are Heterozygous (this tally excludes 0 heterozygous SNPs that were treated as homozygous)
Total autosomal (Chr 1-22): 68.532 % (637580 of 930342 SNPs) are Homozygous (this tally includes 0 heterozygous SNPs that were treated as homozygous)
Processing Completed

DMXX
08-29-2012, 04:29 PM
The "Total autosomal (Chr 1-22) ... Homozygous" values are most relevant to the discussion here and were cited specifically on DNA-Forums when users compared their own results. I recall having a value around AJL's.

One possibly useful inference I can make from the Chr-specific Homozygous results is the range.

Theoretically, those with parents who stem from genetically similar backgrounds that have underwent some form of genetic drift (i.e. a full-blooded Kalash) will have a smaller range across their Chr Homozygous values.

To test this, I've compared my values with yours below.



Username auDNA Homozygosity Average auDNA Homozygosity Range
apophis99942 68.532 % 6.40%
Humata 67.669 % 4.362%


It's hard to clarify whether that assertion holds up or not based on two samples. I wonder what our other users get?

apophis99942
08-29-2012, 04:42 PM
Yeah, two samples is probably nowhere near enough. Plus from what I remember reading, the results largely depend on the version of your submitted file (if it's V2 or V3). What I don't get is why it's held that the ~70% average for auDNA homozygosity delineates an inbred condition. How arbitrary is that and what is that being compared to?

DMXX
08-29-2012, 04:44 PM
I don't think any formal assessment was made into what value confers the status of "inbred". 70% was taken as the threshold on DNA-Forums. Perhaps one of the other former users there can clarify if I'm remembering correctly.

gijoeinfinity
08-29-2012, 07:38 PM
The % basically shows you an overall genetic distance between your parents; it may not detect recent inbreeding such as if your father's parents were first cousins.

My % using this tool is as follows:

V2: 65.82%
V3: 67.98%

But my parent's percentages are much higher:

Father V3: 70.428% - Colonial American
Mother V3: 72.555% - Filipino

My mother's numbers are high, not necessarily because her parents were inbred, but because East Asian populations tend to have higher affinity with one another as opposed to African or European. I'm not sure why this is the case though.

botoole60611
11-24-2012, 07:16 AM
My results are 70.562 %.

I remember when this first came out a couple years back I had a biologist friend explain it to me - that my parents were from the same area.

Bio-dad is 75% New England colonial going back to Mayflower ancestors. My mother is Plymouth and also Acadian.

And my 14th GGM on my mother's side is the brother of my 11th GGF on my father's side, among others.

I have found a few DNA matches that have ancestry connection to both sides of my tree.

Little bit
11-24-2012, 02:37 PM
I've looked at quite of few of these results on the "How inbred are you" thread at 23andme, and here's what I discovered:

-Overall homozygosity increases with (1.) consanguinity, (2.) endogamy, (3.) Northward in Europe, and (4.) having parents from the same gene pool.
-Overall homozygosity decreases with (1.) genetic distance of the parents and (2) living at the crossroads where populations are diverse.
-Consanguinity is most easily observed via auDNA Homozygosity Range. Sometimes just one or 2 chromosomes will show higher-than-average homozygosity, but for individuals who come from cultures that practice cousin marriage, the range can be stunning (67-93%)!
-Overall number of ROH's increases and decreases in the same pattern as overall homozygosity.
-Size of ROH's does too. The more consanguineous, endogamous, or Northern (European) you are, the bigger the ROH's.
-I haven't observed enough samples from distinct populations but I can say with some certainty from the samples I've seen that Europeans, in general, have lower homozygosity numbers than Africans and Asians. There's one 100% African sample I know of, I'm sharing with him at 23andme, and his v2 70.438% blows my higher end N Euro 68.551% v2 results out of the water!
-X homozygosity is interesting for females. My daughter's 75.060% v3 is higher end for European but I've seen it hit the 77% range.
-Check for no-call run's - I see apophis99942 has one on the 11th chromosome. You can research it by plugging 11q11. I know theres a common CNV located there related to obesity:
http://genome.ucsc.edu/cgi-bin/hgTracks?hgHubConnect.destUrl=..%2Fcgi-bin%2FhgTracks&clade=mammal&org=Human&db=hg19&position=chr11%3A55122337-55163740&hgt.positionInput=chr11%3A55122337-55163740&hgt.suggestTrack=knownGene&Submit=submit&hgsid=312218089
-In Europe, Swedes and Lithuanians seem to get the highest homozygosity and ROH's, from what I've seen. You can check Evon_Evon's spreadsheet for comparisons (eastwind87 is Chinese but those are v2 results and she still has top score - I'd really love to see a v3 Chinese sample=) :
https://docs.google.com/spreadsheet/ccc?key=0AmrjskaD3Uj8dGx4N2xGRTZWTHhodGhQQ0s3bTl6Y 0E&hl=en_GB#gid=0

If you want to observe different examples, go to this 23andme thread:
https://www.23andme.com/you/community/thread/3093/

Consanguinity - cousin marriage:
Faris123 June 15, 2011
zack_a Nov 13, 2011 - He also blogged about his v2 results here, notice how much range for the individual chromosomes he has (mine range between 67-70%) http://www.zackvision.com/weblog/2011/01/inbreeding/

Endogamy - French Canadians:
LargoDominus Aug 10, 2011
Eric from Chicontimi Aug 10, 2011

4GP Northern European:
L. Stockhom (Swedish) May 13, 2011
Alina76 (Lithuanian) Nov 13, 2012

Little bit
11-24-2012, 02:39 PM
And here's my outbred N European mother but same gene pool. My mom has very high homozygosity for an outbred American, but her ROH's are small, few over 1.5Mb, and her chromosomes are very stable. Evidently her Irish/English/German ancestors were similar enough to reach higher homozygosity when mixed:

Chr 1 has a ROH of length 303 from position 154924239 to position 155940948 ( 1.02 Mb)
Chr 1 has a ROH of length 200 from position 156063880 to position 156238593 ( 0.17 Mb)
Chr 1 has a ROH of length 275 from position 224936295 to position 225903098 ( 0.97 Mb)
Chr 2 has a ROH of length 533 from position 31549662 to position 33329957 ( 1.78 Mb)
Chr 2 has a ROH of length 368 from position 75288700 to position 76109411 ( 0.82 Mb)
Chr 2 has a ROH of length 253 from position 134727667 to position 135218605 ( 0.49 Mb)
Chr 2 has a ROH of length 258 from position 135722328 to position 136824836 ( 1.10 Mb)
Chr 2 has a ROH of length 201 from position 140019620 to position 140665986 ( 0.65 Mb)
Chr 2 has a ROH of length 502 from position 158193407 to position 159672168 ( 1.48 Mb)
Chr 3 has a ROH of length 439 from position 37034946 to position 37531856 ( 0.50 Mb)
Chr 3 has a ROH of length 297 from position 55802668 to position 56797985 ( 1.00 Mb)
Chr 3 has a ROH of length 202 from position 107794140 to position 108531753 ( 0.74 Mb)
Chr 4 has a ROH of length 261 from position 9915741 to position 10310495 ( 0.39 Mb)
Chr 5 has a ROH of length 223 from position 57503024 to position 58071799 ( 0.57 Mb)
Chr 5 has a ROH of length 339 from position 112218700 to position 113118069 ( 0.90 Mb)
Chr 6 has a ROH of length 1377 from position 30316980 to position 31236567 ( 0.92 Mb)
Chr 6 has a ROH of length 433 from position 31253878 to position 31435991 ( 0.18 Mb)
Chr 6 has a ROH of length 278 from position 33024499 to position 33185918 ( 0.16 Mb)
Chr 6 has a ROH of length 247 from position 122046232 to position 123006095 ( 0.96 Mb)
Chr 7 has a ROH of length 206 from position 98933689 to position 99365451 ( 0.43 Mb)
Chr 7 has a ROH of length 297 from position 116929065 to position 117440972 ( 0.51 Mb)
Chr 8 has a ROH of length 256 from position 19536790 to position 19876970 ( 0.34 Mb)
Chr 10 has a ROH of length 407 from position 94090498 to position 95064403 ( 0.97 Mb)
Chr 11 has a ROH of length 246 from position 5244404 to position 5255790 ( 0.01 Mb)
Chr 11 has a ROH of length 223 from position 9622111 to position 10393873 ( 0.77 Mb)
Chr 11 has a ROH of length 208 from position 47235918 to position 48066048 ( 0.83 Mb)
Chr 11 has a ROH of length 212 from position 81225948 to position 81582575 ( 0.36 Mb)
Chr 12 has a ROH of length 369 from position 103169397 to position 103341908 ( 0.17 Mb)
Chr 14 has a ROH of length 302 from position 41928909 to position 42988346 ( 1.06 Mb)
Chr 14 has a ROH of length 240 from position 73489268 to position 73964278 ( 0.48 Mb)
Chr 16 has a ROH of length 229 from position 2126043 to position 2138252 ( 0.01 Mb)
Chr 16 has a ROH of length 235 from position 16130340 to position 16256678 ( 0.13 Mb)
Chr 16 has a ROH of length 335 from position 30118750 to position 31384687 ( 1.27 Mb)
Chr 17 has a ROH of length 234 from position 48267228 to position 48275866 ( 0.01 Mb)
Chr 17 has a ROH of length 257 from position 50212182 to position 51118173 ( 0.91 Mb)
Chr 18 has a ROH of length 207 from position 24517015 to position 24654150 ( 0.14 Mb)
Chr 18 has a ROH of length 252 from position 66576237 to position 67169994 ( 0.59 Mb)
Chr 19 has a ROH of length 208 from position 37371732 to position 38475375 ( 1.10 Mb)
Chr 20 has a ROH of length 288 from position 48110188 to position 48793362 ( 0.68 Mb)
Chr 22 has a ROH of length 245 from position 28198577 to position 29379731 ( 1.18 Mb)
Chr 22 has a ROH of length 214 from position 42372381 to position 42691238 ( 0.32 Mb)
Chr X has a ROH of length 227 from position 55024559 to position 58178159 ( 3.15 Mb)
Chr X has a ROH of length 593 from position 72351056 to position 78620053 ( 6.27 Mb)
Chr X has a ROH of length 263 from position 153274228 to position 153540977 ( 0.27 Mb)
Chr Y has a ROH of length 1766 from position 2649694 to position 59032809 (56.38 Mb)

Chr 1: 71.618 % (55081 of 76909 SNPs) are homozygous, 284 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 2: 71.325 % (55167 of 77346 SNPs) are homozygous, 271 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 3: 70.037 % (44323 of 63285 SNPs) are homozygous, 233 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 4: 70.740 % (38919 of 55017 SNPs) are homozygous, 218 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 5: 70.753 % (39635 of 56019 SNPs) are homozygous, 189 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 6: 71.082 % (44955 of 63244 SNPs) are homozygous, 292 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 7: 69.756 % (35551 of 50965 SNPs) are homozygous, 207 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 8: 69.330 % (34121 of 49215 SNPs) are homozygous, 168 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 9: 69.695 % (29948 of 42970 SNPs) are homozygous, 148 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 10: 71.158 % (35808 of 50322 SNPs) are homozygous, 190 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 11: 71.148 % (34131 of 47972 SNPs) are homozygous, 208 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 12: 70.606 % (33273 of 47125 SNPs) are homozygous, 193 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 13: 71.373 % (25750 of 36078 SNPs) are homozygous, 137 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 14: 69.907 % (21544 of 30818 SNPs) are homozygous, 89 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 15: 70.358 % (19981 of 28399 SNPs) are homozygous, 106 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 16: 72.241 % (21793 of 30167 SNPs) are homozygous, 107 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 17: 71.066 % (18966 of 26688 SNPs) are homozygous, 102 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 18: 71.892 % (20109 of 27971 SNPs) are homozygous, 88 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 19: 72.697 % (13473 of 18533 SNPs) are homozygous, 143 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 20: 71.876 % (17131 of 23834 SNPs) are homozygous, 74 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 21: 70.859 % ( 9498 of 13404 SNPs) are homozygous, 49 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 22: 71.291 % (10052 of 14100 SNPs) are homozygous, 72 No-Calls, 0 heterozygous SNPs treated as homozygous

Chr X: 74.580 % (19396 of 26007 SNPs) are homozygous, 86 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr Y: 1766 SNPs, 1766 No-Calls, 0 heterozygous SNPs treated as homozygous
mtDNA : 2459 SNPs, 25 No-Calls, 0 heterozygous SNPs treated as homozygous

Total autosomal (Chr 1-22): 0.383 % ( 3568 of 930381 SNPs) are NoCalls
Total autosomal (Chr 1-22): 29.146 % (271172 of 930381 SNPs) are Heterozygous (this tally excludes 0 heterozygous SNPs that were treated as homozygous)
Total autosomal (Chr 1-22): 70.854 % (659209 of 930381 SNPs) are Homozygous (this tally includes 0 heterozygous SNPs that were treated as homozygous)

Private_user
11-24-2012, 05:57 PM
I've looked at quite of few of these results on the "How inbred are you" thread at 23andme, and here's what I discovered:

-Overall homozygosity increases with (1.) consanguinity, (2.) endogamy, (3.) Northward in Europe, and (4.) having parents from the same gene pool.
-Overall homozygosity decreases with (1.) genetic distance of the parents and (2) living at the crossroads where populations are diverse.
-Consanguinity is most easily observed via auDNA Homozygosity Range. Sometimes just one or 2 chromosomes will show higher-than-average homozygosity, but for individuals who come from cultures that practice cousin marriage, the range can be stunning (67-93%)!
-Overall number of ROH's increases and decreases in the same pattern as overall homozygosity.
-Size of ROH's does too. The more consanguineous, endogamous, or Northern (European) you are, the bigger the ROH's.
Wrong (the part in bold). Check all Lithuanians at Evon's spreadsheet again - 6 of us there from all over the country, so, it's fairly representative.
ROH V3. homozygosity (https://docs.google.com/spreadsheet/ccc?key=0AmrjskaD3Uj8dGx4N2xGRTZWTHhodGhQQ0s3bTl6Y 0E&hl=en_GB#gid=0)

Large ROHs are not more abundant than in Southern or Central Europe while overall homozygosity percentages are among the highest in Europe - if not the highest. The two factors aren't related.
There are also 7 Finns in the spreadsheet - they ought to have higher homozigosity scores than us, if what you say was true: Finland is so much further North than Lithuania. But in reality they don't - quite on the contrary.

Little bit
11-24-2012, 10:08 PM
I find big ROH's more common in Northern Europeans but there are always exceptions. Whatever keeps a population from gaining outside admixture whether it be distance, culture, or other forces will, over time, cause that population to lose heterozygosity. Even within Sweden, there is a difference between Northern and Southern populations when it comes to homozygosity, with the far Northern showing a larger number of extended homozygous regions:


Extended homozygous segments

The observed patterns of homozygosity further reinforce the picture of a genetic divide between the southern and northern parts of Sweden. While the differences in the number of extended homozygous segments were mostly small and non-significant for the southern national areas, the counties corresponding to the three northernmost national areas had a larger number of extended homozygous regions, suggestive of an increase in autozygosity. The northern national areas are much more sparsely populated than the southern with vast geographical distances between towns and villages, a fact that may have contributed to the observed loss of heterozygosity. The increased level of genetic homogeneity in the north may be an advantage if a study is set to search for recessive genetic variants with high penetrance, as by means of linkage studies.



http://www.plosone.org/article/info:doi/10.1371/journal.pone.0022547

Private_user
11-25-2012, 10:30 AM
I find big ROH's more common in Northern Europeans but there are always exceptions. Whatever keeps a population from gaining outside admixture whether it be distance, culture, or other forces will, over time, cause that population to lose heterozygosity. Even within Sweden, there is a difference between Northern and Southern populations when it comes to homozygosity, with the far Northern showing a larger number of extended homozygous regions:
http://www.plosone.org/article/info:doi/10.1371/journal.pone.0022547
The quote you posted is about Sweden's internal variation - not about the variation of the whole Europe.
When a study about the whole Europe was made, it showed exactly what I said, i.e. that what you say isn't true.

Not only was the mean ROH length of Lithuanians the second smallest in Europe, the Southern European countries Serbia, Spain, Italy, Croatia, Portugal all had even larger mean ROH lengths than 4gp Ashkenazis - that's comparable to isolated island populations like Cypriots, Sardinians & Orcadians.
http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0034267

I marked Southern European (South East + South West) & Northern European (North East + North West) countries for the sake of illustration and convenience:




Population (Ethnicity or Country)
mean ROH length (cM)


Surui
4.08


Balochi
3.89


Makrani
3.77


Bedouin
3.63


Palestine
3.45


Druze
3.38


Brahui
3.32


Sindhi
3.25


Pathan
3.22


Pakistan
3.17


Karitiana
3.13


Palestinian
3.09


Dominican Republic
2.92


Lebanon
2.91


Armenia
2.9


Pima
2.9


Kalash
2.89


Mozabite
2.79


Burusho
2.78


Iraq
2.77


Biaka Pygmies
2.71


Haiti
2.71


Hazara
2.63


Serbia
2.57


Morocco
2.55


Cyprus
2.52


Sri Lanka
2.52


Turkey
2.5


Egypt
2.47


Brazil
2.45


Jamaica
2.43


Iran
2.41


Orcadian
2.4


Syria
2.4


Colombia
2.4


North Italian
2.39


Croatia
2.38


Bantu (N.E.)
2.38


Portugal
2.37


Spain
2.37


Italy
2.36


Ashkenazi_3GP a
2.35


Ashkenazi_2GP a
2.35


Sardinian
2.35


Belgium
2.35


Lahu
2.35


Mbuti Pygmies
2.35


Colombian
2.34


Greece
2.33


India
2.33


Ashkenazi a
2.32


Russia
2.32


Uygur
2.32


Australia
2.32


Argentina
2.32


French Basque
2.31


Ashkenazi_1GP a
2.31


Slovakia
2.31


Adygei
2.31


Bosnia and Herzegovina
2.3


Denmark
2.3


San
2.3


Yakut
2.3


New Zealand
2.29


Tuscan
2.28


Ukraine
2.27


Bulgaria
2.27


Germany
2.26


Cuba
2.26


Hezhen
2.25


Ecuador
2.24


Norway
2.23


Sweden
2.23


Switzerland
2.23


Poland
2.23


United Kingdom
2.22


Yoruba
2.22


United States of America
2.22


Romania
2.21


Netherlands
2.21


Hungary
2.2


Mexico
2.2


Estonia
2.18


Czech Republic
2.18


France
2.18


Miaozu
2.18


Canada
2.18


Mandenka
2.17


Finland
2.16


Ireland
2.15


She
2.15


Austria
2.13


Papuan
2.12


Russian
2.11


Slovenia
2.1


South Korea
2.1


Iceland
2.09


Macedonia
2.09


Dai
2.07


Lithuania
2.06


Oroqen
2.06


Belarus
2.05


China
2.02


Japan
1.99


South Africa
1.97


Chile
1.95


Taiwan
1.95


Philippines
1.94


Daur
1.93


Maya
1.93


Vietnam
1.93


Tu
1.92


Peru
1.9


Yizu
1.89


Cambodian
1.87


Naxi
1.86


Japanese
1.85


Han
1.84


Melanesian
1.83


Xibo
1.78


Mongolian
1.77




Coining new factually incorrect terms like "ethnically inbred" (which in reality translates to "not actually inbred but I will call it inbred just cause I like redefining the terms") and proliferating them is actually rather offensive.
I get it, your heritage is very mixed - nothing wrong with that in my book. But then why are you trying to create the impression that not having such mixed heritage is somehow inferior by misapplying terms that carry negative connotation (in this case "inbred")?

apophis99942
11-28-2012, 09:11 PM
Does inbreeding work better for some groups than others?

Kamane
06-17-2013, 06:03 PM
ROHs of length at least 200 will be reported.
No-Call runs of length at least 10 will be reported.
No-Calls will be treated as homozygous.
Heterozygous SNPs that are at least 150 SNPs away from the nearest heterozygous SNP will be treated as homozygous.

Chr 2 has a No-Call run of length 10 from position 41238644 to position 41248468 ( 9.82 Kb)
Chr 6 has a No-Call run of length 32 from position 78972930 to position 79031742 (58.81 Kb)
Chr Y has a No-Call run of length 64 from position 2897433 to position 3245636 (348.20 Kb)
Chr Y has a No-Call run of length 16 from position 3310270 to position 3401707 (91.44 Kb)
Chr Y has a No-Call run of length 29 from position 3436718 to position 3490038 (53.32 Kb)
Chr Y has a No-Call run of length 17 from position 3547060 to position 3627909 (80.85 Kb)
Chr Y has a No-Call run of length 17 from position 3640050 to position 3682867 (42.82 Kb)
Chr Y has a No-Call run of length 11 from position 3697126 to position 3711649 (14.52 Kb)
Chr Y has a No-Call run of length 11 from position 3721230 to position 3764211 (42.98 Kb)
Chr Y has a No-Call run of length 36 from position 3781791 to position 4017487 (235.70 Kb)
Chr Y has a No-Call run of length 10 from position 4026698 to position 4065381 (38.68 Kb)
Chr Y has a No-Call run of length 34 from position 4084431 to position 4239428 (155.00 Kb)
Chr Y has a No-Call run of length 56 from position 4262761 to position 4482533 (219.77 Kb)
Chr Y has a No-Call run of length 44 from position 4559101 to position 4723799 (164.70 Kb)
Chr Y has a No-Call run of length 18 from position 4749584 to position 4800467 (50.88 Kb)
Chr Y has a No-Call run of length 38 from position 4804521 to position 4871809 (67.29 Kb)
Chr Y has a No-Call run of length 15 from position 4882982 to position 4907409 (24.43 Kb)
Chr Y has a No-Call run of length 26 from position 4927998 to position 4956740 (28.74 Kb)
Chr Y has a No-Call run of length 41 from position 4957608 to position 5012099 (54.49 Kb)
Chr Y has a No-Call run of length 28 from position 5015824 to position 5083703 (67.88 Kb)
Chr Y has a No-Call run of length 36 from position 5085510 to position 5187330 (101.82 Kb)
Chr Y has a No-Call run of length 38 from position 5203601 to position 5292479 (88.88 Kb)
Chr Y has a No-Call run of length 42 from position 5298470 to position 5366585 (68.11 Kb)
Chr Y has a No-Call run of length 89 from position 5370861 to position 5558366 (187.50 Kb)
Chr Y has a No-Call run of length 28 from position 5577743 to position 5672315 (94.57 Kb)
Chr Y has a No-Call run of length 50 from position 5680126 to position 5908658 (228.53 Kb)
Chr Y has a No-Call run of length 14 from position 5949606 to position 6006768 (57.16 Kb)
Chr Y has a No-Call run of length 13 from position 6019917 to position 6073852 (53.94 Kb)
Chr Y has a No-Call run of length 38 from position 6082930 to position 6736154 (653.22 Kb)
Chr Y has a No-Call run of length 10 from position 13938496 to position 13982729 (44.23 Kb)
Chr Y has a No-Call run of length 10 from position 28495550 to position 28539062 (43.51 Kb)

Chr 1 has a ROH of length 449 from position 60100662 to position 61256553 ( 1.16 Mb)
Chr 1 has a ROH of length 216 from position 64086901 to position 64632885 ( 0.55 Mb)
Chr 1 has a ROH of length 291 from position 94451747 to position 94502922 ( 0.05 Mb)
Chr 1 has a ROH of length 300 from position 94510164 to position 94587687 ( 0.08 Mb)
Chr 1 has a ROH of length 240 from position 100067902 to position 100744798 ( 0.68 Mb)
Chr 1 has a ROH of length 201 from position 108473016 to position 109249795 ( 0.78 Mb)
Chr 1 has a ROH of length 253 from position 155086905 to position 156010787 ( 0.92 Mb)
Chr 1 has a ROH of length 220 from position 158904114 to position 159538241 ( 0.63 Mb)
Chr 1 has a ROH of length 209 from position 179039055 to position 179678643 ( 0.64 Mb)
Chr 1 has a ROH of length 347 from position 184038151 to position 185426382 ( 1.39 Mb)
Chr 1 has a ROH of length 275 from position 223655061 to position 224707177 ( 1.05 Mb)
Chr 2 has a ROH of length 244 from position 179233041 to position 179856777 ( 0.62 Mb)
Chr 2 has a ROH of length 266 from position 234569137 to position 234706167 ( 0.14 Mb)
Chr 3 has a ROH of length 384 from position 62605941 to position 63417340 ( 0.81 Mb)
Chr 3 has a ROH of length 277 from position 65414051 to position 66139937 ( 0.73 Mb)
Chr 3 has a ROH of length 274 from position 128563551 to position 129646689 ( 1.08 Mb)
Chr 3 has a ROH of length 439 from position 147950353 to position 148962041 ( 1.01 Mb)
Chr 4 has a ROH of length 213 from position 53879085 to position 54574146 ( 0.70 Mb)
Chr 4 has a ROH of length 240 from position 131629960 to position 132600769 ( 0.97 Mb)
Chr 5 has a ROH of length 366 from position 28316657 to position 29585580 ( 1.27 Mb)
Chr 5 has a ROH of length 287 from position 129697384 to position 131556309 ( 1.86 Mb)
Chr 5 has a ROH of length 361 from position 135217810 to position 136376050 ( 1.16 Mb)
Chr 5 has a ROH of length 212 from position 143589949 to position 144465810 ( 0.88 Mb)
Chr 6 has a ROH of length 497 from position 31106177 to position 31326011 ( 0.22 Mb) (1 heterozygous SNPs treated as homozygous)
Chr 6 has a ROH of length 533 from position 31678774 to position 32127477 ( 0.45 Mb) (1 heterozygous SNPs treated as homozygous)
Chr 6 has a ROH of length 313 from position 32206687 to position 32382966 ( 0.18 Mb)
Chr 6 has a ROH of length 207 from position 111424015 to position 112182030 ( 0.76 Mb)
Chr 6 has a ROH of length 344 from position 130885909 to position 131884112 ( 1.00 Mb)
Chr 7 has a ROH of length 298 from position 1326861 to position 2393947 ( 1.07 Mb)
Chr 7 has a ROH of length 218 from position 50729681 to position 51462597 ( 0.73 Mb)
Chr 7 has a ROH of length 365 from position 86851097 to position 87229430 ( 0.38 Mb)
Chr 7 has a ROH of length 302 from position 98933689 to position 99585441 ( 0.65 Mb)
Chr 8 has a ROH of length 218 from position 79766499 to position 80576128 ( 0.81 Mb)
Chr 9 has a ROH of length 259 from position 19867614 to position 20404474 ( 0.54 Mb)
Chr 9 has a ROH of length 216 from position 34866726 to position 35685669 ( 0.82 Mb)
Chr 9 has a ROH of length 363 from position 99411960 to position 100890591 ( 1.48 Mb) (1 heterozygous SNPs treated as homozygous)
Chr 9 has a ROH of length 920 from position 105430482 to position 107686354 ( 2.26 Mb)
Chr 9 has a ROH of length 217 from position 123653598 to position 124356876 ( 0.70 Mb)
Chr 9 has a ROH of length 237 from position 130660810 to position 131609974 ( 0.95 Mb)
Chr 10 has a ROH of length 249 from position 37758910 to position 43066414 ( 5.31 Mb)
Chr 10 has a ROH of length 248 from position 98157460 to position 98903394 ( 0.75 Mb)
Chr 11 has a ROH of length 210 from position 17574588 to position 18164687 ( 0.59 Mb)
Chr 11 has a ROH of length 660 from position 99881170 to position 101399510 ( 1.52 Mb)
Chr 12 has a ROH of length 445 from position 9029686 to position 10192794 ( 1.16 Mb)
Chr 12 has a ROH of length 234 from position 18276779 to position 18884896 ( 0.61 Mb)
Chr 13 has a ROH of length 215 from position 63969262 to position 64727530 ( 0.76 Mb)
Chr 14 has a ROH of length 204 from position 75186450 to position 75879718 ( 0.69 Mb)
Chr 15 has a ROH of length 403 from position 27505136 to position 28924405 ( 1.42 Mb) (1 heterozygous SNPs treated as homozygous)
Chr 15 has a ROH of length 305 from position 48211710 to position 48988951 ( 0.78 Mb)
Chr 15 has a ROH of length 326 from position 79321517 to position 80011975 ( 0.69 Mb)
Chr 15 has a ROH of length 289 from position 96186627 to position 96806647 ( 0.62 Mb)
Chr 16 has a ROH of length 544 from position 2085295 to position 2208889 ( 0.12 Mb) (1 heterozygous SNPs treated as homozygous)
Chr 16 has a ROH of length 231 from position 31542415 to position 47060239 (15.52 Mb)
Chr 16 has a ROH of length 211 from position 80937545 to position 81278265 ( 0.34 Mb)
Chr 16 has a ROH of length 260 from position 83656056 to position 83995250 ( 0.34 Mb)
Chr 17 has a ROH of length 202 from position 46474118 to position 47053828 ( 0.58 Mb)
Chr 19 has a ROH of length 235 from position 11651810 to position 12636822 ( 0.99 Mb)
Chr 20 has a ROH of length 278 from position 37923447 to position 38669077 ( 0.75 Mb)
Chr 21 has a ROH of length 468 from position 44823479 to position 46097193 ( 1.27 Mb)
Chr 21 has a ROH of length 208 from position 47571209 to position 48100155 ( 0.53 Mb)

Kamane
06-17-2013, 06:10 PM
pt. 2:


Chr 1: 73.674 % (56662 of 76909 SNPs) are homozygous, 1898 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 2: 70.711 % (54692 of 77346 SNPs) are homozygous, 1829 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 3: 72.137 % (45652 of 63285 SNPs) are homozygous, 1560 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 4: 70.727 % (38912 of 55017 SNPs) are homozygous, 1337 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 5: 70.169 % (39308 of 56019 SNPs) are homozygous, 1358 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 6: 72.118 % (45610 of 63244 SNPs) are homozygous, 1729 No-Calls, 2 heterozygous SNPs treated as homozygous
Chr 7: 71.475 % (36427 of 50965 SNPs) are homozygous, 1333 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 8: 69.410 % (34160 of 49215 SNPs) are homozygous, 1253 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 9: 71.656 % (30790 of 42969 SNPs) are homozygous, 1074 No-Calls, 1 heterozygous SNPs treated as homozygous
Chr 10: 69.882 % (35166 of 50322 SNPs) are homozygous, 1207 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 11: 71.283 % (34196 of 47972 SNPs) are homozygous, 1207 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 12: 72.032 % (33945 of 47125 SNPs) are homozygous, 1209 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 13: 71.298 % (25723 of 36078 SNPs) are homozygous, 852 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 14: 72.383 % (22307 of 30818 SNPs) are homozygous, 815 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 15: 71.127 % (20200 of 28400 SNPs) are homozygous, 691 No-Calls, 1 heterozygous SNPs treated as homozygous
Chr 16: 71.900 % (21690 of 30167 SNPs) are homozygous, 843 No-Calls, 1 heterozygous SNPs treated as homozygous
Chr 17: 73.685 % (19665 of 26688 SNPs) are homozygous, 778 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 18: 70.637 % (19758 of 27971 SNPs) are homozygous, 593 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 19: 73.107 % (13549 of 18533 SNPs) are homozygous, 665 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 20: 72.694 % (17326 of 23834 SNPs) are homozygous, 566 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 21: 72.792 % ( 9757 of 13404 SNPs) are homozygous, 345 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 22: 69.837 % ( 9847 of 14100 SNPs) are homozygous, 522 No-Calls, 0 heterozygous SNPs treated as homozygous

Chr X: 5.502 % ( 1431 of 26007 SNPs) are homozygous, 1128 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr Y: 1766 SNPs, 1023 No-Calls, 0 heterozygous SNPs treated as homozygous
mtDNA : 2459 SNPs, 106 No-Calls, 0 heterozygous SNPs treated as homozygous

Total autosomal (Chr 1-22): 2.543 % ( 23664 of 930381 SNPs) are NoCalls
Total autosomal (Chr 1-22): 28.487 % (265039 of 930381 SNPs) are Heterozygous (this tally excludes 5 heterozygous SNPs that were treated as homozygous)
Total autosomal (Chr 1-22): 71.513 % (665342 of 930381 SNPs) are Homozygous (this tally includes 5 heterozygous SNPs that were treated as homozygous)

Ian B
06-19-2013, 02:03 AM
OK, but for the benefit of a newcomer, what does it all mean?

BMG
08-22-2013, 01:18 PM
ROHs of length at least 200 will be reported.
No-Call runs of length at least 10 will be reported.
No-Calls will be treated as homozygous.
Heterozygous SNPs that are at least 150 SNPs away from the nearest heterozygous SNP will be treated as homozygous.

Chr 1 has a ROH of length 250 from position 90360894 to position 91391381 ( 1.03 Mb)
Chr 5 has a ROH of length 513 from position 107157057 to position 109525303 ( 2.37 Mb)
Chr 6 has a ROH of length 327 from position 34600990 to position 35643648 ( 1.04 Mb)
Chr 11 has a ROH of length 317 from position 80023860 to position 80950946 ( 0.93 Mb)
Chr 12 has a ROH of length 227 from position 100516973 to position 101487777 ( 0.97 Mb)
Chr 14 has a ROH of length 292 from position 41787965 to position 43365045 ( 1.58 Mb)
Chr 16 has a ROH of length 217 from position 35143083 to position 47037436 (11.89 Mb)

Chr 1: 70.955 % (41476 of 58454 SNPs) are homozygous, 31 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 2: 70.051 % (39902 of 56961 SNPs) are homozygous, 31 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 3: 69.750 % (32509 of 46608 SNPs) are homozygous, 30 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 4: 69.415 % (27730 of 39948 SNPs) are homozygous, 16 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 5: 69.989 % (29103 of 41582 SNPs) are homozygous, 14 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 6: 70.188 % (33317 of 47468 SNPs) are homozygous, 23 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 7: 69.856 % (26270 of 37606 SNPs) are homozygous, 23 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 8: 67.415 % (24639 of 36548 SNPs) are homozygous, 17 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 9: 69.933 % (22661 of 32404 SNPs) are homozygous, 17 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 10: 70.475 % (27226 of 38632 SNPs) are homozygous, 21 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 11: 69.684 % (25186 of 36143 SNPs) are homozygous, 24 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 12: 70.327 % (24672 of 35082 SNPs) are homozygous, 16 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 13: 68.976 % (18976 of 27511 SNPs) are homozygous, 16 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 14: 70.091 % (16121 of 23000 SNPs) are homozygous, 8 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 15: 70.030 % (14985 of 21398 SNPs) are homozygous, 7 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 16: 69.664 % (15657 of 22475 SNPs) are homozygous, 10 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 17: 70.162 % (14010 of 19968 SNPs) are homozygous, 3 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 18: 71.107 % (15276 of 21483 SNPs) are homozygous, 7 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 19: 67.904 % (10096 of 14868 SNPs) are homozygous, 7 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 20: 71.214 % (12963 of 18203 SNPs) are homozygous, 6 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 21: 69.340 % ( 7011 of 10111 SNPs) are homozygous, 3 No-Calls, 0 heterozygous SNPs treated as homozygous
Chr 22: 70.424 % ( 7253 of 10299 SNPs) are homozygous, 3 No-Calls, 0 heterozygous SNPs treated as homozygous

Total autosomal (Chr 1-22): 0.048 % ( 333 of 696752 SNPs) are NoCalls
Total autosomal (Chr 1-22): 30.099 % (209713 of 696752 SNPs) are Heterozygous (this tally excludes 0 heterozygous SNPs that were treated as homozygous)
Total autosomal (Chr 1-22): 69.901 % (487039 of 696752 SNPs) are Homozygous (this tally includes 0 heterozygous SNPs that were treated as homozygous)

Processing Completed.