{"id":7498,"date":"2018-11-01T17:45:10","date_gmt":"2018-11-01T17:45:10","guid":{"rendered":"http:\/\/www.jmhartley.com\/HBlog\/?p=7498"},"modified":"2018-11-01T17:45:10","modified_gmt":"2018-11-01T17:45:10","slug":"visual-phasing-six-siblings-with-the-fox-spreadsheet-part-3-chromosome-2","status":"publish","type":"post","link":"http:\/\/www.jmhartley.com\/HBlog\/2018\/11\/01\/visual-phasing-six-siblings-with-the-fox-spreadsheet-part-3-chromosome-2\/","title":{"rendered":"Visual Phasing Six Siblings with the Fox Spreadsheet: Part 3 – Chromosome 2"},"content":{"rendered":"

In Part 1<\/a>, I downloaded the Steven Fox Spreadsheet and built up the information for six siblings and 17 cousins. Then I did the visual phasing on the X Chromosome. In Part 2<\/a>, I finished Chromosome 1 for 6 siblings, with a heavy dependence on cousin matches.<\/p>\n

Visual Phasing Chromosome 2<\/h2>\n

Here are the 15 comparisons for my six siblings. There are 5, 4, 3, 2, then 1 comparison. I think that is where the 15 comes from.<\/p>\n

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I don’t see too many odd things here.<\/p>\n

Here I added a bunch of crossovers. I don’t know if it is better to put in too few and add later or too many and erase later. I’m not too worried if I have them perfect as I will be checking them against cousin matches.<\/p>\n

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I’ll start with cousin Maury. I think that’s how his name is spelled. Where we match represents the DNA I got from my paternal Hartley grandfather:<\/p>\n

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I need to stick the blue matches above for Jim, Joel, Heidi and Lori. I see one crossover for Heidi where her Hartley DNA stops and above and below her, Jim and Lori’s Hartley DNA continues on to the right. To the right of Heidi’s crossover, the only other choice on the paternal side is Frazer, so I’ll add that in.<\/p>\n

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I have the first crossover identified. It is for Heidi, it is paternal and it is at position 53.5M. I’ll put this into a spreadsheet as it is helpful information to have if you ever do raw data phasing or if you want to add your grandparents to Gedmatch:<\/p>\n

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[The M for Heidi is wrong. It should be a P.]<\/span><\/p>\n

I could also infer that the segments above and below the Hartley matches would be Frazer matches. I’ll add those now. If I’m wrong, I can correct them later. However, again, on the paternal side, there are two choices from where the DNA came from.<\/p>\n

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Adding a Maternal Cousin Match to Chromosome 2<\/h3>\n

Cousin Anita is a Rathfelder cousin.<\/p>\n

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It looks like there are few crossovers here. However, the representations of where the relative positions of the matches are can be misleading. I think that I will try assign as many crossovers as I can. Here is what I get from Anita’s matches:<\/p>\n

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Here is a summary of the crossovers from the first two cousin matches:<\/p>\n

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I didn’t get a position number for Jim’s crossover as they are not displaying correctly on the spreadsheet.<\/p>\n

Next, Check the Gedmatch Comparisons<\/h3>\n

Here is one issue I see right away:<\/p>\n

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In the Gedmatch comparison between Heidi and Lori, there is a no match area between Segment H and F in red. The answer appears to be that Heidi has an additional crossover in the area of the L and F maternal crossovers at 103 and 105M. The Heidi crossover should be at about 104, based on the Heidi and Jim (V) comparison:<\/p>\n

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In Lori’s crossover, she went from Rathfelder to Lentz. In order for Heidi and Lori to continue not matching, Heidi needs to change from Lentz to Rathfelder.<\/p>\n

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The above gedmatch comparison is Lori compared to Heidi. Between crossovers L and H there is a very short segment where Lori and Heidi are HIR. They don’t match H to L. Then L to H they match on Lentz (green) only. Then Heidi and Lori go back quickly to not matching again.<\/p>\n

Cousin Joyce on the Hartley Side<\/h3>\n

Cousin Joyce has some Hartley segments for the left side of my family’s Chromosome 2:<\/p>\n

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These matches start at about zero and go to 9M. That is at about the third vertical line above (crossover) belonging to D who is me (Joel). This causes a problem as it goes through Sharon’s crossover. When I look more closely, I see that Sharon’s crossover is at 9M and mine is at 12M:<\/p>\n

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That means I have to bring back the orange one small segment:<\/p>\n

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While I was working on this, I made a guess that I (D) had a paternal crossover right after Sharon. I put this into my spreadsheet:<\/p>\n

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At 7M, I have a crossover for Lori, but I don’t know if it is maternal or paternal yet. I also looked up the last crossover position for Jim at gedmatch.<\/p>\n

It looks like Joyce could help clean up the right side of Chromosome 2:<\/p>\n

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The bottom blue bar is for Heidi and it shows her crossover. Heidi’s crossover is at 226M. Note that I show three crossovers in a row above, but only have two initials. I’ll say that the extra crossover is for Heidi:<\/p>\n

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The circled areas are in the comparison of Jim (V) to Heidi and Jon (F) to Heidi. Heidi is common in both. I had mentioned in a previous Blog that a change from no match to FIR or from FIR to no match could indicate a crossover for a person on a paternal and maternal side in close succession. That appears to be the case here.<\/p>\n

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The spreadsheet is important, because the visual part of visual phasing can throw you off. That means that the visuals don’t always line up well, so it is important to depend on the position numbers. This is especially important where the crossovers are close together.<\/p>\n

Here are Heidi’s crossovers on the right:<\/p>\n

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This creates another problem as Heidi’s Lent in Green has to get back to purple Rathfelder on the left, and I don’t have any crossovers for Heidi between the two. This means that either Heidi doesn’t have a crossover on the left or she needs another in the middle. Confused? You bet I am. I’ll worry about this later.<\/p>\n

Deciphering the Right End of Chromosome 2 – Paternal Side<\/h3>\n

Hartley cousin Beth helps figure out the right hand side of the Chromosome. Ends of Chromosomes can be difficult to interpret.<\/p>\n

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Lori’s match is off by about one half million positions from the other three matches. I don’t know if that is significant. It may indicate a crossover that I don’t have.<\/p>\n

Here is how I started to fill in the right hand side of Chromosome 2:<\/p>\n

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