DCG Cladogram Upgrades
Posted: Mon, 2022-Feb-14 7:22 am
A few small upgrades were made to the DCG Cladogram:
In a related note, we are preparing to move the DCG Cladogram to the new, experimental CP086569.2 reference Y chromosome that has been released recently by the Telomere-To-Telomere Consortium. It is hoped this is the beginning of COMPLETE Y chromosome testing. Commercially available testing technology is still slightly lagging in the ability to accurately sequence the complete Y chromosome. The cost and error rate of Long Read Sequence (LRS) technologies such as Oxford Nanopore Technologies and PacBio HiFi reads are dropping and it is hoped that within the next couple of years we will see commercial testing services offering LRS tests of 50,000 bp or higher reads instead of today's technology of 100 to 400 bp reads. That is over 100X improvement. This should eliminate all the current problematic regions of the Y chromosome that are too repetitive for today's short reads to accurately sequence.
- Each clade now shows by small icons at the bottom of the clade box which Y-Haplotrees it can be found on.
- Each mutation within a clade phylogenetic node (box) will now also show which Y-Haplotrees it can be found on in the pop-up box that appears when the mouse hovers over the mutation name. The identification consists of 3 letter designations that are hopefully self evident: FTD (Family Tree DNA), TBT (The Big Tree), YFL (YFull), YDW (YDNA Warehouse), and YSQ (YSEQ GmbH).
- The YFull R1b-DF104 Live YTree has been incorporated into the DCG Cladogram as much as it can be. Since there is no public cross reference between YFull IDs and FTD IDs, the men on the YFull Live YTree cannot be added to the DCG Cladogram, just the clades. There is not always a perfect fit even with the clades due to the different data samples each analysis company works with.
In a related note, we are preparing to move the DCG Cladogram to the new, experimental CP086569.2 reference Y chromosome that has been released recently by the Telomere-To-Telomere Consortium. It is hoped this is the beginning of COMPLETE Y chromosome testing. Commercially available testing technology is still slightly lagging in the ability to accurately sequence the complete Y chromosome. The cost and error rate of Long Read Sequence (LRS) technologies such as Oxford Nanopore Technologies and PacBio HiFi reads are dropping and it is hoped that within the next couple of years we will see commercial testing services offering LRS tests of 50,000 bp or higher reads instead of today's technology of 100 to 400 bp reads. That is over 100X improvement. This should eliminate all the current problematic regions of the Y chromosome that are too repetitive for today's short reads to accurately sequence.