A Third of Mitochondria in Chromosome 1

[felix]

Configuration Guide for Y-STR Kit

I uploaded a small configuration guide here, which helps to fix any problems in Y-STR Kit

Configuration Guide: Y-STR Kit Guide.pdf

This helps to resolve any Y-STR issues.

[felix]

For DYS393, there are only 12 repeats and the motif is correct in all places I looked. Hence, I am not sure how FTDNA calculates the value to have 13.

For DYS390, the last 2 repeats does not match with the motif and doing a manual count leads to only 25 matching FTDNA instead of 27 because...

[felix]

No I need the details.

When you click on the numbers, it will take you to the actual repeat display. That's what I want to see....

[felix]

If DYS 303 and 390 are 100 reliable, you go to the details and count the repeats yourself to see the value you getting for Y-STR. That's exactly what is in the BAM.

I can fix if the repeats are different when counted manually and what the program reports at the top. However, I cannot...

[felix]

What is the reliability of those values? If the program says not reliable, then they are not to be used and will be off....

[felix]

The only problem is, 99% reliable isn't really 99% accurate value because it takes only the available sites into consideration for reliability calculation and that 1% still has a 50% change of mutation on one site which can reduce the Y-STR values to 1 or 2. I compared my results with Y-DNA 64 with...

[felix]

So 4 values in YDNA12 match, which is good to hear. For (null or 0) I believe there are are no values in the Y location. Regarding -2 and -1 deltas, are they unreliable? What are the reliability percentages? If you click on the numbers, you can actually go down to look into the repeats and the missing...

[felix]

Fixed the bug and reuploaded....

[felix]

The differences can be fixed. How much is the difference? Just 1 or 2? How does the detailed fasta like display with actual repeats look for those mismatches?...

[felix]

It's late here and will fix this bug by tomorrow.

But, if you place the BAM file in a path that doesn't have spaces, does it work? How much is it accurate and the reliability percentage?...

[felix]

Finally, I was able to write a tool to extract Y-STR from BAM myself. The tool is at the below link.

Link: Y-STR Kit

Let me know if there are any inconsistencies in Y-STR values.

It can extract all the 111 FTDNA Y-STR panel markers....

[felix]

These tools are not accurate since it is based on imputations. To confirm, you must do the actual tests with FTDNA....

[felix]

RSRS version 2



Yes, I am very much interested. Since these are non random and are from mtDNA originally, this will help in correcting the RSRS sequence details using data from chromosomes by aligning several overlapping sequence occurring in multiple locations.
...

[felix]

When I was doing some research on human genome, I noticed that a third of Mitochondria is also located within Chromosome 1. The MtDNA RSRS sequence from 3914 to 9730 position is identical to the chromosome segment from position 629084 to 634899 (GRCh38) or position 564464 to 570279 (ucsc/hg19). It is...

[felix]

If you had done your autosomal DNA testing and you want to know the genotype of an untested SNP, this is the tool. SNP prophet predicts your genotype for an untested SNP using your autosomal DNA. It has an offline version and an online version.The offline is huge but does not require any internet, nor...