Polish Iron age autosomal dna (Eurogenes k13 results)

[vbnetkhio]

MZ_103, Goth from Masłomęcz, Poland/Ukraine border 200–400 AD

0.110709 Genotype rate

Component%
North_Atlantic36,33%
Baltic42,99%
West_Med12,40%
East_Med0,30%
South_Asian0,08%
East_Asian0,20%
Oceanian2,05%
Northeast_African4,76%
Sub-Saharan0,89%


Mixed Mode:
1 81,64% Estonian + 18,36% French_Basque @ 6,345
2 76,95% Lithuanian + 23,05% French_Basque @ 6,597
3 78,52% Estonian + 21,48% Southwest_French @ 6,885
4 78,52% Estonian + 21,48% Spanish_Cantabria @ 6,909
5 80,86% Estonian + 19,14% Spanish_Aragon @ 7,056
6 79,30% Estonian + 20,70% Spanish_Castilla_Y_Leon @ 7,144
7 80,08% Estonian + 19,92% Spanish_Castilla_La_Mancha @ 7,187
8 65,23% Lithuanian + 34,77% Southwest_English @ 7,259
9 78,52% Estonian + 21,48% Spanish_Galicia @ 7,354
10 79,30% Estonian + 20,70% Spanish_Cataluna @ 7,385

Least-squares method.

Using 1 populations approximation
1 100% Southwest_Finnish @ 9,537
2 100% Polish @ 10,536
3 100% South_Polish @ 11,834
4 100% Estonian @ 12,122
5 100% Finnish @ 12,616
6 100% Ukrainian @ 13,025
7 100% Belorussian @ 13,358
8 100% North_Swedish @ 13,546
9 100% Estonian_Polish @ 13,548
10 100% Russian_Smolensk @ 13,701

Using 2 populations approximation
1 50% Estonian + 50% East_German @ 8,181
2 50% Polish + 50% North_Swedish @ 8,309
3 50% North_Swedish + 50% Estonian_Polish @ 8,346
4 50% Southwest_Finnish + 50% Polish @ 8,397
5 50% Lithuanian + 50% Swedish @ 8,409
6 50% North_Swedish + 50% Lithuanian @ 8,598
7 50% Belorussian + 50% North_Swedish @ 8,715
8 50% Lithuanian + 50% Icelandic @ 8,719
9 50% North_Swedish + 50% Russian_Smolensk @ 8,720
10 50% Estonian_Polish + 50% Swedish @ 8,823

Using 3 populations approximation
1 33% Lithuanian + 33% Lithuanian + 33% Southwest_English @ 7,275
2 33% Lithuanian + 33% Lithuanian + 33% Southeast_English @ 7,600
3 33% Lithuanian + 33% Lithuanian + 33% Orcadian @ 7,750
4 33% Lithuanian + 33% Lithuanian + 33% West_Scottish @ 7,863
5 33% Polish + 33% Estonian + 33% Swedish @ 7,937
6 33% East_Finnish + 33% Lithuanian + 33% Southwest_English @ 7,956
7 33% Lithuanian + 33% Lithuanian + 33% Irish @ 7,958
8 33% Polish + 33% Estonian + 33% Icelandic @ 7,976
9 33% Estonian + 33% Estonian + 33% Southwest_English @ 7,987
10 33% Estonian + 33% Estonian + 33% Southeast_English @ 8,012

Using 4 populations approximation
1 25% Lithuanian + 25% Lithuanian + 25% Lithuanian + 25% French_Basque @ 6,667
2 25% Estonian + 25% Estonian + 25% Estonian + 25% Southwest_French @ 7,044
3 25% Estonian + 25% Estonian + 25% Estonian + 25% Spanish_Cantabria @ 7,145
4 25% Estonian + 25% Estonian + 25% Estonian + 25% Spanish_Castilla_Y_Leon @ 7,380
5 25% Estonian + 25% Estonian + 25% Finnish + 25% Southwest_French @ 7,409
6 25% Estonian + 25% Estonian + 25% Estonian + 25% French_Basque @ 7,444
7 25% Estonian + 25% Estonian + 25% Estonian + 25% Spanish_Galicia @ 7,543
8 25% Estonian + 25% Estonian + 25% Finnish + 25% Spanish_Cantabria @ 7,568
9 25% Estonian + 25% Estonian + 25% Ukrainian + 25% Southwest_English @ 7,588
10 25% Estonian + 25% Estonian + 25% Estonian + 25% Spanish_Cataluna @ 7,600

[Dušan]

Hmm how to interpret this?
Seems to much for noise.



Component %
North_Atlantic 36,33%
Baltic 42,99%
West_Med 12,40%
East_Med 0,30%
South_Asian 0,08%
East_Asian 0,20%
Oceanian 2,05%
Northeast_African 4,76%
Sub-Saharan 0,89%

[vbnetkhio]

here's the file, if you want to run it trough other calcs:

https://easyupload.io/9gd0eh

[vbnetkhio]

Hmm how to interpret this?
Seems to much for noise.

it has around 20k snps which is kind of low quality, but since we have so little ancient dna from this area, it's very useful.

[Leto]

Basically an ethnic Pole.

[smd555]

here's the file, if you want to run it trough other calcs:

https://easyupload.io/9gd0eh

Сan you tell the algorithm how you converted from bam to raw? Did you use only bcftools mpileup?
And what about another ancient samples - are they insufficient quality?

[vbnetkhio]

Сan you tell the algorithm how you converted from bam to raw? Did you use only bcftools mpileup?
And what about another ancient samples - are they insufficient quality?

No, this one just had the most reads out of the Maslomecz samples, so I checked it first.

the conversion has more steps, i'll write a tutorial later.

[Lemminkäinen]

Hmm how to interpret this?
Seems to much for noise.

What I have seen the African in ancient European samples comes from mapping errors.

With no East African, a bit less West Mediterranean and 3-4 Siberian it is me!

[Roy]

Basically an ethnic Pole.

Not exactly a mainstream one but still could be.

[CommonSense]

Hmm how to interpret this?
Seems to much for noise.

It means the sample is of very low quality and shouldn't be used to draw any conclusions just yet.

[Arzanene]

Masłomęcz_Goth,36.33,42.99,12.40,0,0.30,0,0.08,0.2 0,0,0,2.05,4.76,0.89

Target: Masłomęcz_Goth
Distance: 4.5473% / 4.54729031 | ADC: 0.25x RC
56.5 Latvian
22.4 Sweden_Svealand_East
17.2 French_Basque
3.9 Ethiopian_Gumuz


Target: Masłomęcz_Goth
Distance: 5.3477% / 5.34767192 | ADC: 0.25x RC
65.8 Lithuanian
16.0 Swedish
14.7 French_Basque
3.5 Ethiopian_Gumuz

balto-germanic?

[vbnetkhio]

Сan you tell the algorithm how you converted from bam to raw? Did you use only bcftools mpileup?
And what about another ancient samples - are they insufficient quality?

first upload your file, then in bcftools mpileup select this file under "input BAM/CRAM", and select hg19 under "Select reference genome", and then you can execute the algorythm. When it finishes it will output a BCF file and it will be added to your history.

then after that run "bcftools call" on that BCF file output from the first step, just select the file and run it, and you'll get another BCF file. in this step you can already choose to output a VCF file but it will probably be too big and take too long to download and convert.

because of that I also run "bcftools filter" on the second BCF file. select the second bcf file, then upload this file : https://easyupload.io/769eny , then under Restrict To > Regions select "Operate on Regions specified in a history dataset", and select this dataset you uploaded (new.tsv), and for your output type select "uncompressed VCF".

then you can download this VCF file, and convert it to 23andme with DNAKitStudio.

for this file, I started with the fastq file, not BAM. in this case there is one extra step at the begining. convert the fastq to BAM with "map with bwa-mem", you also need to select hg19 reference genome, "single" under "Single or Paired-end reads", and then select your fastq file and run it. then you'll have a BAM and you can do the mpileup and the rest.

[smd555]

first upload your file, then in bcftools mpileup select this file under "input BAM/CRAM", and select hg19 under "Select reference genome", and then you can execute the algorythm. When it finishes it will output a BCF file and it will be added to your history.

then after that run "bcftools call" on that BCF file output from the first step, just select the file and run it, and you'll get another BCF file. in this step you can already choose to output a VCF file but it will probably be too big and take too long to download and convert.

because of that I also run "bcftools filter" on the second BCF file. select the second bcf file, then upload this file : https://easyupload.io/769eny , then under Restrict To > Regions select "Operate on Regions specified in a history dataset", and select this dataset you uploaded (new.tsv), and for your output type select "uncompressed VCF".

then you can download this VCF file, and convert it to 23andme with DNAKitStudio.

for this file, I started with the fastq file, not BAM. in this case there is one extra step at the begining. convert the fastq to BAM with "map with bwa-mem", you also need to select hg19 reference genome, "single" under "Single or Paired-end reads", and then select your fastq file and run it. then you'll have a BAM and you can do the mpileup and the rest.

I have converted another sample (MZ_106) to vcf and then to 13andme. But it doesn`t run in Admixture Studio. What`s the reason? Can it be connected with bad quality - or I have chosen some wrong settings converting it?

ERROR - index is out of range. The index must be a positive number, and its size should not exceed the collection size :

https://i.ibb.co/BLmkjrn/2021-08-28-220158.png (https://ibb.co/9nJP2VZ)

[vbnetkhio]

I have converted another sample (MZ_106) to vcf and then to 13andme. But it doesn`t run in Admixture Studio. What`s the reason? Can it be connected with bad quality - or I have chosen some wrong settings converting it?

ERROR - index is out of range. The index must be a positive number, and its size should not exceed the collection size :

https://i.ibb.co/BLmkjrn/2021-08-28-220158.png (https://ibb.co/9nJP2VZ)

you did something wrong, your version has zero snps. (0 genotype rate) did you use the bam or fastq? maybe their bam files are corrupt and it's better to use the fastq. it doesn't take much longer either.

they are here:
https://ftp.cngb.org/pub/gigadb/pub/10.5524/100001_101000/100310/Raw_data/

106 is split into 2 files, so you have to convert them both and merge them with dnakitstudio in the end.

[smd555]

you did something wrong, your version has zero snps. (0 genotype rate) did you use the bam or fastq? maybe their bam files are corrupt and it's better to use the fastq. it doesn't take much longer either.

they are here:
https://ftp.cngb.org/pub/gigadb/pub/10.5524/100001_101000/100310/Raw_data/

106 is split into 2 files, so you have to convert them both and merge them with dnakitstudio in the end.

I`m downloading these fastq now. Can you check my vcf from bam file? I shared it in my google drive.

[vbnetkhio]

I`m downloading these fastq now. Can you check my vcf from bam file? I shared it in my google drive.

yeah, it's empty, there's no snps.

[smd555]

you did something wrong, your version has zero snps. (0 genotype rate) did you use the bam or fastq? maybe their bam files are corrupt and it's better to use the fastq. it doesn't take much longer either.

they are here:
https://ftp.cngb.org/pub/gigadb/pub/10.5524/100001_101000/100310/Raw_data/

106 is split into 2 files, so you have to convert them both and merge them with dnakitstudio in the end.


Have I to convert them paired or single by "map with bwa-mem"? I tried the first part single - it doesnt convert:



https://i.ibb.co/kgX9yyq/2021-08-29-122154.png (https://ibb.co/HDqx22G)



PS Are those two files MZ106?:
106_GGATCAA_L006_R1_001.fastq.gz
106_GGATCAA_L006_R1_002.fastq.gz

[vbnetkhio]

Have I to convert them paired or single by "map with bwa-mem"? I tried the first part single - it doesnt convert:



https://i.ibb.co/kgX9yyq/2021-08-29-122154.png (https://ibb.co/HDqx22G)

single. did you select the hg19 reference genome? full name is "Human (Homo Sapiens) (b37): hg19"



PS Are those two files MZ106?:
106_GGATCAA_L006_R1_001.fastq.gz
106_GGATCAA_L006_R1_002.fastq.gz

yes

[smd555]

single. did you select the hg19 reference genome? full name is "Human (Homo Sapiens) (b37): hg19"


Yes:

https://i.ibb.co/2yZ18db/2021-08-29-132148.png (https://ibb.co/t4LTZDd)

[vbnetkhio]

Yes:

https://i.ibb.co/2yZ18db/2021-08-29-132148.png (https://ibb.co/t4LTZDd)

which error do you get? (click on 11 in history for more info)

[vbnetkhio]

Yes:

https://i.ibb.co/2yZ18db/2021-08-29-132148.png (https://ibb.co/t4LTZDd)

are your fastq files damaged maybe? they should have 283.02 and 217.06 MB

[smd555]

which error do you get? (click on 11 in history for more info)

This?:

https://i.ibb.co/0B02rjN/2021-08-29-135658.png (https://ibb.co/bH4mXgh)

[vbnetkhio]

This?:

https://i.ibb.co/0B02rjN/2021-08-29-135658.png (https://ibb.co/bH4mXgh)

it says you are not logged in. did you register an account?

[smd555]

it says you are not logged in. did you register an account?

Can you check my vcf from fastq files (part1 and part2)? I`v shared them in my google drive.

[vbnetkhio]

Can you check my vcf from fastq files (part1 and part2)? I`v shared them in my google drive.

it's very low quality, if you did everything right. it's probably that, because 106 has very few reads. you can try with MZ 100, it's on second place by read number.

sample reads
103 6539551
100 2494647
88 1548942
94 1247768
92 1066147
89 926111
111 696740
110 621407
102 619286
93 457702
105 289604
90 200066
91 179957
99 159295
109 112541
114 104474
95 22557
97 17401
113 17310
98 12112
112 11463
108 8958
101 7049
106 6993
104 6933
96 6177
107 5816

[smd555]

it's very low quality, if you did everything right. it's probably that, because 106 has very few reads. you can try with MZ 100, it's on second place by read number.



If I get you right - I have to convert each separately part to raw, and then to merge two raws? Or I have to merge two vcfs?

[vbnetkhio]

If I get you right - I have to convert each separately part to raw, and then to merge two raws? Or I have to merge two vcfs?

i merge the two 23andme raws at the end. maybe there's a better way but this works too. i merge them with dnakitstudio.

[smd555]

My result of MZ100. Typical Goth:

FINAL ADMIXTURE PROPORTIONS:
----------------------------
49.28% North_Atlantic
33.88% Baltic
10.31% West_Med
2.47% West_Asian
0.00% East_Med
0.02% Red_Sea
0.07% South_Asian
0.00% East_Asian
1.09% Siberian
0.00% Amerindian
0.51% Oceanian
0.09% Northeast_African
2.28% Sub-Saharan

Mixed Mode:
1 80,08% Icelandic + 19,92% Estonian @ 3,986
2 71,48% Icelandic + 28,52% Southwest_Finnish @ 4,023
3 78,52% Icelandic + 21,48% Finnish @ 4,145
4 50,39% North_Swedish + 49,61% Icelandic @ 4,189
5 50,39% Icelandic + 49,61% North_Swedish @ 4,189
6 83,20% Icelandic + 16,80% Lithuanian @ 4,284
7 81,64% Icelandic + 18,36% East_Finnish @ 4,319
8 87,89% Swedish + 12,11% Southwest_Finnish @ 4,379
9 73,05% Norwegian + 26,95% Southwest_Finnish @ 4,405
10 74,61% Swedish + 25,39% North_Swedish @ 4,411

Least-squares method.

Using 1 populations approximation
1 100% Swedish @ 4,808
2 100% Norwegian @ 7,109
3 100% North_Swedish @ 7,158
4 100% Icelandic @ 7,160
5 100% North_Dutch @ 9,264
6 100% Danish @ 9,268
7 100% North_German @ 9,737
8 100% Orcadian @ 10,838
9 100% Irish @ 11,644
10 100% West_Scottish @ 12,260

Using 2 populations approximation
1 50% North_Swedish + 50% Icelandic @ 4,188
2 50% Norwegian + 50% North_Swedish @ 4,482
3 50% Swedish + 50% North_Swedish @ 4,788
4 50% Swedish + 50% Swedish @ 4,808
5 50% West_Scottish + 50% Southwest_Finnish @ 5,098
6 50% North_Swedish + 50% North_Dutch @ 5,181
7 50% North_Swedish + 50% Orcadian @ 5,289
8 50% North_Swedish + 50% Irish @ 5,415
9 50% Irish + 50% Southwest_Finnish @ 5,418
10 50% North_Swedish + 50% Danish @ 5,431

Using 3 populations approximation
1 33% Icelandic + 33% Icelandic + 33% Southwest_Finnish @ 4,163
2 33% Swedish + 33% North_Swedish + 33% Icelandic @ 4,267
3 33% Norwegian + 33% Icelandic + 33% Southwest_Finnish @ 4,326
4 33% Swedish + 33% Swedish + 33% North_Swedish @ 4,453
5 33% Swedish + 33% Norwegian + 33% North_Swedish @ 4,472
6 33% Norwegian + 33% Norwegian + 33% Southwest_Finnish @ 4,582
7 33% North_Swedish + 33% North_Swedish + 33% Icelandic @ 4,613
8 33% North_Swedish + 33% Icelandic + 33% Icelandic @ 4,615
9 33% North_Swedish + 33% North_Swedish + 33% West_Scottish @ 4,657
10 33% Norwegian + 33% North_Swedish + 33% Icelandic @ 4,679

Using 4 populations approximation
1 25% Icelandic + 25% Icelandic + 25% Icelandic + 25% Southwest_Finnish @ 4,080
2 25% North_Swedish + 25% North_Swedish + 25% Icelandic + 25% Icelandic @ 4,188
3 25% Icelandic + 25% Icelandic + 25% Icelandic + 25% Estonian @ 4,235
4 25% Norwegian + 25% Norwegian + 25% Icelandic + 25% Southwest_Finnish @ 4,256
5 25% Icelandic + 25% Icelandic + 25% Icelandic + 25% Finnish @ 4,277
6 25% Swedish + 25% Swedish + 25% North_Swedish + 25% Icelandic @ 4,358
7 25% Swedish + 25% Swedish + 25% Swedish + 25% North_Swedish @ 4,411
8 25% Norwegian + 25% Norwegian + 25% Norwegian + 25% Southwest_Finnish @ 4,427
9 25% Norwegian + 25% Norwegian + 25% North_Swedish + 25% North_Swedish @ 4,482
10 25% Swedish + 25% Swedish + 25% Norwegian + 25% North_Swedish @ 4,513

[vbnetkhio]

My result of MZ100. Typical Goth:

FINAL ADMIXTURE PROPORTIONS:
----------------------------
49.28% North_Atlantic
33.88% Baltic
10.31% West_Med
2.47% West_Asian
0.00% East_Med
0.02% Red_Sea
0.07% South_Asian
0.00% East_Asian
1.09% Siberian
0.00% Amerindian
0.51% Oceanian
0.09% Northeast_African
2.28% Sub-Saharan

Mixed Mode:
1 80,08% Icelandic + 19,92% Estonian @ 3,986
2 71,48% Icelandic + 28,52% Southwest_Finnish @ 4,023
3 78,52% Icelandic + 21,48% Finnish @ 4,145
4 50,39% North_Swedish + 49,61% Icelandic @ 4,189
5 50,39% Icelandic + 49,61% North_Swedish @ 4,189
6 83,20% Icelandic + 16,80% Lithuanian @ 4,284
7 81,64% Icelandic + 18,36% East_Finnish @ 4,319
8 87,89% Swedish + 12,11% Southwest_Finnish @ 4,379
9 73,05% Norwegian + 26,95% Southwest_Finnish @ 4,405
10 74,61% Swedish + 25,39% North_Swedish @ 4,411

Least-squares method.

Using 1 populations approximation
1 100% Swedish @ 4,808
2 100% Norwegian @ 7,109
3 100% North_Swedish @ 7,158
4 100% Icelandic @ 7,160
5 100% North_Dutch @ 9,264
6 100% Danish @ 9,268
7 100% North_German @ 9,737
8 100% Orcadian @ 10,838
9 100% Irish @ 11,644
10 100% West_Scottish @ 12,260

Using 2 populations approximation
1 50% North_Swedish + 50% Icelandic @ 4,188
2 50% Norwegian + 50% North_Swedish @ 4,482
3 50% Swedish + 50% North_Swedish @ 4,788
4 50% Swedish + 50% Swedish @ 4,808
5 50% West_Scottish + 50% Southwest_Finnish @ 5,098
6 50% North_Swedish + 50% North_Dutch @ 5,181
7 50% North_Swedish + 50% Orcadian @ 5,289
8 50% North_Swedish + 50% Irish @ 5,415
9 50% Irish + 50% Southwest_Finnish @ 5,418
10 50% North_Swedish + 50% Danish @ 5,431

Using 3 populations approximation
1 33% Icelandic + 33% Icelandic + 33% Southwest_Finnish @ 4,163
2 33% Swedish + 33% North_Swedish + 33% Icelandic @ 4,267
3 33% Norwegian + 33% Icelandic + 33% Southwest_Finnish @ 4,326
4 33% Swedish + 33% Swedish + 33% North_Swedish @ 4,453
5 33% Swedish + 33% Norwegian + 33% North_Swedish @ 4,472
6 33% Norwegian + 33% Norwegian + 33% Southwest_Finnish @ 4,582
7 33% North_Swedish + 33% North_Swedish + 33% Icelandic @ 4,613
8 33% North_Swedish + 33% Icelandic + 33% Icelandic @ 4,615
9 33% North_Swedish + 33% North_Swedish + 33% West_Scottish @ 4,657
10 33% Norwegian + 33% North_Swedish + 33% Icelandic @ 4,679

Using 4 populations approximation
1 25% Icelandic + 25% Icelandic + 25% Icelandic + 25% Southwest_Finnish @ 4,080
2 25% North_Swedish + 25% North_Swedish + 25% Icelandic + 25% Icelandic @ 4,188
3 25% Icelandic + 25% Icelandic + 25% Icelandic + 25% Estonian @ 4,235
4 25% Norwegian + 25% Norwegian + 25% Icelandic + 25% Southwest_Finnish @ 4,256
5 25% Icelandic + 25% Icelandic + 25% Icelandic + 25% Finnish @ 4,277
6 25% Swedish + 25% Swedish + 25% North_Swedish + 25% Icelandic @ 4,358
7 25% Swedish + 25% Swedish + 25% Swedish + 25% North_Swedish @ 4,411
8 25% Norwegian + 25% Norwegian + 25% Norwegian + 25% Southwest_Finnish @ 4,427
9 25% Norwegian + 25% Norwegian + 25% North_Swedish + 25% North_Swedish @ 4,482
10 25% Swedish + 25% Swedish + 25% Norwegian + 25% North_Swedish @ 4,513

thanks for the conversion :thumb001:

it seems that Goths and some kind of Balto-Slavs were living side by side.

[smd555]

it's very low quality, if you did everything right. it's probably that, because 106 has very few reads. you can try with MZ 100, it's on second place by read number.

sample reads
103 6539551
100 2494647
88 1548942
94 1247768
92 1066147
89 926111
111 696740
110 621407
102 619286
93 457702
105 289604
90 200066
91 179957
99 159295
109 112541
114 104474
95 22557
97 17401
113 17310
98 12112
112 11463
108 8958
101 7049
106 6993
104 6933
96 6177
107 5816

How can I see the sample reads? And how can I find the samples from another works in this database? For example POH13 from Moravia.

[vbnetkhio]

How can I see the sample reads? And how I can find the samples from another works in this database? For example POH13 from Moravia.

That study with POH13 was deleted from the nucleotide archive, it can't be downloaded anymore.

here is the supplementary file of the Polish study:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5965364/bin/gix044_adna_microorganisms_figlerowicz_supplementa ry_tables.xlsx

i went by the number of mapped hg19 reads column. maybe there's a better method, but idk.

[smd555]

Thanks a lot!

[vbnetkhio]

My result of MZ100. Typical Goth:

FINAL ADMIXTURE PROPORTIONS:
----------------------------
49.28% North_Atlantic
33.88% Baltic
10.31% West_Med
2.47% West_Asian
0.00% East_Med
0.02% Red_Sea
0.07% South_Asian
0.00% East_Asian
1.09% Siberian
0.00% Amerindian
0.51% Oceanian
0.09% Northeast_African
2.28% Sub-Saharan

Mixed Mode:
1 80,08% Icelandic + 19,92% Estonian @ 3,986
2 71,48% Icelandic + 28,52% Southwest_Finnish @ 4,023
3 78,52% Icelandic + 21,48% Finnish @ 4,145
4 50,39% North_Swedish + 49,61% Icelandic @ 4,189
5 50,39% Icelandic + 49,61% North_Swedish @ 4,189
6 83,20% Icelandic + 16,80% Lithuanian @ 4,284
7 81,64% Icelandic + 18,36% East_Finnish @ 4,319
8 87,89% Swedish + 12,11% Southwest_Finnish @ 4,379
9 73,05% Norwegian + 26,95% Southwest_Finnish @ 4,405
10 74,61% Swedish + 25,39% North_Swedish @ 4,411

Least-squares method.

Using 1 populations approximation
1 100% Swedish @ 4,808
2 100% Norwegian @ 7,109
3 100% North_Swedish @ 7,158
4 100% Icelandic @ 7,160
5 100% North_Dutch @ 9,264
6 100% Danish @ 9,268
7 100% North_German @ 9,737
8 100% Orcadian @ 10,838
9 100% Irish @ 11,644
10 100% West_Scottish @ 12,260

Using 2 populations approximation
1 50% North_Swedish + 50% Icelandic @ 4,188
2 50% Norwegian + 50% North_Swedish @ 4,482
3 50% Swedish + 50% North_Swedish @ 4,788
4 50% Swedish + 50% Swedish @ 4,808
5 50% West_Scottish + 50% Southwest_Finnish @ 5,098
6 50% North_Swedish + 50% North_Dutch @ 5,181
7 50% North_Swedish + 50% Orcadian @ 5,289
8 50% North_Swedish + 50% Irish @ 5,415
9 50% Irish + 50% Southwest_Finnish @ 5,418
10 50% North_Swedish + 50% Danish @ 5,431

Using 3 populations approximation
1 33% Icelandic + 33% Icelandic + 33% Southwest_Finnish @ 4,163
2 33% Swedish + 33% North_Swedish + 33% Icelandic @ 4,267
3 33% Norwegian + 33% Icelandic + 33% Southwest_Finnish @ 4,326
4 33% Swedish + 33% Swedish + 33% North_Swedish @ 4,453
5 33% Swedish + 33% Norwegian + 33% North_Swedish @ 4,472
6 33% Norwegian + 33% Norwegian + 33% Southwest_Finnish @ 4,582
7 33% North_Swedish + 33% North_Swedish + 33% Icelandic @ 4,613
8 33% North_Swedish + 33% Icelandic + 33% Icelandic @ 4,615
9 33% North_Swedish + 33% North_Swedish + 33% West_Scottish @ 4,657
10 33% Norwegian + 33% North_Swedish + 33% Icelandic @ 4,679

Using 4 populations approximation
1 25% Icelandic + 25% Icelandic + 25% Icelandic + 25% Southwest_Finnish @ 4,080
2 25% North_Swedish + 25% North_Swedish + 25% Icelandic + 25% Icelandic @ 4,188
3 25% Icelandic + 25% Icelandic + 25% Icelandic + 25% Estonian @ 4,235
4 25% Norwegian + 25% Norwegian + 25% Icelandic + 25% Southwest_Finnish @ 4,256
5 25% Icelandic + 25% Icelandic + 25% Icelandic + 25% Finnish @ 4,277
6 25% Swedish + 25% Swedish + 25% North_Swedish + 25% Icelandic @ 4,358
7 25% Swedish + 25% Swedish + 25% Swedish + 25% North_Swedish @ 4,411
8 25% Norwegian + 25% Norwegian + 25% Norwegian + 25% Southwest_Finnish @ 4,427
9 25% Norwegian + 25% Norwegian + 25% North_Swedish + 25% North_Swedish @ 4,482
10 25% Swedish + 25% Swedish + 25% Norwegian + 25% North_Swedish @ 4,513

could you share his 23andme file? i want to merge him with 103.

[smd555]

could you share his 23andme file? i want to merge him with 103.

I shared it. I also added samples 88 and 94 (their K13 results in my next post). Of course, I cannot vouch for the quality of my conversion.

[smd555]

Results for samples MZ_88 and MZ_94:

MZ_88


FINAL ADMIXTURE PROPORTIONS:
----------------------------
41.13% North_Atlantic
29.16% Baltic
15.60% West_Med
0.03% West_Asian
0.00% East_Med
4.23% Red_Sea
0.00% South_Asian
0.07% East_Asian
0.00% Siberian
0.00% Amerindian
3.59% Oceanian
0.90% Northeast_African
5.28% Sub-Saharan

1 58,20% Finnish + 41,80% French_Basque @ 8,730
2 65,23% Southwest_Finnish + 34,77% French_Basque @ 8,903
3 68,36% North_Swedish + 31,64% Spanish_Cantabria @ 9,001
4 67,58% North_Swedish + 32,42% Spanish_Galicia @ 9,035
5 67,58% North_Swedish + 32,42% Southwest_French @ 9,066
6 57,42% Estonian + 42,58% French_Basque @ 9,106
7 58,20% Southwest_Finnish + 41,80% Spanish_Cantabria @ 9,226
8 83,20% North_Swedish + 16,80% Sardinian @ 9,262
9 55,08% East_Finnish + 44,92% French_Basque @ 9,288
10 70,70% North_Swedish + 29,30% Spanish_Extremadura @ 9,419

Least-squares method.

Using 1 populations approximation
1 100% East_German @ 12,483
2 100% Swedish @ 13,194
3 100% Austrian @ 13,598
4 100% North_German @ 13,654
5 100% South_Dutch @ 14,120
6 100% North_Swedish @ 14,178
7 100% Icelandic @ 14,197
8 100% North_Dutch @ 14,421
9 100% Danish @ 14,692
10 100% West_German @ 14,714

Using 2 populations approximation
1 50% East_Finnish + 50% French_Basque @ 9,799
2 50% Southwest_Finnish + 50% Spanish_Cantabria @ 9,812
3 50% Finnish + 50% Spanish_Cantabria @ 9,815
4 50% Lithuanian + 50% French_Basque @ 9,883
5 50% Southwest_Finnish + 50% Southwest_French @ 9,915
6 50% Finnish + 50% French_Basque @ 9,917
7 50% Estonian + 50% French_Basque @ 9,959
8 50% Southwest_French + 50% Finnish @ 10,023
9 50% Southwest_Finnish + 50% Spanish_Galicia @ 10,119
10 50% Spanish_Cantabria + 50% Estonian @ 10,177

Using 3 populations approximation
1 33% Southwest_Finnish + 33% Southwest_Finnish + 33% French_Basque @ 8,917
2 33% North_Swedish + 33% North_Swedish + 33% Spanish_Cantabria @ 9,019
3 33% North_Swedish + 33% North_Swedish + 33% Spanish_Galicia @ 9,037
4 33% North_Swedish + 33% North_Swedish + 33% Southwest_French @ 9,071
5 33% Southwest_Finnish + 33% Ukrainian_Lviv + 33% French_Basque @ 9,277
6 33% Southwest_Finnish + 33% South_Polish + 33% French_Basque @ 9,309
7 33% North_Swedish + 33% North_Swedish + 33% Spanish_Castilla_Y_Leon @ 9,463
8 33% North_Swedish + 33% North_Swedish + 33% Spanish_Extremadura @ 9,531
9 33% North_Swedish + 33% North_Swedish + 33% Portuguese @ 9,538
10 33% North_Swedish + 33% North_Swedish + 33% Spanish_Castilla_La_Mancha @ 9,636

Using 4 populations approximation
1 25% Finnish + 25% Finnish + 25% Spanish_Cantabria + 25% French_Basque @ 9,046
2 25% Finnish + 25% Finnish + 25% Spanish_Castilla_Y_Leon + 25% French_Basque @ 9,052
3 25% Finnish + 25% Finnish + 25% Portuguese + 25% French_Basque @ 9,148
4 25% North_Swedish + 25% North_Swedish + 25% North_Swedish + 25% Spanish_Cantabria @ 9,290
5 25% North_Swedish + 25% North_Swedish + 25% North_Swedish + 25% Spanish_Galicia @ 9,395
6 25% North_Swedish + 25% North_Swedish + 25% North_Swedish + 25% Southwest_French @ 9,405
7 25% North_Swedish + 25% North_Swedish + 25% North_Swedish + 25% Spanish_Extremadura @ 9,546
8 25% North_Swedish + 25% North_Swedish + 25% Icelandic + 25% Spanish_Galicia @ 9,586
9 25% North_Swedish + 25% North_Swedish + 25% North_Swedish + 25% Spanish_Castilla_La_Mancha @ 9,607
10 25% North_Swedish + 25% North_Swedish + 25% North_Swedish + 25% Spanish_Aragon @ 9,649

MZ_94


FINAL ADMIXTURE PROPORTIONS:
----------------------------
51.56% North_Atlantic
25.72% Baltic
4.30% West_Med
2.77% West_Asian
11.65% East_Med
0.00% Red_Sea
0.00% South_Asian
2.69% East_Asian
0.03% Siberian
1.28% Amerindian
0.00% Oceanian
0.00% Northeast_African
0.00% Sub-Saharan

Mixed Mode:
1 94,14% Danish + 5,86% Yemenite_Jew @ 10,220
2 91,80% Norwegian + 8,20% Yemenite_Jew @ 10,220
3 94,92% Danish + 5,08% Lebanese_Druze @ 10,509
4 91,02% Norwegian + 8,98% Lebanese_Druze @ 10,552
5 95,70% Danish + 4,30% Saudi @ 10,609
6 94,92% Danish + 5,08% Palestinian @ 10,638
7 94,14% North_Dutch + 5,86% Yemenite_Jew @ 10,691
8 95,70% Danish + 4,30% Egyptian @ 10,701
9 91,02% Icelandic + 8,98% Yemenite_Jew @ 10,720
10 95,70% Danish + 4,30% Lebanese_Christian @ 10,734

Least-squares method.

Using 1 populations approximation
1 100% Danish @ 11,168
2 100% North_Dutch @ 11,751
3 100% North_German @ 11,964
4 100% Norwegian @ 12,356
5 100% Southeast_English @ 12,474
6 100% Icelandic @ 12,876
7 100% Orcadian @ 13,001
8 100% Swedish @ 13,513
9 100% West_Scottish @ 13,725
10 100% Irish @ 13,970

Using 2 populations approximation
1 50% Danish + 50% Danish @ 11,168
2 50% Danish + 50% North_Dutch @ 11,430
3 50% Danish + 50% North_German @ 11,443
4 50% Danish + 50% Southeast_English @ 11,532
5 50% Danish + 50% Norwegian @ 11,652
6 50% North_Dutch + 50% North_German @ 11,692
7 50% North_German + 50% Southeast_English @ 11,697
8 50% North_Dutch + 50% North_Dutch @ 11,751
9 50% Norwegian + 50% Southeast_English @ 11,802
10 50% North_Dutch + 50% Southeast_English @ 11,854

Using 3 populations approximation
1 33% Danish + 33% Danish + 33% Danish @ 11,168
2 33% Danish + 33% Danish + 33% North_German @ 11,323
3 33% Danish + 33% Danish + 33% North_Dutch @ 11,336
4 33% Danish + 33% Danish + 33% Southeast_English @ 11,342
5 33% Danish + 33% North_German + 33% Southeast_English @ 11,448
6 33% Danish + 33% Danish + 33% Norwegian @ 11,464
7 33% Danish + 33% North_Dutch + 33% North_German @ 11,485
8 33% Danish + 33% North_Dutch + 33% North_Dutch @ 11,531
9 33% Danish + 33% North_Dutch + 33% Southeast_English @ 11,539
10 33% Danish + 33% Danish + 33% West_German @ 11,584

Using 4 populations approximation
1 25% Danish + 25% Danish + 25% Danish + 25% Danish @ 11,168
2 25% Danish + 25% Danish + 25% Danish + 25% Southeast_English @ 11,272
3 25% Danish + 25% Danish + 25% Danish + 25% North_German @ 11,273
4 25% Danish + 25% Danish + 25% Danish + 25% North_Dutch @ 11,291
5 25% Danish + 25% Danish + 25% North_German + 25% Southeast_English @ 11,350
6 25% Danish + 25% Danish + 25% Danish + 25% Norwegian @ 11,380
7 25% Danish + 25% Danish + 25% Danish + 25% West_German @ 11,380
8 25% Danish + 25% Danish + 25% North_Dutch + 25% North_German @ 11,394
9 25% Danish + 25% Danish + 25% North_Dutch + 25% Southeast_English @ 11,412
10 25% Danish + 25% Danish + 25% North_Dutch + 25% North_Dutch @ 11,430

[vbnetkhio]

merged files:

20% genotype rate



FINAL ADMIXTURE PROPORTIONS:
----------------------------
42.07% North_Atlantic
37.45% Baltic
11.95% West_Med
1.95% West_Asian
0.05% East_Med
0.01% Red_Sea
0.01% South_Asian
0.22% East_Asian
0.65% Siberian
0.00% Amerindian
1.47% Oceanian
1.17% Northeast_African
3.00% Sub-Saharan

Mixed Mode:
1 52,73% Estonian + 47,27% Southwest_English @ 4,480
2 50,39% Southwest_English + 49,61% Estonian @ 4,608
3 53,52% Southwest_English + 46,48% Lithuanian @ 4,869
4 51,17% Orcadian + 48,83% Estonian @ 5,031
5 50,39% Estonian + 49,61% Orcadian @ 5,052
6 57,42% Orcadian + 42,58% Lithuanian @ 5,079
7 50,39% Lithuanian + 49,61% Southwest_English @ 5,120
8 50,39% Estonian + 49,61% Southeast_English @ 5,167
9 50,39% Southeast_English + 49,61% Estonian @ 5,179
10 51,95% Estonian + 48,05% West_Scottish @ 5,185

Least-squares method.

Using 1 populations approximation
1 100% North_Swedish @ 7,076
2 100% Southwest_Finnish @ 10,343
3 100% Swedish @ 10,507
4 100% East_German @ 11,399
5 100% North_German @ 13,710
6 100% Norwegian @ 13,912
7 100% Icelandic @ 13,986
8 100% Austrian @ 14,074
9 100% South_Polish @ 14,924
10 100% Danish @ 14,981

Using 2 populations approximation
1 50% Estonian + 50% Southwest_English @ 4,577
2 50% Orcadian + 50% Estonian @ 5,042
3 50% Southwest_English + 50% Lithuanian @ 5,074
4 50% Estonian + 50% Southeast_English @ 5,171
5 50% Estonian + 50% Irish @ 5,211
6 50% Estonian + 50% West_Scottish @ 5,229
7 50% West_Scottish + 50% Lithuanian @ 5,523
8 50% Icelandic + 50% Polish @ 5,643
9 50% Icelandic + 50% Estonian @ 5,662
10 50% North_Dutch + 50% Estonian @ 5,677

Using 3 populations approximation
1 33% Icelandic + 33% Icelandic + 33% Lithuanian @ 5,462
2 33% Southwest_Finnish + 33% Southwest_Finnish + 33% Southwest_English @ 5,528
3 33% Swedish + 33% Swedish + 33% Estonian @ 5,634
4 33% Swedish + 33% Swedish + 33% Estonian_Polish @ 5,671
5 33% North_Swedish + 33% Swedish + 33% Polish @ 5,682
6 33% Norwegian + 33% Icelandic + 33% Lithuanian @ 5,702
7 33% Swedish + 33% Swedish + 33% Lithuanian @ 5,718
8 33% Swedish + 33% Swedish + 33% Polish @ 5,756
9 33% East_German + 33% Norwegian + 33% Estonian @ 5,872
10 33% Southwest_Finnish + 33% Southwest_Finnish + 33% Southeast_English @ 5,882

Using 4 populations approximation
1 25% Southwest_English + 25% Southwest_English + 25% East_Finnish + 25% Lithuanian @ 5,009
2 25% Orcadian + 25% Orcadian + 25% Estonian + 25% Estonian @ 5,042
3 25% Orcadian + 25% Orcadian + 25% Estonian + 25% Lithuanian @ 5,181
4 25% Orcadian + 25% Orcadian + 25% Estonian + 25% Estonian_Polish @ 5,362
5 25% Orcadian + 25% Orcadian + 25% Estonian + 25% Belorussian @ 5,416
6 25% Icelandic + 25% Icelandic + 25% South_Polish + 25% Estonian @ 5,453
7 25% Southwest_English + 25% Southwest_English + 25% Estonian_Polish + 25% Lithuanian @ 5,488
8 25% Swedish + 25% Swedish + 25% East_German + 25% Estonian @ 5,502
9 25% Orcadian + 25% Orcadian + 25% Estonian + 25% Russian_Smolensk @ 5,503
10 25% Southwest_English + 25% Southwest_English + 25% Estonian_Polish + 25% East_Finnish @ 5,612


^results are much more reliable after merging.

[vbnetkhio]

if these were a mix of Goths and Venedi, it seems Venedi were Baltic-like, and lacked the Med admixtures of modern Poles and Ukrainians from this area.

[smd555]

merged files:

20% genotype rate



FINAL ADMIXTURE PROPORTIONS:
----------------------------
42.07% North_Atlantic
37.45% Baltic
11.95% West_Med
1.95% West_Asian
0.05% East_Med
0.01% Red_Sea
0.01% South_Asian
0.22% East_Asian
0.65% Siberian
0.00% Amerindian
1.47% Oceanian
1.17% Northeast_African
3.00% Sub-Saharan

Mixed Mode:
1 52,73% Estonian + 47,27% Southwest_English @ 4,480
2 50,39% Southwest_English + 49,61% Estonian @ 4,608
3 53,52% Southwest_English + 46,48% Lithuanian @ 4,869
4 51,17% Orcadian + 48,83% Estonian @ 5,031
5 50,39% Estonian + 49,61% Orcadian @ 5,052
6 57,42% Orcadian + 42,58% Lithuanian @ 5,079
7 50,39% Lithuanian + 49,61% Southwest_English @ 5,120
8 50,39% Estonian + 49,61% Southeast_English @ 5,167
9 50,39% Southeast_English + 49,61% Estonian @ 5,179
10 51,95% Estonian + 48,05% West_Scottish @ 5,185

Least-squares method.

Using 1 populations approximation
1 100% North_Swedish @ 7,076
2 100% Southwest_Finnish @ 10,343
3 100% Swedish @ 10,507
4 100% East_German @ 11,399
5 100% North_German @ 13,710
6 100% Norwegian @ 13,912
7 100% Icelandic @ 13,986
8 100% Austrian @ 14,074
9 100% South_Polish @ 14,924
10 100% Danish @ 14,981

Using 2 populations approximation
1 50% Estonian + 50% Southwest_English @ 4,577
2 50% Orcadian + 50% Estonian @ 5,042
3 50% Southwest_English + 50% Lithuanian @ 5,074
4 50% Estonian + 50% Southeast_English @ 5,171
5 50% Estonian + 50% Irish @ 5,211
6 50% Estonian + 50% West_Scottish @ 5,229
7 50% West_Scottish + 50% Lithuanian @ 5,523
8 50% Icelandic + 50% Polish @ 5,643
9 50% Icelandic + 50% Estonian @ 5,662
10 50% North_Dutch + 50% Estonian @ 5,677

Using 3 populations approximation
1 33% Icelandic + 33% Icelandic + 33% Lithuanian @ 5,462
2 33% Southwest_Finnish + 33% Southwest_Finnish + 33% Southwest_English @ 5,528
3 33% Swedish + 33% Swedish + 33% Estonian @ 5,634
4 33% Swedish + 33% Swedish + 33% Estonian_Polish @ 5,671
5 33% North_Swedish + 33% Swedish + 33% Polish @ 5,682
6 33% Norwegian + 33% Icelandic + 33% Lithuanian @ 5,702
7 33% Swedish + 33% Swedish + 33% Lithuanian @ 5,718
8 33% Swedish + 33% Swedish + 33% Polish @ 5,756
9 33% East_German + 33% Norwegian + 33% Estonian @ 5,872
10 33% Southwest_Finnish + 33% Southwest_Finnish + 33% Southeast_English @ 5,882

Using 4 populations approximation
1 25% Southwest_English + 25% Southwest_English + 25% East_Finnish + 25% Lithuanian @ 5,009
2 25% Orcadian + 25% Orcadian + 25% Estonian + 25% Estonian @ 5,042
3 25% Orcadian + 25% Orcadian + 25% Estonian + 25% Lithuanian @ 5,181
4 25% Orcadian + 25% Orcadian + 25% Estonian + 25% Estonian_Polish @ 5,362
5 25% Orcadian + 25% Orcadian + 25% Estonian + 25% Belorussian @ 5,416
6 25% Icelandic + 25% Icelandic + 25% South_Polish + 25% Estonian @ 5,453
7 25% Southwest_English + 25% Southwest_English + 25% Estonian_Polish + 25% Lithuanian @ 5,488
8 25% Swedish + 25% Swedish + 25% East_German + 25% Estonian @ 5,502
9 25% Orcadian + 25% Orcadian + 25% Estonian + 25% Russian_Smolensk @ 5,503
10 25% Southwest_English + 25% Southwest_English + 25% Estonian_Polish + 25% East_Finnish @ 5,612


^results are much more reliable after merging.

How did you merged them? By standard algorithm in DNAKitStudio?

[vbnetkhio]

How did you merged them? By standard algorithm in DNAKitStudio?

Yes

[smd555]

Yes

My result, I have an Admixture Studio v.2.50:


41.19% North_Atlantic
38.03% Baltic
13.03% West_Med
0.55% West_Asian
0.05% East_Med
0.00% Red_Sea
0.00% South_Asian
1.11% East_Asian
0.16% Siberian
0.00% Amerindian
1.53% Oceanian
2.18% Northeast_African
2.17% Sub-Saharan

[vbnetkhio]

My result, I have an Admixture Studio v.2.50:

The order you merge them in matters, because if they have different alleles on the same position, one gets overwritten.

I aldo added that low quality one you converted first but i think it contributed badically 0 snps.

[smd555]

The order you merge them in matters, because if they have different alleles on the same position, one gets overwritten.

I aldo added that low quality one you converted first but i think it contributed badically 0 snps.

What are the advantages of merging them?

PS I still have a question about the samples from Moravia. Is there any data on sample LIB3(Italian-like) or the results of K-13? G25 in this case does not interest me.

[vbnetkhio]

What are the advantages of merging them?

PS I still have a question about the samples from Moravia. Is there any data on sample LIB3(Italian-like) or the results of K-13? G25 in this case does not interest me.

The individual samples have a lot of noise and unrealistic components, so you can't do an accurate comparison with other samples and populations, When you merge them that's fixed.

That study isn't published yet, and the data was just temporarily available. It will probably be available again when the study is published.

[vbnetkhio]

Given these results, proto-Slavs must've come from a small area in the extreme Southeast of Poland and the extreme Southwest of Ukraine.

[smd555]

Given these results, proto-Slavs must've come from a small area in the extreme Southeast of Poland and the extreme Southwest of Ukraine.

Ukrainian archeologists (not of them, but many) connect the origin of the Prague-Korchak culture with a local group of the Chernyakhiv culture of the upper Transnistria. Belarussian archeologists instead are developing a version of the origin of the Prague-Korchak culture on the basis of the late Zarubynets sites of the middle Pripyat basin (Belarussian territory). Each version has its advantages and disadvantages.

[vbnetkhio]

Ukrainian archeologists (not of them, but many) connect the origin of the Prague-Korchak culture with a local group of the Chernyakhiv culture of the upper Transnistria. Belarussian archeologists instead are developing a version of the origin of the Prague-Korchak culture on the basis of the late Zarubynets sites of the middle Pripyat basin (Belarussian territory). Each version has its advantages and disadvantages.

Linguists and Archaeologists place the homeland in many different parts of Poland and Ukraine, there are multiple conflicting theories.

But if the Balto-Slavs in Maslomecz were Estonian like, then the proper Slavs had to come from somewhere further south.

[smd555]

.......
because of that I also run "bcftools filter" on the second BCF file. select the second bcf file, then upload this file : https://easyupload.io/769eny , then under Restrict To > Regions select "Operate on Regions specified in a history dataset", and select this dataset you uploaded (new.tsv), and for your output type select "uncompressed VCF".......


"FILE NOT FOUND" - Can you refresh it?