# Mother doesn't match, but maternal cousin does

### Mother doesn't match, but maternal cousin does

Posted: 1365281633000
Classification: Query
This post was deleted by the author on 21 Apr 2014 2:20AM GMT

### Re: Mother doesn't match, but maternal cousin does

Posted: 1365290023000
Classification: Query
Do you have access to the raw data for your 2C1R (the shorthand I use for second cousin once removed in my spreadsheet)? If so, you could run David Pike's utility to compare yourself and your mother to the 2C1R. Every segment where you and your 2C1R match should be found in your mother.

http://www.math.mun.ca/~dapike/FF23utils/pair-comp.php

Now you and your 2C1R could match the Hagler in different places, so this experiment doesn't necessarily prove anything for that riddle. It's just a way of confirming that things are proceeding in an orderly fashion for the three of you. If your Hagler connection is interested in pursuing this, his/her raw data would probably clear up the mystery.

### Re: Mother doesn't match, but maternal cousin does

Posted: 1365295829000
Classification: Query
This post was deleted by the author on 21 Apr 2014 2:21AM GMT

### Re: Mother doesn't match, but maternal cousin does

Posted: 1365358492000
Classification: Query
I didn't mention this, but the default value of 500 consecutive matching SNPs is probably too low for the current chips. I'd suggest 1000 SNPs nowadays. That trims the list of matching segments down to these.

Chr 1 length 26559 from position 33419206 to position 165047786 (131.63 Mb)
Chr 1 length 2636 from position 165355350 to position 174969271 ( 9.61 Mb)
Chr 1 length 2779 from position 235760817 to position 244544458 ( 8.78 Mb)
Chr 3 length 3196 from position 61495 to position 8055996 ( 7.99 Mb)
Chr 4 length 2608 from position 71566 to position 10105797 ( 10.03 Mb)
Chr 5 length 5483 from position 150901699 to position 172067768 ( 21.17 Mb)
Chr 6 length 1379 from position 98896667 to position 106006902 ( 7.11 Mb)
Chr 6 length 4325 from position 137617136 to position 154274843 ( 16.66 Mb)
Chr 8 length 4644 from position 129309414 to position 146293414 ( 16.98 Mb)
Chr 9 length 1612 from position 134355421 to position 139033054 ( 4.68 Mb)
Chr 10 length 10991 from position 31086001 to position 80959517 ( 49.87 Mb)
Chr 10 length 2808 from position 125254416 to position 132603123 ( 7.35 Mb)
Chr 13 length 2256 from position 108473323 to position 115103529 ( 6.63 Mb)
Chr 15 length 1191 from position 27311111 to position 33259043 ( 5.95 Mb)
Chr 15 length 4665 from position 62095573 to position 83250767 ( 21.16 Mb)
Chr 15 length 5342 from position 87162259 to position 102398631 ( 15.24 Mb)
Chr 18 length 3119 from position 13034 to position 8894977 ( 8.88 Mb)
Chr 21 length 1464 from position 28147728 to position 33522718 ( 5.37 Mb)

Assuming the list you posted is for yourself vs your maternally related cousin, all of those segments should also appear in your Mom.

The starting and ending points don't need to be exact. There are two reasons your segment boundaries might not match the ones in your Mom's list. One is recombination: she may not have given you the entire segment.

The other is "fuzzy boundaries." We are only checking to see if at least one of your two alleles is the same as at least one of your match's two alleles. We don't actually know which of your alleles came from your father and which from your mother. Sometimes a few paternal alleles can make it appear that the long consecutive run of half-identical SNPs is continuing.

### Re: Mother doesn't match, but maternal cousin does

Posted: 1388515844000
Classification: Query
You might also upload them to gedmatch.com . I think it's very easy to use and has a 3D Chromosome viewer that shows where you intersect. You can list several people in this at the same time
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