International Society of Genetic Genealogy Wiki ISOGG Wiki

A Y-sequence is a substantial part of the Y-chromosome DNA which, according to hg19, is 59,373,566 bases long. See the Y-DNA SNP testing chart for a technical comparison of Y-sequence testing and other forms of Y-SNP testing.

Comparison table

This chart has been compiled as a subset of ChrisR/current_NextGenSeq_testing#NGS_comparison_table. FGC = Full Genomes Corporation, FTDNA = Family Tree DNA, see also Y-DNA SNP testing chart and Autosomal DNA testing comparison chart.

	FGC WGS 30×	FGC WGS GenomeGuide	FGC WGS 4×	FGC WGS 2×	FGC Y-Elite 2.1	FTDNA BigY
Introduced	Summer 2014	Early 2016	July 2015	July 2015	May 2015	November 2013
Price	$1250 ($42/×)	$700 ($47/×)	$395 ($99/×)	$280 ($140/×)	$645	$575
Sequenced DNA focus	whole genome	whole genome	whole genome	whole genome	Y-DNA, mtDNA	Y-DNA
Read depth, read length, Method	30× 150 bp (or 10 mb)	~15× 150 bp	4× 150 bp	2× 150 bp	80× 150 bp	60× 100 bp
Upgrade options	$55 per 1× + $100 data fee	price difference + $100 data fee	price difference + $100 data fee	price difference + $100 data fee	2nd order for 60×	-
Y ≥1× coverage (FGC)	~22.9 mbp 92% hg19	~ 22.3 mbp?	~17.7 mbp 72% hg19	? mbp	~22.0 mbp 89% hg19	~16 mbp 65% hg19 (14-23 mbp)
Y Callable Loci (GATK) (FGC qual.-read-lenght)	~14.9 mbp	~13.2 mbp hg19	~1.1 mbp hg19	~0.4 mbp hg19	~14.8 mbp hg19? ~13.5 mbp hg38	~8.8 mbp hg19 ~8.6 mbp hg38
Y Method Analysis (YFull)	Mean/Av. 21× Median 12× ~22.8 mbp ~0.3 Gb BAM ~2900? SNPs ?/111 STRs	?	Mean/Av. 9× Median 4× ~87% Y-cov-hg19 ~0.1 Gb BAM 2,764 known + 243 novel SNPs ~81/111 STRs	?	Mean/Av. ~47-72× Median ~31-47× 22 mbp ~1.2 Gb BAM ~2750 SNPs ~107/111 STRs	Mean/Av. -91× Median 47-60× ~13.9 mbp ~0.8 Gb BAM ~2050 SNPs ~96/111 STRs
mt Method Analysis		~100% FMS Mean/Av. >1000X			92-100% FMS	~69% FMS Mean/Av. ~13-41X (0-100%)
at/X Method ~3,60 mill. SNPs expected	~3.60 mill. SNPs (~100%) ca. 22.5x? Coverage ca. 95%.	~3.52 mill. SNPs (~98%)	~1.75 mill. SNPs (~49%)		not included	not included

FGC Y-Elite

Since 2013 Full Genomes Corp. provides the raw data in BAM file format along with interpretation results. Download is possible after Account login or with Account Sharing from Amazon Simple Storage Service (S3).

• Y-Elite 1.0: BAM files contain ca. 22.7 Mbp in approx. 9 GB.

FGC WGS

Since 2014 Full Genomes Corp. provides the Raw Data in BAM file format along with interpretation results. BAM files according to read depth (data amount) are delivered online or by hard drive / USB stick.

BigY Raw Data Window

FTDNA Big Y

Since 2013 Family Tree DNA provides VCF (and BED) for download on the Big Y results page > Download Raw Data. BAM files for Big Y deliver ca. 13.9 Mbp in approx. 1 GB. The BAM file needs to be requested by filling out a Contact Us Form request and choosing the Big Y BAM Request category. After some business days (in May 2016 it takes ca. 2-3 weeks) the link should be available Big Y results page > Download Raw Data > Download BAM. Additionally a "Share BAM" function is available which creates a temporarily valid link to download the BAM file (expires after 1 hour). Upload to YFull with the "Link to a sharing file" normally works.

FTDNA Walk Through the Y

From 2007-2013 Walk Through the Y delivered 300,000 - 600,000 base pairs. The technology used was not NextGenSeq but the details are mentioned here.

See also

• Next generation sequencing
• Full Genomes Corporation
• Family Tree DNA
• Y-DNA tools
• YFull
• FGC Full Y Chromosome Sequencing at anthrogenica.com
• Next Generation Sequencing Statistics GRCh38 by James Kane (haplogroup-r.org)