MAS Solutions Genealogical Research Platform

Research platform

A workbench for the Sudanese J1 lineage.

A curated Y-DNA reference collection for the Sudanese J1 (J-M267) cluster centred on J-FGC15175, with tools to place a haplotype on the project tree, read the phylogeny, measure genetic distance, and date divergences — built for the genetic-genealogy and research community.

The tools

BY3 Placement

Compare a haplotype to the curated project members: nearest matches, core-cluster judgement, and candidate subclades. Honest by design — names a cluster, not a guaranteed terminal SNP.

BY3 Tree

The project phylogeny from J-BY2 down through the core node J-FGC15175, with member counts at every node.

Y-STR Distance

Genetic distance between two Y-STR haplotypes with correct multi-copy marker handling (FTDNA infinite-allele model).

TMRCA

Time to most recent common ancestor with a 95% interval — SNP-based (preferred) or STR-based, assumptions stated.

cM Predictor

Turn shared centimorgans into ranked candidate relationships (Shared cM Project v4.0).

Reference

Haplogroup nomenclature, tree versions, testing platforms, and a working glossary.

Scope: genealogy & research only. This platform does not interpret medical or health variants — that requires a licensed clinician. TMRCA and relationship figures are model-dependent estimates; always cite the tree build behind any claim.

About this platform

Compiled & developed by

Mustafa Adil Suhail

Independent Researcher in Manuscripts & Genealogy
Bachelor of Science — Medical Laboratories
Hematology & Immunology

For inquiries: Mustafa.adil.suhail@gmail.com

With the support of the Jaalyeen Genealogy Project on FamilyTreeDNA.

A MAS Solutions research initiative. © MAS Solutions — the reference collection and its compilation are proprietary to MAS Solutions and provided for research reference only; data may not be exported, copied, or redistributed.

Autosomal relatedness

Shared-ancestor estimator.

Enter how many centimorgans (cM) two people share on an autosomal test (FTDNA Family Finder, 23andMe, Ancestry, MyHeritage). The tool translates that into roughly how far back their common ancestor sits — in plain words. Ranges are the real Shared cM Project v4.0 (Bettinger, 2020).

Total shared cM

Largest segment cM (optional)

Married within the same lineage / community (endogamy) — tick if, over generations, this line has mostly married within the same tribe or extended family (very common, and normal). Shared DNA is higher in this case, so the common ancestor is usually further back than a standard reading suggests.

Autosomal cM measures overall relatedness across all lines — not the paternal (nasab) line specifically. For the direct male line, Y-STR / SNP is the evidence; cM is supporting, and it is sensitive to intermarriage. For exact relationship-probability percentages (from Ancestry’s simulations), cross-check DNA Painter — note it assumes no endogamy.

Y-STR Genetic Distance

FTDNA modified infinite-allele model. Enter markers as NAME=value, comma-separated. Multi-copy markers use hyphens, e.g. DYS385=11-14, DYS464=12-14-15-16.

Kit A haplotype Kit B haplotype

BY3 Subclade Placement

For haplogroup J1 (J-M267) and its downstream branches. Your haplotype is compared to the loaded project members: the tool finds your nearest known members, judges whether you sit inside the core cluster or on an outlier branch (by distance to the group modal), and lists the candidate subclades. In a tight J1 group STRs place you in a cluster but rarely pin the exact terminal SNP — Big Y does that.

Query haplotype (NAME=value, comma-separated; multi-copy hyphenated, e.g. DYS385=13-19, DYS464=12-14-16-17)

Hold-out mode — exclude exact (GD 0) matches before predicting. Use when the sample is already in the reference set, so you get a genuine prediction rather than a lookup.

Force a side call — always assign a parent side (J-FGC15168 / J-FGC72765 / J-FTH24463) by nearest side-modal, even when it's a near tie. STR only, ~70% reliable in leave-one-out, not confirmed. For comparison against the honest mode above.

Have your own Y-STR results from FTDNA, YSEQ, YFull or any other provider (a row of marker names + one row of values)? Use Load STR results (CSV) to place that sample against the collection — any CSV whose columns are standard marker names (DYS…, YCAII, CDY, Y-GATA-H4) is accepted. Your file is read in the browser and is not stored.

Reference set

A curated collection of de-identified J1 project members (ID, subclade, country, STR markers — personal names are never stored). The collection is read-only; the two tools below show how the method performs and the group’s consensus haplotype, without exposing individual records.

Placement is honest by design: it names your cluster and closest branches, not a guaranteed terminal SNP. Confirm the subclade with Big Y-700 (or a J1 SNP pack), and cite the tree build (ISOGG/YFull).

Phylogeny

BY3 Project Tree.

The phylogeny of the curated reference collection, rooted at J-BY2 and running down through the core node J-FGC15175. Each node shows how many members sit in that subtree. Click a node to list its members. Branch labels are SNP-only.

Core cluster (J-FGC15175) J-FGC15168 side J-FGC72765 side J-FTH24463 side other node FTDNA+ = terminal branch also attested on FamilyTreeDNA (samples outside the project)

Click any node above to see its members.

TMRCA Calculator

Time to Most Recent Common Ancestor, with a 95% confidence interval. SNP-based dating (Big Y / WGS) is far more reliable than STR-based; both are shown with their assumptions stated. Poisson CI via Byar's approximation.

Method

Generation length (yrs)

"Present" calendar year

Reference

Quick, citable facts. Tree versions move — confirm live builds where noted.

Current tree & reference versions to cite

YFull YTreeVersioned (v11, v12, v13…). Confirm the live build at yfull.com; don't quote a version from memory. ISOGG Y-treeLong-running community Y-DNA tree (isogg.org/tree). PhyloTree mtBuild 17 (18 Feb 2016) — still the last official mtDNA build. Reference seqsrCRS (default difference reference) and RSRS (phylogenetically rooted). Shared cM Projectv4.0 (March 2020), hosted on DNA Painter.

File formats

Chain: FASTQ reads → align → BAM/SAM → call → VCF variants. FASTA = reference/consensus sequence.

Format	What it is	Genealogy use
FASTQ	Raw reads + Phred quality	Read counts / QC (pre-alignment)
FASTA	Sequence, no quality	Reference (rCRS), consensus regions
BAM/SAM	Aligned reads (BAM = binary)	Coverage/depth at a SNP; feeds YFull
VCF	Variants vs reference	Y-SNP / mt calls → haplogroup
Vendor raw	Array genotype table (~600–700k)	Autosomal matching; top-level Y/mt only

Phred quality scores

Q201% error — acceptableQ300.1% error — good (common threshold)Q400.01% error — high

Illumina uses Phred+33 encoding. Always check depth AND quality before trusting a single call.

Haplogroup nomenclature

Prefer terminal-SNP shorthand (e.g. R-M269, I-M253, J-M267) over unstable long-form (R1b1a2). Your terminal SNP = the deepest confirmed-derived SNP you carry. STRs match & estimate time; SNPs define the tree.

Testing platforms

Platform	Tech	Y / mt	Autosomal
FamilyTreeDNA	Array + NGS	Y-37/67/111, Big Y-700 · mtFull	Family Finder
YSEQ	Sanger/NGS/WGS	SNPs, packs, WGS	—
YFull	BAM analysis	YTree, TMRCA, novel variants	—
23andMe	Array ~600k	top-level only	yes (+health)
AncestryDNA	Array ~700k	none reported	yes (largest DB, no browser)
MyHeritage	Array	—	yes (has browser)
Nebula	WGS 30×	full resolution	yes (FASTQ/BAM/VCF)

Glossary

cMCentimorgan — unit of genetic distance; total shared cM indexes relatedness. IBD / IBSIdentical by descent (real shared ancestor) vs by state (chance); segments <7 cM often IBS. EndogamyIntermarriage within a closed group inflates shared cM; matches look closer than they are. SNP / STRSNPs define haplogroups (near-permanent); STRs mutate fast, used for matching. Terminal SNPDeepest branch-defining SNP you're confidently derived (+) for. TMRCATime to most recent common ancestor — always report the confidence interval. Triangulation3+ people matching on the same segment ⇒ shared ancestor for that segment. Modal haplotypeConsensus marker values for a group; a reference to measure GD against. G25Global25 coordinates for admixture distance modeling (model-relative).