Nebula Genomics (30x Whole Genome Sequencing)

@Jovialis
If you compare the Nebula coordinates vs 23andme, Ancestry, LivDNA, … Which is the closest and the farthest from Nebula?

Ancestry gives you the most coverage out of those, 23andme, and LivingDNA are tied for the least. The bulk of the Superkit came from what Ancestry provided.
 
Ancestry gives you the most coverage out of those, 23andme, and LivingDNA are tied for the least. The bulk of the Superkit came from what Ancestry provided.

thanks :) … so for those without a combined Kit, their best coordinates and results might be through AncestryDNA.
 
@Salento

Indeed, Ancestry is probably the best mainstream genotyping consumer genomics company to obtain your raw data.

Here is my updated Dodecad distance results for Nebula:

Distance to:Nebula
1.88010638Italian_Abruzzo
3.84724577Italian_Apulia
4.96997988Italian_Lazio
5.09004912Greek_Central
5.15633591Italian_Campania
5.26680017Italian_Marche
5.36386987Greek_Lemnos
5.37535115Italian_Sicily
5.65294613Greek_Athens
6.17855970Greek_Foca
6.88314608Greek_Peloponnese
7.89715772Albanian
8.24733896Italian_Calabria
8.28775000Ashkenazi_Jews
8.29598698Greek_Thrace
8.44739605Moldovan_Jewish
8.50125873Italian_Romagna
8.71546327Greek_Izmir
8.82405236Greek_Thessaly
9.18807379Greek_Thessaloniki
9.36855378Greek_Fournoi
10.46934095Bulgarian_Thrace
10.49634698Greek_Crete
11.21442821Albanian_Kosovo
11.52890715Italian_Tuscany

 
Here is the original spread sheet for Dodecad:

Distance to:Nebula
6.80801733C_Italian
8.00835813O_Italian
8.25956415S_Italian_Sicilian
8.44261216Sicilian
8.54508046Greek
10.47327074Tuscan
11.26364506Ashkenazy_Jews
11.32732978Ashkenazi
11.38397119TSI30
15.05379022Sephardic_Jews
16.61730423Morocco_Jews
17.22097558N_Italian
18.95840974North_Italian
19.61347496Bulgarian
20.07642897Bulgarians
20.96617276Romanians
24.20628844Turkish
24.79345881Cypriots
26.70302230Turks
27.86819693Lebanese
27.99393506Baleares
29.34935093Canarias
29.39324072Galicia
29.55520935Extremadura
30.00664093Portuguese

 
Dodecad Globe 13 results:

Distance to:Jovialis:Nebula
2.65588027Greek_D
5.00656569C_Italian_D
6.51534343Sicilian_D
6.52577198S_Italian_Sicilian_D
8.05553847Ashkenazi_D
8.41972090Ashkenazy_Jews
9.42187349Tuscan
10.08532102TSI30
10.53649372O_Italian_D
15.58511149Sephardic_Jews
16.36177558Morocco_Jews
16.40602633N_Italian_D
16.99122421North_Italian
18.69148737Turkish_Aydin_Ho
19.07945754Bulgarians_Y
19.62166405Bulgarian_D
21.68662491Romanians
21.86878369Turkish_Cypriot_D
22.01239878Cypriots
22.31622056Canarias_1KG
23.28513904Murcia_1KG
23.41955807Baleares_1KG
24.10248327Portuguese_D
24.42338429Turkish_D
24.46135115Extremadura_1KG

 
Ancient Rome Test in Dodecad G13

Distance to:Jovialis:Nebula
1.80922635C6:Imperial_Mediterranean:R835:Civitanova_Marche
2.69957404C6:Late_Antiquity_Mediterranean:R118:S_Ercolano_Necropolis_Ostia
2.89001730C6:Medieval_Mediterranean:R970:Tivoli_Palazzo_Cianti
2.93651154C6:Medieval_Mediterranean:R57:Villa_Magna
3.12512400C6:Imperial_Mediterranean:R836:Civitanova_Marche
3.21353388C6:Medieval_Mediterranean:R969:Tivoli_Palazzo_Cianti
3.32625916C6:Medieval_Mediterranean:R1290:Villa_Magna
3.41651870C6:Medieval_Mediterranean:R52:Villa_Magna
3.48716217C6:Medieval_Mediterranean:R59:Villa_Magna
3.79902619C6:Late_Antiquity_Mediterranean:R121:S_Ercolano_Necropolis_Ostia
4.02554344C6:Imperial_Mediterranean:R131:Via_Paisiello_Necropolis
4.06814454C6:Imperial_Mediterranean:R49:Centocelle_Necropolis
4.47909589C6:Medieval_Mediterranean:R60:Villa_Magna
4.57123616C6:Medieval_Mediterranean:R973:Tivoli_Palazzo_Cianti
4.74308971C5:Late_Antiquity_Eastern_Mediterranean:R122:S_Ercolano_Necropolis_Ostia
4.77853534C6:Medieval_Mediterranean:R58:Villa_Magna
4.83627956C6:Medieval_Mediterranean:R64:Villa_Magna
4.86082298C6:Medieval_Mediterranean:R54:Villa_Magna
4.95681349C5:Late_Antiquity_Eastern_Mediterranean:R32:Mausole_di_Augusto
5.38665945C6:Late_Antiquity_Mediterranean:R107:Crypta_Balbi
5.53368774C6:Medieval_Mediterranean:R56:Villa_Magna
5.54973873C6:Late_Antiquity_Mediterranean:R36:Celio
5.62045372C6:Imperial_Mediterranean:R1549:Monterotondo
5.62926283C6:Late_Antiquity_Mediterranean:R117:S_Ercolano_Necropolis_Ostia
5.77807927C6:Medieval_Mediterranean:R1283:Cancelleria

 
With the dietary health snips alone I was very tempted, but it also seems your calculator results had a huge improvement? (or am I missunderstanding, seems like your distances decreased).

I could only dream of 1.6 diatance atm. but that might have to do with my autosomal mix. Wonder if anything would drop me below 4 for averaged pops, and 2.5 for single tab.

Does the 30x ever go on sale?
 
thanks :) … so for those without a combined Kit, their best coordinates and results might be through AncestryDNA.

Jovialis: Thanks for sharing your Nebula information. So that is lots of SNPS, I assume your Super Kit is a combined Ancestry, 23 and something else. and you still almost have 1 million more SNPs.

Salento: I agree with what you are suggesting based on Jovialis results, Ancestry is the best results for me as well. They just have so many more reference populations than any other Company that I have seen and read about.
 
With the dietary health snips alone I was very tempted, but it also seems your calculator results had a huge improvement? (or am I missunderstanding, seems like your distances decreased).

I could only dream of 1.6 diatance atm. but that might have to do with my autosomal mix. Wonder if anything would drop me below 4 for averaged pops, and 2.5 for single tab.

Does the 30x ever go on sale?

I think they do go on sale every now and then, you should check around holidays like Christmas.

Ancestry is pretty sufficient for high accuracy for raw data. But if you want total accuracy, I would go with a 30x Genome sequencing service. Nebula for the most part has been pretty good in terms of service. Though I did have to follow up with them to make sure they're on top of it. Overall, I'd give them 4 out of 5 stars, because the process took longer than expected. Nevertheless, they give you good files to work with.

The CRAM was of particular value to me, because I turned it into a BAM with WGSextract beta 3, which I then turned into a combined raw data file, providing 99.99% genotype coverage.
 
Despite having 99th percentile testosterone levels, and apparently 100th percentile for psychosis :petrified:; I am saved by the fact that I have a large brain volume. I also know for a fact that I have a high IQ due to testing as a child. Because if I were low IQ with a smaller brain, I'd likely be a criminal, in prison:

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I think they do go on sale every now and then, you should check around holidays like Christmas.

Ancestry is pretty sufficient for high accuracy for raw data. But if you want total accuracy, I would go with a 30x Genome sequencing service. Nebula for the most part has been pretty good in terms of service. Though I did have to follow up with them to make sure they're on top of it. Overall, I'd give them 4 out of 5 stars, because the process took longer than expected. Nevertheless, they give you good files to work with.

The CRAM was of particular value to me, because I turned it into a BAM with WGSextract beta 3, which I then turned into a combined raw data file, providing 99.99% genotype coverage.

Jovialis: So the Nebula Genomics test you did. Do you get a file similar to say Ancestry, etc that you can easily download and then run in GEDMATCH or Admixture studio, etc.? That 99.9% coverage you are referring to, that is doing the Nebula Genomics test? or is that 99.8% the 1 million or so SNPs you got from Nebula plus the other approximately 1 million from your Ancestry+23/Me+ I assume NATGENO, etc?

Thanks for sharing some your results, really interesting.
 
Very interesting.

Say I get Ancestry, can I run it through Nebula to get those reports?

Those reports look lit!!!
 
@PT

My superkit was a combination of 23andme V5, Ancestry DNA, Living DNA, Helix geno 2.0, and FTDNA.

FilenameCalculatorGenotype ratio
Nebula GenomicsDodecad K12b99.99%
SuperkitDodecad K12b94.64%
AncestryDNADodecad K12b91.20%
Nat Geo Helix 2.0Dodecad K12b43.58%
FTDNADodecad K12b40.00%
Living DNADodecad K12b28.19%
23andme_V5Dodecad K12b28.09%

UWDjxP9.png
 
Very interesting.

Say I get Ancestry, can I run it through Nebula to get those reports?

Those reports look lit!!!

If you're particularly interested in the reports, I'd go with the 30x nebula test. Ancestry, while sufficient for looking at ancestry, would give you limited or skewed reports. Also, there is an annoying issue with e-mails if you upload raw data. If you want to test with nebula, use a different e-mail than the one you used to upload the raw data.
 
@PT

My superkit was a combination of 23andme V5, Ancestry DNA, Living DNA, Helix geno 2.0, and FTDNA.

FilenameCalculatorGenotype ratio
Nebula GenomicsDodecad K12b99.99%
SuperkitDodecad K12b94.64%
AncestryDNADodecad K12b91.20%
Nat Geo Helix 2.0Dodecad K12b43.58%
FTDNADodecad K12b40.00%
Living DNADodecad K12b28.19%
23andme_V5Dodecad K12b28.09%

UWDjxP9.png

I think because the genotype coverage was so low, the imputation decided to lump me in with a more predominate genotype for Southern Italians, which is why 23andme and living DNA puts me between Abruzzo, Campania, and Sicily. Nevertheless, the higher genotype coverage shows that there is a fairly significant shift from that.
 
Jovialis: Thanks for the information in post #41. Wow so Ancestry really does provide more genotype coverage vs. the other ones you have used. I can see that your Superkit and Nebula plots you between Apulia, Lazio and Abruzzo similar to where your Ancestry DNA file plots you. Nice little Natural experiment you ran there. I think I may do that as well.

Thanks again for the PCA plot with all your various Files

PT
 
Jovialis: Thanks again for that PCA plot. I used my 3 files, Ancestry, 23ME and NATGENO and combined Ancestry_23ME and plotted them vs. the Dodecad 12B updated Modern Italian populations. All of them are in the same neighborhood but Ancestry individually gives me the closest Distances vs. 23_ME and NATGENO and my Combined Ancestry/23ME tightens up the estimates among Sicily, Campania and Abruzzo. NATGENO has me a little more Western shifted I think due to NATGENO assigning me a large WEST_MED component (14%, 2nd behind the Italian_Southern Europe of 71%), which they consider (Sardinia, Corsica and NW Italy to Southern France and Iberia) part of.

Again thanks for that PCA plot of yours, as when I did mine the way you presented it, really provides a nice picture

FbNqWsG.jpg



Distance to:PalermoTrapani_ANCESTRY
3.55695094Italian_Campania
3.83109645Italian_Abruzzo
4.03399306Italian_Sicily
5.85703850Italian_Calabria
6.29590343Italian_Apulia
6.47651913Ashkenazi_Jews
7.04365275Italian_Marche
7.18862991Moldovan_Jewish
7.65706210Italian_Lazio
7.90179726Greek_Lemnos
8.92854971Italian_Jews
9.03374230Greek_Foca
9.04327927Greek_Athens
9.04979005Greek_Central
9.35666073Greek_Fournoi


Distance to:PalermoTrapani_NATGENO
5.80251670Italian_Campania
5.81831591Italian_Abruzzo
6.25112790Italian_Sicily
7.02488890Italian_Marche
7.77297240Italian_Lazio
7.77398225Italian_Calabria
7.96713248Ashkenazi_Jews
8.17665580Italian_Apulia
8.68283940Moldovan_Jewish
9.90486244Greek_Lemnos
9.91812986Italian_Jews
10.00520864Italian_Romagna
10.27486253Greek_Athens
10.32988867Greek_Central
10.78454450Greek_Foca


Distance to:PalermoTrapani23_ME
5.36401902Italian_Abruzzo
5.60141946Italian_Sicily
5.74162869Italian_Campania
7.07688943Italian_Marche
7.10671513Italian_Apulia
7.46454285Italian_Lazio
7.60805494Ashkenazi_Jews
7.63214911Italian_Calabria
8.06370882Moldovan_Jewish
8.74444967Greek_Lemnos
9.43181319Greek_Central
9.55031413Greek_Athens
9.94718051Italian_Jews
9.99860490Greek_Foca
10.12975321Italian_Romagna

Distance to:PalermoTrapani_ANCESTRY_23ME
3.56992997Italian_Campania
3.77608263Italian_Abruzzo
3.98449495Italian_Sicily
5.86301970Italian_Calabria
6.23848539Italian_Apulia
6.45569516Ashkenazi_Jews
7.01391360Italian_Marche
7.14076326Moldovan_Jewish
7.60876468Italian_Lazio
7.86122764Greek_Lemnos
8.94503773Italian_Jews
8.98608925Greek_Foca
8.98801424Greek_Athens
8.99696616Greek_Central
9.33669106Greek_Fournoi

 

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