Regarding the title, I would like to emphasize, assuming no recent endogamy. To be clear, let's say they're distant enough that any endogamy would be expected to be less than 5 continuous centimorgans. Another way of asking this is "Do the different chromosome pairs have matches independently of each other?"
I was working on trying to manually join my father and my cousins' raw DNA files in specific areas to strengthen a target person's match results in a similar manner as the Lazarus tool found on GEDMATCH.com.
Side note: the Lazarus tool isn't an option because I don't have the raw DNA files for each person who I know has matching segments to my target person, so I have to infer segment sequences based on the raw data I do have.
I see that there are two alleles, one from each chromosome pair inherited by my father.
My question is whether both of those alleles from each chromosome that are paired have independent matches on the same segment or is it such that on any given segment only paternal matches or only maternal matches can be there regardless of there being two complete copies of each chromosome?
Are these DNA strands more like a coin with two sides and each side can have its own paternal or maternal matches along equivalent segments?
So far, in the DNA painting I've been doing, I see very little overlap between paternal and maternal matches, so this could just be fuzzy areas on the ends from differences in testing services and perhaps some endogamy 5 or 6 generations ago in a couple of places.
If I were to 100% complete this DNA paint-job, should I expect that half of each paternal side and each maternal side will remain blank, or should I expect 100% coverage of each chromosome paired for a total of 46 fully-accounted-for chromosomes? I understand that won't happen in reality due to data unavailability, but theoretically, for the purpose of clarification, I am asking this.
Hypothetical: Chromosome 1 from position 12,000,000 to 180,000,000 there is a matching relative on my grandfather's side, does that mean the match is only for one of the chromosome pairs and there are really two different "Chromosome 1, 12,000,000 - 180,000,000" one for my grandmother, and one for my grandfather such as a "Chromosome 1A" and "Chromosome 1B" each with independent sequences to find matches for?
For example, chromosome 6 in this image contains a significant section where I have known matches for paternal and maternal ancestors. Does this imply endogamy, or is this expected and does not imply endogamy and I simply haven't added enough data to encounter this in many places yet?