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Y-DNA next generation sequencing

From 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
[1]
Read depth,
read length,
Method 		30×
150 bp (or 10 mb)[2] 		~15×
150 bp 		4×
150 bp 		2×
150 bp 		80×
150 bp 		60×
100 bp
Upgrade options $55 per 1× + $100 data fee[3] price difference
+ $100 data fee 		price difference
+ $100 data fee[4] 		price difference
+ $100 data fee[4] 		2nd order
for 60× [5] 		-
Y ≥1× coverage
(FGC) 		~22.9 mbp [6]
92% hg19 		~ 22.3 mbp? ~17.7 mbp [6]
72% hg19 		? mbp ~22.0 mbp [6]
89% hg19 		~16 mbp
65% hg19
(14-23 mbp)[7]
Y Callable Loci (GATK)
(FGC qual.-read-lenght) 		~14.9 mbp [8] ~13.2 mbp hg19[9] ~1.1 mbp hg19 ~0.4 mbp hg19 ~14.8 mbp hg19?[10]
~13.5 mbp hg38[11] 		~8.8 mbp hg19[12]
~8.6 mbp hg38[11]
Y Method
Analysis (YFull) 		Mean/Av. 21×
Median 12×
~22.8 mbp
~0.3 Gb BAM
~2900? SNPs
?/111 STRs 		? [13] 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 [6]
~2750 SNPs[14]
~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 [9]

92-100% FMS [15] ~69% FMS [1]
Mean/Av. ~13-41X [16]
(0-100%)[7]
at/X Method
~3,60 mill. SNPs expected 		~3.60 mill. SNPs
(~100%)[17]
ca. 22.5x?
Coverage ca. 95%. 		~3.52 mill. SNPs
(~98%)[9] 		~1.75 mill. SNPs
(~49%)[17]
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

References

  1. ↑ 1.0 1.1 until April 2015 BAM file included mtDNA data, after it is omitted
  2. ↑ $2750 pilot project long read whole genome Chromium technology, Justin Loe, FGC, 2016-09-02, Forum http://www.anthrogenica.com/showthread.php?742-Full-Y-Chromosome-Sequencing-Phase-III-Pilot&p=184229&viewfull=1#post184229
  3. ↑ Justin Loe, FGC, 2016-09-20, Forum http://www.anthrogenica.com/showthread.php?742-Full-Y-Chromosome-Sequencing-Phase-III-Pilot&p=187847&viewfull=1#post187847
  4. ↑ 4.0 4.1 Justin Loe, FGC, 2015-11-29, Forum http://www.anthrogenica.com/showthread.php?742-Full-Y-Chromosome-Sequencing-Phase-III-Pilot&p=123473&viewfull=1#post123473
  5. ↑ Justin Loe, FGC, 2015-12-15, http://www.anthrogenica.com/showthread.php?742-Full-Y-Chromosome-Sequencing-Phase-III-Pilot&p=126856#post126856
  6. ↑ 6.0 6.1 6.2 6.3 Justin Loe, email message, 28 Dec 2015 and AG Forum 2016-01 http://www.anthrogenica.com/showthread.php?742-Full-Y-Chromosome-Sequencing-Phase-III-Pilot&p=131470&viewfull=1#post131470
  7. ↑ 7.0 7.1 Jim Kane, Which Y-DNA NGS test to take? November 12, 2015, http://www.it2kane.org/2015/11/which-ngs-test-to-take/
  8. ↑ Justin Loe, E-Mail 2016-06-10
  9. ↑ 9.0 9.1 9.2 Justin Loe, E-Mail 2016-02
  10. ↑ Justin Loe, AG Forum 2016-03 http://www.anthrogenica.com/showthread.php?742-Full-Y-Chromosome-Sequencing-Phase-III-Pilot&p=146390&viewfull=1#post146390
  11. ↑ 11.0 11.1 JamesKane, AG Forum 2016-03 http://www.anthrogenica.com/showthread.php?742-Full-Y-Chromosome-Sequencing-Phase-III-Pilot&p=146667&viewfull=1#post146667
  12. ↑ Vince Tilroe analysis of FGC raw-data from Greg Magoon, shared by Iain McDonald, 2 Dec 2015
  13. ↑ based on a single sample with initial QC problems YF05650
  14. ↑ Justin Loe, AG Forum 2016-01 http://www.anthrogenica.com/showthread.php?742-Full-Y-Chromosome-Sequencing-Phase-III-Pilot&p=132860&viewfull=1#post132860
  15. ↑ Justin Loe, Batch 9006, email message, 28 Dec 2015
  16. ↑ Petr, Forum post: Full Y Chromosome Sequencing: Phase III Pilot, 2015-12-25, http://www.anthrogenica.com/showthread.php?742-Full-Y-Chromosome-Sequencing-Phase-III-Pilot&p=128756&viewfull=1#post128756
  17. ↑ 17.0 17.1 Justin Loe, AG Forum 2016-01 http://www.anthrogenica.com/showthread.php?742-Full-Y-Chromosome-Sequencing-Phase-III-Pilot&p=134491&viewfull=1#post134491
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