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DNAChron A New High Precision Y-chromosome Haplogroup Tree, Free To Upload Now!
Introduction
DNAChron is a new upload site for Y chromosome DNA sequencing data on Y-chromosome haplogroup tree. DNAChron is not just another Y tree, because of not satisfied with current Y trees's age estimated method, which discard almost half of all SNPs, and all INDELs, that lead to loss on accuracy. We developed a new algorithm to get as much as possible precision on mutation analysis and age estimation, then DNAChron is born.
We hope this new algorithm can make help to discover more unknown history. Chronicle your unique story in the past.
Overview
- High precision mutation analysis. On average, we can find 30%~100% more mutations per haplogroup than other Y-trees. Based on the existing data, more private mutations can be found for you. Find more subclades that can be merged on the rapid expanded haplogroup, clarify the relationship between haplogroups. Your newly discovered mutation will be named with prefix C (Chronicle).
- Analyse in whole Y-chromosome sequence, totally use 18M data. Free to remap bam/cram/fastq data with Hg38 reference while retain the data mapping to T2T reference(CP086569.2). Activate the potential of your whole genome sequencing data.
- High precision age estimation. We can provide the probability distribution diagram of different years. The pricision of effective age estimation is increased by 3~5 times.
- Real age estimation, when dealing with continuous expand haplogroups, like R-L151, there will be no age contradiction between upstream and downstream, and there will be no deviation between age difference and mutation number between haplogroups. Solve the systematic deviation of the traditional algorithm that the more subclades, the smaller the estimation age is.
- Provide matching between ISOGG of different versions and YTree. Help quickly understand the main haplogroup. Help find the corresponding relationship between the historical ISOGG ID found in a large number of papers and network information and the current haplogroup.
- For samples with low coverage of sequencing data, it can also show you which subclades may be merged with in addition to the current tree location, or even belong to the downstream of a sibling subclade. That is, the tree uncertainty.
- By registering, you can browse the analysis results and raw data of more than 7000 public samples.
- Rapid, automatically and standardized analysis process. You can get result within 3 working days after importing data.
- Abundant function: mutation, haplogroup and ISOGG search, browsing raw data, browsing reference sequence, browsing mutation info, personal information publish, etc.
- Datacenter in Singapore.
- The DNAChron Y-tree is under construction, FREE to upload now!
DNAChron VS Others
|
DNAChron |
Others |
| Mutation analysis precision |
On average, 60 years per mutation. It is easier to clarify the rapid expanded haplogroup. |
On average, 80~100 years per mutation. |
| Confidence interval |
Yes, with probability distribution diagram |
Provide 95% CI range, or nothing. |
| True confidence interval |
Yes |
The age is estimated according to fixed around 8M data range, which does not change with sample. Nowadays, commercial sequencing can cover more than 14M. |
| Age estimation precision |
Highest precision can reach 60 years per mutation. |
Fix to more than 100 year per mutation |
| Real age estiamtion |
Yes |
The relationship between upstream and downstream is not considered. May have age contradiction between upstream and downstream, and there may be serious deviation between age difference and mutation number between haplogroups |
| Accuracy of age estimation increases with the number of samples |
Yes |
When the number of samples and subclades increases to a certain extent, the accuracy cannot be further improved due to the contradiction between upstream and downstream age estimation. |
Snapshots （Can't paste image now）
New find in widely known Haplogroups:
Age estimations :
No contradiction age estimation between upstream and downstream:
Browse public sample:
Browse historical ISOGG tree, and get it's matching YTree node:
Information publication:
High Precision Mutation Analysis
- No pre-defined mask region, all region on Y-chromosome will be analysed. DNAChron can find out small piece of stable region in many traditionally discarded regions.
- The stability of each muation is verified by whole y-tree.
- Support to find SNP, INDEL and MNP/complex
On average, we can find 30%~100% more mutations per haplogroup than other Y-trees.
High Precision Age Estimation
- With the benefit of high precision mutation analysis, the tree is more accuracy, and we can find more mutations for age estimation.
- All 18M bases are used for age estimation, and include every muation type: SNP, INDEL, MNP/complex. DNAChron can get a much higher mutation rate than traditional algorithm.
- The calculation of mutation rate depends on the actual sample coverage, data include low coverage data and whole sequence data can get it's real age estimateion probability distribution.
- The probability distribution can transfer between haplogroups, there will be no age contradiction between upstream and downstream, and there will be no deviation between age difference and mutation number between haplogroups.
- Each haplogroup's age estimation have an extra independent condition from upstream.
Mutations
To provide an offline, standard, batch process tools for conversion and search on mutation names and positions from ybrowse. We create a github repository dnachronYdb .
- Download only the delta, don't need to download whole hundreds of megabytes data every time.
- Exceed the max 1048576 row limitation of Excel, can search on all mutation info at one time.
- Using database index, search mutation names and positions efficiently.
- Standardize indel mutation, left alignment, and unify REF and ALT formats.
- Add additional mutation naming date. For mutations with repeated name, the earliest name can be selected according to the naming date.
- Using the database format, you can use program to batch process mutation names and position conversion. Please check the processing tools we provide. Github repository dnachronYdb-putils .
Privacy & Security
DNAChron will store your registration information, tester information, analysis result information and genetic information data separately on the cloud, and protect them in all aspects through reasonable and feasible security measures such as technology, hardware and management process.
Detail privacy policy please view on the website.
Reference
The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes
Generation of high-resolution a priori Y-chromosome phylogenies using “next-generation” sequencing data
The Y-chromosome point mutation rate in humans
Defining a New Rate Constant for Y-Chromosome SNPs based on Full Sequencing Data
Improved Models of Coalescence Ages of Y-DNA Haplogroups
The study of human Y chromosome variation through ancient DNA
Present-Day DNA Contamination in Ancient DNA Datasets
Computational challenges in the analysis of ancient DNA
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