Admixtools ancIBD github

Jovialis · Jan 26, 2024

GitHub - hringbauer/ancIBD: Detecting IBD within low coverage ancient DNA data. Development Repository for software package that contains code for manuscript.

Detecting IBD within low coverage ancient DNA data. Development Repository for software package that contains code for manuscript. - GitHub - hringbauer/ancIBD: Detecting IBD within low coverage an...

github.com

So who is the genius that is going to figure this one out?

Jovialis · Jan 26, 2024

Hmm, looks like you first need to convert aDNA files to VCF format, and impute them with GLIMPES, which a pretty massive first step.

FASTQ to SAM to BAM to Sorted-BAM to VCF is a pretty large undertaking for just a single file.

Thus, the ability for us to get ahead of the curve, and figure out which samples are best to use before they even come out in papers is possible. But it would require a herculean undertaking by several members of the community, merely just to convert the samples to VCF.

Though most samples come as sorted BAMs already on ENA. So to endeavor to do a wide-scale project is feasible. If it is FASTQ, forget it.

Jovialis · Jan 26, 2024

BAMs to VCF
VCF imputed in GLIMPES
Imputed files processed in ancIBD
Identify best samples to use in qpAdm

That's how the hobbyist community would get ahead of the curve from academic papers.

Salento · Jan 27, 2024

Jovialis said:
BAMs to VCF

VCF imputed in GLIMPES

Imputed files processed in ancIBD

Identify best samples to use in qpAdm

That's how the hobbyist community would get ahead of the curve from academic papers.

Hi Jovialis, here is a link with the Imputed VCF and Eigenstrat Antonio_2019 (includes a non imputed VCF called with the "1000 Genomes"), but they are not GLIMPES ..they are Beagles Imputed. The VCF contains all the samples, but they can be extracted individually, ... or convert the VCF to plink and extract each sample to VCF.
The Link: (after download ... untar, then navigate and untar again)

ancient_rome_web.tar.gz

drive.google.com

from: http://web.stanford.edu/group/pritchardlab/dataArchive.html

I converted the Imputed VCF into a "Reich" 1240k and HO Eigenstrat/Plink, ... with 1240K: about 96% coverage per sample ... I played around with it: converting, extracting, merging, ... Here is the Link:

AncientRome-1240K_and_HO_Imputed

MediaFire is a simple to use free service that lets you put all your photos, documents, music, and video in a single place so you can access them anywhere and share them everywhere.

www.mediafire.com

One output ... imputed R437 dodK12b:

Code:

R437_cov-96.29%,6.30,0,3.19,0,32.31,11.57,0,0,11.85,0.70,34.01,0.07

Salento · Jan 31, 2024

Found a GLIMPSE VCF, after filtering I extracted, edited the heads, and tested the Antonio_2019 samples, ... we know that R53 and R54 are related.

Some Resuts:

IBD

iid1	iid2	max_IBD	sum_IBD>8.0	n_IBD>8.0	sum_IBD>12.0	n_IBD>12.0	sum_IBD>16.0	n_IBD>16.0	sum_IBD>20.0	n_IBD>20.0
R53	R54	28.0063986778259	80.6819975376129	4	72.3859965801239	3	72.3859965801239	3	72.3859965801239	3
R54	R64	33.1764996051788	75.3223031759262	3	64.697203040123	2	64.697203040123	2	64.697203040123	2
R52	R53	32.5489997863769	62.9499077796936	3	53.7110030651093	2	53.7110030651093	2	53.7110030651093	2
R53	R64	53.3635973930359	53.3635973930359	1	53.3635973930359	1	53.3635973930359	1	53.3635973930359	1
R9	R17	12.1754944324493	21.9883859157562	2	12.1754944324493	1	0	0	0	0
R11	R15	10.3309035301209	19.3359971046448	2	0	0	0	0	0	0
R54	R60	12.4449014663696	12.4449014663696	1	12.4449014663696	1	0	0	0	0

CH_ALL

Start	End	StartM	EndM	length	lengthM	ch	iid1	iid2
4606	18543	0.577737	1.41346001625061	13937	0.835723042488098	15	R53	R54
17905	31857	1.186976	1.99431502819061	13952	0.807339072227478	1	R53	R54
17011	26303	1.140008	1.72522497177124	9292	0.585216999053955	1	R54	R64
17938	26303	1.188959	1.72522497177124	8365	0.536265969276428	1	R53	R64
10466	22910	0.627808	1.16144394874573	12444	0.533635973930359	3	R53	R64
717	8656	0.095289	0.584698975086212	7939	0.489409975707531	20	R53	R54
2607	8377	0.224026	0.659416019916534	5770	0.435390025377274	16	R53	R54
20	4130	0.014738	0.448329985141754	4110	0.433591985143721	17	R53	R64
12222	17141	0.789812028408051	1.17709004878998	4919	0.387278020381927	18	R53	R54
27088	33001	1.29929494857788	1.68000900745392	5913	0.380714058876038	8	R53	R54
5872	8528	0.649466	1.02555799484253	2656	0.37609201669693	19	R54	R64
4035	10914	0.308542	0.656117022037506	6879	0.347575008869171	7	R53	R54
836	6893	0.132061	0.478502005338669	6057	0.346441000699997	14	R53	R64

VCF files:

Public Archive: 917f1ac64148c3800ab7baa29402d088

erda.ku.dk

some example:
... after filtering: VCFs Head Editing:
bcftools head Romans_1.vcf.gz > 1header.hr
bcftools head Romans_2.vcf.gz > 2header.hr
bcftools head Romans_3.vcf.gz > 3header.hr
...and so on

Edit all Heads with the one below (copy and paste), replace ##contig=<ID=1> to 2header.hr with ##contig=<ID=2> save it, ...and so on.
##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=30/10/2021 - 05:10:05
##source=GLIMPSE_phase v1.0.0
##contig=<ID=1>
##INFO=<ID=RAF,Number=A,Type=Float,Description="ALT allele frequency in the reference panel">
##INFO=<ID=AF,Number=A,Type=Float,Description="ALT allele frequency computed from DS/GP field across target samples">
##INFO=<ID=INFO,Number=A,Type=Float,Description="Imputation information or quality score">
##INFO=<ID=BUF,Number=A,Type=Integer,Description="Is it a variant site falling within buffer regions? (0=no/1=yes)">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Unphased genotypes">
##FORMAT=<ID=DS,Number=1,Type=Float,Description="Genotype dosage">
##FORMAT=<ID=GP,Number=3,Type=Float,Description="Genotype posteriors">
##FORMAT=<ID=HS,Number=1,Type=Integer,Description="Sampled haplotype pairs packed into intergers (max: 16 pairs, see NMAIN header line)">
##NMAIN=15
##INFO=<ID=pan_troglodytes,Number=1,Type=String,Description="allele observed in pan_troglodytes">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths (high-quality bases)">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
##INFO=<ID=MASK_1000G,Number=0,Type=Flag,Description="SNP is in 1000G strict mask region">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##reference=ftp://ftp.1000genomes.ebi.ac.uk//vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz
##bcftools_viewVersion=1.13+htslib-1.13
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT R1 R2 R3 R4 R5 R6 R7 R8 R9 R10 R11 R15 R16 R17 R18 R19 R22 R24 R25 R26 R27 R28 R29 R30 R31 R32 R33 R34 R35 R36 R37 R38 R39 R40 R41 R42 R43 R44 R45 R47 R49 R50 R51 R52 R53 R54 R55 R56 R57 R58 R59 R60 R61 R62 R63 R64 R65 R66 R67 R68 R69 R70 R71 R72 R73 R75 R76 R78 R80 R81 R104 R105 R106 R107 R108 R109 R110 R111 R113 R114 R115 R116 R117 R118 R120 R121 R122 R123 R125 R126 R128 R130 R131 R132 R133 R134 R136 R137 R435 R436 R437 R473 R474 R475 R835 R836 R850 R851 R969 R970 R973 R1014 R1015 R1016 R1021 R1219 R1220 R1221 R1224 R1283 R1285 R1286 R1287 R1288 R1289 R1290 R1543 R1544 R1545 R1547 R1548 R1549 R1550 R1551

Now we replace the Heads:
bcftools reheader -h 1header.hr Romans_1.vcf.gz > Romans_chr1.vcf.gz
bcftools reheader -h 2header.hr Romans_2.vcf.gz > Romans_chr2.vcf.gz
bcftools reheader -h 3header.hr Romans_3.vcf.gz > Romans_chr3.vcf.gz
... and so on

Jovialis · Jan 31, 2024

Thank you so much for this Salento,

I've been slacking, but I'm happy to see that you're endeavoring to undertake this analysis.

I look forward to the future!

Jovialis · Jan 31, 2024

https://twitter.com/x/status/1752716368087076940

Jovialis · Jan 31, 2024

@Salento

Would you be able to test C_Italian_N, and C_Italian_ChL relative tot he pertinent Roman samples? As well as modern samples?

I hope it isn't asking for a lot, but it would really be ground breaking, imo

Admixtools - C_Italian_N/ChL to Model Iron Age & Modern Italians

Only ITS5 had a sub-optimal p-vaule, but the other metrics looked good. Here are modern Italian populations using C_Italian_N and C_Italian_ChL, along with Steppe_EMBA, and Iran_N_CHG. Since TSI and the North can be modeled with WHG, it works with the ChL central Italian sample since there was...

www.eupedia.com

Jovialis · Jan 31, 2024

@Salento

Another senario to explore ancIBD analysis with C6 Imperial Romans vs Modern Italian populations.

As well as C5 vs Modern Italian.

Salento · Feb 1, 2024

Jovialis said:
@Salento

Would you be able to test C_Italian_N, and C_Italian_ChL relative tot he pertinent Roman samples? As well as modern samples?

I hope it isn't asking for a lot, but it would really be ground breaking, imo

Admixtools - C_Italian_N/ChL to Model Iron Age & Modern Italians

Only ITS5 had a sub-optimal p-vaule, but the other metrics looked good. Here are modern Italian populations using C_Italian_N and C_Italian_ChL, along with Steppe_EMBA, and Iran_N_CHG. Since TSI and the North can be modeled with WHG, it works with the ChL central Italian sample since there was...

www.eupedia.com

I don't have any imputed modern samples. This is the IBD (closest samples), I uploaded the chr files:

Antonio_2019_ibd

MediaFire is a simple to use free service that lets you put all your photos, documents, music, and video in a single place so you can access them anywhere and share them everywhere.

www.mediafire.com

The ch_all_C_Ita_N-C_Ita_ChL file has the relations of R6 R10 R2 R3 R8 R9 R19 R16 R17 R18 R4 R5 R1014 with the R samples, ... the ch_all_Antonio_2019 file has the complete relations of all the samples.

iid1	iid2	max_IBD	sum_IBD>8.0	n_IBD>8.0	sum_IBD>12.0	n_IBD>12.0	sum_IBD>16.0	n_IBD>16.0	sum_IBD>20.0	n_IBD>20.0
R53	R54	28.0063986778259	80.6819975376129	4	72.3859965801239	3	72.3859965801239	3	72.3859965801239	3
R54	R64	33.1764996051788	75.3223031759262	3	64.697203040123	2	64.697203040123	2	64.697203040123	2
R52	R53	32.5489997863769	62.9499077796936	3	53.7110030651093	2	53.7110030651093	2	53.7110030651093	2
R53	R64	53.3635973930359	53.3635973930359	1	53.3635973930359	1	53.3635973930359	1	53.3635973930359	1
C_Ita_N_R9	C_Ita_N_R17	12.1754944324493	21.9883859157562	2	12.1754944324493	1	0	0	0	0
R11	R15	10.3309035301209	19.3359971046448	2	0	0	0	0	0	0
R54	R60	12.4449014663696	12.4449014663696	1	12.4449014663696	1	0	0	0	0
R56	R58	11.5373015403748	11.5373015403748	1	0	0	0	0	0	0
C_Ita_N_R6	C_Ita_N_R19	11.2657964229584	11.2657964229584	1	0	0	0	0	0	0
R7	R11	10.1803958415985	10.1803958415985	1	0	0	0	0	0	0
C_Ita_N_R8	C_Ita_N_R18	10.130500793457	10.130500793457	1	0	0	0	0	0	0
C_Ita_N_R10	C_Ita_ChL_R1014	9.81310009956359	9.81310009956359	1	0	0	0	0	0	0
R65	R973	9.791100025177	9.791100025177	1	0	0	0	0	0	0
C_Ita_N_R2	C_Ita_N_R9	9.52811241149902	9.52811241149902	1	0	0	0	0	0	0
R64	R65	9.16879177093505	9.16879177093505	1	0	0	0	0	0	0
R969	R973	8.83970260620117	8.83970260620117	1	0	0	0	0	0	0
R1015	R1021	8.82660150527954	8.82660150527954	1	0	0	0	0	0	0
C_Ita_N_R18	C_Ita_N_R19	8.78140330314636	8.78140330314636	1	0	0	0	0	0	0
C_Ita_N_R16	C_Ita_N_R18	8.39280188083648	8.39280188083648	1	0	0	0	0	0	0
R115	R123	8.35940241813659	8.35940241813659	1	0	0	0	0	0	0
C_Ita_N_R17	C_Ita_N_R19	8.33070278167724	8.33070278167724	1	0	0	0	0	0	0
R25	R28	8.21419954299926	8.21419954299926	1	0	0	0	0	0	0
R850	R1543	8.13609361648559	8.13609361648559	1	0	0	0	0	0	0

Jovialis · Feb 1, 2024

@Salento

How about Imperial era-Late Antiquity C6 (as well as IA 437) and C5 vs medieval Italian samples? That would be the next best thing.

@Pax Augusta

I recall you have access to modern Italian samples, providing them to Salento for the purpose of ancIBD analysis would be much appreciated.

Salento · Feb 3, 2024

Jovialis said:
@Salento

How about Imperial era-Late Antiquity C6 (as well as IA 437) and C5 vs medieval Italian samples? That would be the next best thing.

@Pax Augusta

I recall you have access to modern Italian samples, providing them to Salento for the purpose of ancIBD analysis would be much appreciated.

Hi Jovialis,
I found the link of the IBD study and they provide an ancient-samples V54.1file, but it just contains the chromosome matches between the samples. Not all samples passed their quality filters. I sorted the file by the chromosomes, then split it into 22 files, and then I ran the ancIBD. I am providing the link below. I also found an already processed ancIBD for Eurasia and have included that below as well. I used one of your files as info about the V54.1 sample.

Accurate detection of identity-by-descent segments in human ancient DNA - Nature Genetics

ancIBD identifies identity-by-descent regions in ancient DNA using a hidden Markov model optimized for these low-coverage data. Analysis of 4,248 individuals demonstrates that ancIBD can identify up to sixth-degree relatives and provides genealogical insights into ancient populations.

www.nature.com

ibds_Anc_v54_Anc_Eurasia

MediaFire is a simple to use free service that lets you put all your photos, documents, music, and video in a single place so you can access them anywhere and share them everywhere.

www.mediafire.com

Jovialis · Feb 5, 2024

Salento said:
Hi Jovialis,
I found the link of the IBD study and they provide an ancient-samples V54.1file, but it just contains the chromosome matches between the samples. Not all samples passed their quality filters. I sorted the file by the chromosomes, then split it into 22 files, and then I ran the ancIBD. I am providing the link below. I also found an already processed ancIBD for Eurasia and have included that below as well. I used one of your files as info about the V54.1 sample.

Accurate detection of identity-by-descent segments in human ancient DNA - Nature Genetics

ancIBD identifies identity-by-descent regions in ancient DNA using a hidden Markov model optimized for these low-coverage data. Analysis of 4,248 individuals demonstrates that ancIBD can identify up to sixth-degree relatives and provides genealogical insights into ancient populations.

www.nature.com

ibds_Anc_v54_Anc_Eurasia

MediaFire is a simple to use free service that lets you put all your photos, documents, music, and video in a single place so you can access them anywhere and share them everywhere.

www.mediafire.com

Would you be able to test R437 against Imperial samples, Late Antiquity sample and MA samples of C6?

I would also think Imperial samples vs Late Antiquity, and Late Antiquity vs MA would be great.

Salento · Feb 7, 2024

Jovialis said:
Would you be able to test R437 against Imperial samples, Late Antiquity sample and MA samples of C6?

I would also think Imperial samples vs Late Antiquity, and Late Antiquity vs MA would be greatI

I uploaded the v54.1 (Reich) AncIBD (Post #12).
It takes some time to go through the samples … sorting.
The V54_ibd_ind.tsv file is a summary of closer relations, the V54_ch_all.tsv file could contain Ancestral connections, I Think : )

Salento · Feb 16, 2024

I merged and processed all the Ancient Italians in the v54.1 and the Allentoft.
I extracted 220 ibd files and 306 ch files, each file is dedicated to a sample ... kind of a chr. deep dive.
... the download link:

Ancient_ibd_Italy

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www.mediafire.com

Salento · Feb 16, 2024

R437
ibd

iid1	iid2	max_IBD	sum_IBD>8.0
R10340_IA_Tarq_Monter	R437_IA	10.0826025	10.0826025
SUC001_Sardinia_EBA	R437_IA	8.1436992	8.1436992

Chrs:

Start	End	StartM	EndM	length	lengthM	ch	iid1	iid2
45356	46257	1.501041	1.593661	633	0.09262	1	NEO830_C_Marche_Fontenoce	R437_IA
45624	46257	1.501041	1.593661	633	0.09262	1	C6-R118_LA	R437_IA
45749	46350	1.500539	1.619487	748	0.118948	1	R437_IA	C6-R835_Imperial
45568	46441	1.499977	1.620654	873	0.120677	1	R437_IA	R850_IA
45737	46350	1.537566	1.619487	616	0.081921	1	R437_IA	R1015_IA
45724	46219	1.492525	1.577133	1133	0.084608	1	R437_IA	C5-R1548_Imperial
45624	46257	1.503838	1.593661	573	0.089823	1	R437_IA	C6-R1549_Imperial
45739	46350	1.537566	1.619487	616	0.081921	1	R437_IA	RISE487-Copper-Age
19946	46257	1.501079	1.593661	624	0.092582	1	C6-R64_Medieval_EarlyModern	R437_IA
36269	46068	1.489244	1.573993	1082	0.084749	1	C4-R70_Imperial	R437_IA
11507	46257	1.500574	1.593661	651	0.093087	1	C3-R80_Imperial	R437_IA
20858	23422	0.715169	0.796606	2564	0.081437	4	SUC001_Sardinia_EBA	R437_IA
31566	34584	1.01244	1.077913	3018	0.065473	4	SUC002_Sardinia_EBA_Nuragic	R437_IA
4676	7537	0.264554	0.338146	2861	0.073592	4	R1291_Medieval	R437_IA
33546	36490	1.056392	1.123901	2944	0.067509	4	TAQ004_Etruscan	R437_IA
58124	60029	1.367146	1.427351	1905	0.060205	6	R10337_o-IA	R437_IA
53676	55260	1.576529	1.643901	1584	0.067372	7	I15942_Sardinia_N	R437_IA
7572	9718	0.275359	0.340871	2146	0.065512	11	C6-R125_Imperial	R437_IA
24072	27190	0.927009	1.027835	3118	0.100826	16	R10340_IA_Tarq_Monter	R437_IA
1570	3007	0.107968	0.17155	1437	0.063582	21	CL83_North_EarlyMedieval_Langobards_1	R437_IA

Salento · Feb 16, 2024

R850
ibd:

iid1	iid2	max_IBD	sum_IBD>8.0	n_IBD>8.0
R850_IA	C5-R1543_Imperial	9.755802	17.9197	2

chrs:

Start	End	StartM	EndM	length	lengthM	ch	iid1	iid2
45560	46110	1.488374	1.575059	1261	0.086685	1	C7-R109_LA	R850_IA
45684	46441	1.537566	1.620654	707	0.083088	1	R18_Central_Ita_N	R850_IA
45624	46423	1.500673	1.620281	804	0.119608	1	R27_Sardinia_C_BA	R850_IA
45086	46253	1.496666	1.593597	789	0.096931	1	C7-R37_Imperial	R850_IA
45568	46441	1.499977	1.620654	873	0.120677	1	R437_IA	R850_IA
70274	47001	1.548331	1.628971	1234	0.08064	1	R473_IA	R850_IA
29008	46535	1.500554	1.621222	930	0.120668	1	C5-R69_Imperial	R850_IA
18	46395	1.500574	1.62015	789	0.119576	1	C6-R835_Imperial	R850_IA
30543	46519	1.508284	1.620918	795	0.112634	1	R850_IA	C6-R973_Medieval_EarlyModern
38676	40447	1.135862	1.197236	1771	0.061374	2	R850_IA	SUA005_Sardinia_EBA
47491	51612	1.300313	1.397871	4121	0.097558	3	R850_IA	C5-R1543_Imperial
20356	50506	1.315567	1.397206	3417	0.081639	3	R850_IA	C5-R1543_Imperial
40893	44067	1.174066	1.251555	3174	0.077489	5	CSN013_Etruscan	R850_IA
50679	52362	1.422227	1.497685	1683	0.075458	11	R850_IA	R6_Central_Ita_N
27234	28763	1.069454	1.133757	1529	0.064303	15	PRZ001_Etruscan	R850_IA
45552	2171	0.050574	0.140218	1364	0.089644	21	C2-R19_N	R850_IA

Salento · Feb 16, 2024

R1
ibd

iid1	iid2	max_IBD	sum_IBD>8.0	n_IBD>8.0
R11105-BA	R1_Proto-Villanovan	8.033007	8.033007	1

chrs

Start	End	StartM	EndM	length	lengthM	ch	iid1	iid2
48987	50862	1.660108	1.721329	1875	0.061221	1	C6-R136_LA	R1_Proto-Villanovan
45684	45990	1.487406	1.572117	1225	0.084711	1	R1_Proto-Villanovan	C7-R1224_Medieval_EarlyModern
38244	39786	1.122371	1.187115	1542	0.064744	2	MA82_Sardinia_BA_Nuragic_o	R1_Proto-Villanovan
73003	74956	2.011579	2.072362	1953	0.060783	2	C6-R125_Imperial	R1_Proto-Villanovan
73135	75256	2.014162	2.078809	2121	0.064647	2	TAQ023_Etruscan	R1_Proto-Villanovan
57715	59609	1.544242	1.605667	1894	0.061425	3	VOL001_Etruscan	R1_Proto-Villanovan
1507	2914	0.049938	0.112881	1407	0.062943	3	f1R_Pompeii_Roman	R1_Proto-Villanovan
11750	13878	0.426289	0.487623	2128	0.061334	10	VK535_Medieval	R1_Proto-Villanovan
54804	56258	1.646655	1.706911	1454	0.060256	10	R11109_Roman_Imperial	R1_Proto-Villanovan
15729	18023	0.543262	0.604112	2294	0.06085	10	BRC003_Broion_BA	R1_Proto-Villanovan
3799	5379	0.217258	0.282348	1580	0.06509	14	C6-R1549_Imperial	R1_Proto-Villanovan
22913	25733	0.947304	1.016473	2820	0.069169	15	R11104-BA	R1_Proto-Villanovan
22644	25733	0.936143	1.016473	3089	0.08033	15	R11105-BA	R1_Proto-Villanovan
26728	28189	1.042964	1.107793	1461	0.064829	15	R11112_Roman_Imperial	R1_Proto-Villanovan
5622	7688	0.438118	0.502726	2066	0.064608	19	C6-R51_Imperial	R1_Proto-Villanovan
2596	4469	0.154807	0.225011	1873	0.070204	21	R10363_IA_Tarq_Monter	R1_Proto-Villanovan

Salento · Feb 16, 2024

R2
ibd

iid1	iid2	max_IBD	sum_IBD>8.0	n_IBD>8.0	sum_IBD>12.0	n_IBD>12.0	sum_IBD>16.0	n_IBD>16.0	sum_IBD>20.0	n_IBD>20.0
R2_N	R3_N	19.0733999	38.1451994	2	38.1451994	2	38.1451994	2	0	0
R2_N	R9_Central_Ita_N	9.572196	38.0495071	4	0	0	0	0	0	0
R16_Central_Ita_N	R2_N	22.072506	22.072506	1	22.072506	1	22.072506	1	22.072506	1
R2_N	R16_Central_Ita_N	16.2611008	16.2611008	1	16.2611008	1	16.2611008	1	0	0
UZZ075_Sicily_N_Stentinello	R2_N	9.8846018	9.8846018	1	0	0	0	0	0	0
UZZ061_Sicily_MN	R2_N	9.6159995	9.6159995	1	0	0	0	0	0	0
I10372_Sicily_LBA	R2_N	8.6050987	8.6050987	1	0	0	0	0	0	0
R2_N	R435_IA	8.1303	8.1303	1	0	0	0	0	0	0
R2_N	R8_Central_Ita_N	8.0846997	8.0846997	1	0	0	0	0	0	0
R17_Central_Ita_N	R2_N	8.0645993	8.0645993	1	0	0	0	0	0	0

chrs

Start	End	StartM	EndM	length	lengthM	ch	iid1	iid2
2005	3806	0.137596995	0.216137007	1801	0.078540012	1	R27_Sardinia_C_BA	R2_N
24957	27259	0.930208981	0.991662979	2302	0.061453998	1	TAQ011_EarlyMedieval	R2_N
45615	46692	1.500581	1.625437021	1082	0.124855995	1	NEO834_N_Lazio_Mora_Cavorso	R2_N
45628	47051	1.549553	1.630337	1265	0.080783963	1	R2_N	C4-R126_Imperial
45738	47051	1.549553	1.630337	1265	0.080783963	1	R2_N	R474_IA
45568	46350	1.537566	1.619487047	616	0.081921101	1	R2_N	RISE487-Copper-Age
71684	75789	1.990731955	2.086445093	4105	0.095713139	2	R2_N	R9_Central_Ita_N
89367	91361	2.497324944	2.583375931	1994	0.086050987	2	I10372_Sicily_LBA	R2_N
91037	92739	2.568685055	2.630580902	1702	0.061895847	2	SEC001_Sardinia_LateC	R2_N
90167	91607	2.527739048	2.588927984	1440	0.061188936	2	VK537_Medieval	R2_N
24430	74321	1.990732	2.086453915	4047	0.09572196	2	R2_N	R9_Central_Ita_N
58133	60273	1.554507017	1.631090999	2140	0.076583982	3	ORC003_Sardinia_BA_Nuragic	R2_N
6564	9372	0.313910991	0.386018991	2808	0.072108001	4	SEC001_Sardinia_LateC	R2_N
45025	64935	1.89795	2.019859076	2527	0.121909022	4	R2_N	R8_Central_Ita_N
7290	13148	0.285535008	0.476269007	5858	0.190733999	5	R2_N	R3_N
63196	64923	1.761191964	1.822545052	1727	0.061353087	5	MA89_Sardinia_C_o	R2_N
34377	12916	0.285551	0.476269007	5765	0.190717995	5	R2_N	R3_N
45569	2097	0.001231	0.101108	2075	0.099877	5	R2_N	R8_Central_Ita_N
44731	52681	1.211635947	1.432361007	7950	0.22072506	8	R16_Central_Ita_N	R2_N
51751	53850	1.400908947	1.461097956	2099	0.060189009	8	CAM001_Etruscan	R2_N
34469	51787	1.269736	1.432347059	4823	0.162611008	8	R2_N	R16_Central_Ita_N
507	2183	0.013436	0.082525	1676	0.069089	9	I11442_Sicily_EBA	R2_N
15891	19014	0.535694003	0.600072026	3123	0.064378023	9	SEC001_Sardinia_LateC	R2_N
45789	2111	0.001721	0.082567997	2104	0.080846997	9	R2_N	R8_Central_Ita_N
18572	20584	0.619316995	0.695451021	2012	0.076134026	10	R435_IA	R2_N
46760	48954	1.36146903	1.423848033	2194	0.062379003	10	UZZ061_Sicily_MN	R2_N
45682	20297	0.619317	0.700619996	2098	0.081303	10	R2_N	R435_IA
52059	54434	1.482099056	1.576629043	2375	0.094529986	11	R2_N	R9_Central_Ita_N
39117	41880	1.075420976	1.136703968	2763	0.061282992	11	R10_Central_Ita_N	R2_N
52310	53941	1.494881988	1.556825995	1631	0.061944008	11	R6_Central_Ita_N	R2_N
25570	27757	0.757281005	0.817951977	2187	0.060670972	11	R16_Central_Ita_N	R2_N
45023	53446	1.482099	1.576629043	2337	0.094529986	11	R2_N	R9_Central_Ita_N
7618	9883	0.334344	0.404110998	2265	0.069766998	12	R6_Central_Ita_N	R2_N
19989	21816	0.655708015	0.72073698	1827	0.065028965	13	R10359_IA_Tarq_Monter	R2_N
19765	21720	0.645138979	0.718185008	1955	0.073046029	13	R10340_IA_Tarq_Monter	R2_N
1665	3107	0.286956996	0.349321008	1442	0.062364012	15	I15941_Sardinia_N	R2_N
5665	7303	0.481649995	0.54222703	1638	0.060577035	15	SUA005_Sardinia_EBA	R2_N
18067	19894	0.812776029	0.875326991	1827	0.062550962	15	SUC001_Sardinia_EBA	R2_N
1147	2646	0.251805991	0.318470001	1499	0.06666401	15	I16163_Sardinia_IA_2	R2_N
5630	7532	0.47794801	0.545428991	1902	0.067480981	15	TAQ018_Etruscan	R2_N
45684	3200	0.253735	0.353794992	2035	0.100059986	15	R2_N	R3_N
32833	586	0.137574	0.220005006	579	0.082431003	15	R2_N	VK536_Medieval
20699	22973	0.866717994	0.962877989	2274	0.096159995	17	UZZ061_Sicily_MN	R2_N
45724	4767	0.191418	0.272370994	1474	0.080952987	17	R2_N	R8_Central_Ita_N
45077	27676	1.156899	1.24238205	968	0.085483074	17	R2_N	R9_Central_Ita_N
6506	8287	0.366118014	0.42987299	1781	0.063754976	18	I15941_Sardinia_N	R2_N
45396	4585	0.147845	0.266223997	2152	0.118378997	18	NEO695_N_Marche_Maddalena_di_Muccia	R2_N
8087	10467	0.513391972	0.61223799	2380	0.098846018	19	UZZ075_Sicily_N_Stentinello	R2_N
11938	13325	0.46726501	0.529644012	1387	0.062379003	21	SUA007_Sardinia_EBA	R2_N
7222	9458	0.309733987	0.386642009	2236	0.076908022	21	R1014_ChL	R2_N
2501	4305	0.220531002	0.301176995	1804	0.080645993	22	R17_Central_Ita_N	R2_N

Salento · Feb 16, 2024

R6
ibd

iid1	iid2	max_IBD	sum_IBD>8.0	n_IBD>8.0	sum_IBD>12.0	n_IBD>12.0
R6_Central_Ita_N	R29_Sardinia_C_BA	10.9028995	21.1015969	2	0	0
R6_Central_Ita_N	R16_Central_Ita_N	8.5166991	17.0313969	2	0	0
UZZ061_Sicily_MN	R6_Central_Ita_N	13.1358027	13.1358027	1	13.1358027	1
R6_Central_Ita_N	C2-R19_N	11.2821996	11.2821996	1	0	0
R6_Central_Ita_N	MA89_Sardinia_C_o	9.1458999	9.1458999	1	0	0
R6_Central_Ita_N	R8_Central_Ita_N	8.8931918	8.8931918	1	0	0
NEO695_N_Marche_Maddalena_di_Muccia	R6_Central_Ita_N	8.8316977	8.8316977	1	0	0
R6_Central_Ita_N	R25_Sardinia_EBA_Nuragic	8.5776031	8.5776031	1	0	0
R6_Central_Ita_N	SUC002_Sardinia_EBA_Nuragic	8.5735023	8.5735023	1	0	0
R6_Central_Ita_N	RISE486-EBA	8.0664992	8.0664992	1	0	0

chrs

StartM	EndM	length	lengthM	ch	iid1	iid2
2.270176888	2.331826925	2348	0.061650038	1	R6_Central_Ita_N	I3743_Sardinia_EBA
2.161165953	2.222141981	1531	0.060976028	1	R6_Central_Ita_N	R5_Central_Ita_ChL
2.581681967	2.655436039	1753	0.073754072	1	ETR007_EarlyMedieval	R6_Central_Ita_N
1.499846	1.619487047	783	0.119641066	1	R4_Central_Ita_ChL	R6_Central_Ita_N
1.007086992	1.074638009	2391	0.067551017	2	R6_Central_Ita_N	I15941_Sardinia_N
1.00297296	1.079401016	2693	0.076428056	2	R6_Central_Ita_N	SUA007_Sardinia_EBA
0.516057014	0.58691299	2417	0.070855975	2	R6_Central_Ita_N	R24_Sardinia_N_o
0.625850976	0.691034973	4170	0.065183997	3	R6_Central_Ita_N	R17_Central_Ita_N
1.369027019	1.434453964	2972	0.065426946	3	R10342_IA_Tarq_Monter	R6_Central_Ita_N
0.967778981	1.047595978	2060	0.079816997	3	CAM002_Etruscan	R6_Central_Ita_N
0.648832	0.761654019	5841	0.112821996	3	R6_Central_Ita_N	C2-R19_N
0.529264987	0.594753981	2454	0.065488994	5	R6_Central_Ita_N	I10364_Sardinia_LBA
0.407887995	0.47646901	2054	0.068581015	5	R6_Central_Ita_N	SUA006_Sardinia_BA_Nuragic
0.086907998	0.147057995	1341	0.060149997	5	R6_Central_Ita_N	C4-R1551_Imperial
0.664951026	0.729852021	3410	0.064900994	5	R1014_ChL	R6_Central_Ita_N
0.234761	0.304394007	2291	0.069633007	6	R6_Central_Ita_N	MA79_Sardinia_N_o
1.345520973	1.413957	2320	0.068436027	6	R1014_ChL	R6_Central_Ita_N
1.653275967	1.719377995	2290	0.066102028	6	R1554_Bivio_Roman	R6_Central_Ita_N
1.788967013	1.920325041	3443	0.131358027	6	UZZ061_Sicily_MN	R6_Central_Ita_N
1.450299025	1.51109004	1356	0.060791016	7	R6_Central_Ita_N	CL63_North_EarlyMedieval_Langobards_2
0.023104001	0.086871997	1508	0.063767996	7	R6_Central_Ita_N	ORC006_Sardinia_BA_Nuragic
1.048071027	1.120669007	2663	0.07259798	7	R6_Central_Ita_N	SUA006_Sardinia_BA_Nuragic
0.829534	0.917850971	2675	0.088316977	8	NEO695_N_Marche_Maddalena_di_Muccia	R6_Central_Ita_N
0.016723	0.108181998	2209	0.091458999	9	R6_Central_Ita_N	MA89_Sardinia_C_o
0.438704997	0.502655983	1595	0.063950986	9	R6_Central_Ita_N	SUA003_Sardinia_BA_Nuragic
0.720899999	0.794071019	1844	0.07317102	9	R6_Central_Ita_N	R29_Sardinia_C_BA
0.694546998	0.773594022	1859	0.079047024	10	R6_Central_Ita_N	MA79_Sardinia_N_o
0.068690002	0.142934993	1941	0.074244991	10	R27_Sardinia_C_BA	R6_Central_Ita_N
0.349999994	0.459028989	3876	0.109028995	10	R6_Central_Ita_N	R29_Sardinia_C_BA
0.357235	0.459221989	3570	0.101986974	10	R6_Central_Ita_N	R29_Sardinia_C_BA
0.641763	0.740872979	1113	0.099110007	10	R6_Central_Ita_N	C4-R1551_Imperial
1.494881988	1.556825995	1631	0.061944008	11	R6_Central_Ita_N	R2_N
1.51612103	1.576606035	1456	0.060485005	11	R6_Central_Ita_N	ORC008_Sardinia_BA_Nuragic
1.422227025	1.497684956	1683	0.075457931	11	R850_IA	R6_Central_Ita_N
1.373710036	1.462641954	2565	0.088931918	11	R6_Central_Ita_N	R8_Central_Ita_N
0.334344	0.404110998	2265	0.069766998	12	R6_Central_Ita_N	R2_N
0.02138	0.082427002	1374	0.061047003	12	R6_Central_Ita_N	C5-R1545_Imperial
0.642802	0.708263993	1942	0.065461993	12	R6_Central_Ita_N	SUA007_Sardinia_EBA
0.999324024	1.062018037	1474	0.062694013	13	R6_Central_Ita_N	R29_Sardinia_C_BA
0.446166992	0.519152999	2732	0.072986007	14	R6_Central_Ita_N	R5_Central_Ita_ChL
1.004974961	1.077105999	1935	0.072131038	14	R6_Central_Ita_N	SEC004_Sardinia_LateC
0.532817006	0.59325999	1697	0.060442984	16	R6_Central_Ita_N	MA79_Sardinia_N_o
0.471539	0.566242993	2045	0.094704002	16	R6_Central_Ita_N	C2-R19_N
0.126094997	0.199433997	1628	0.073339	17	R6_Central_Ita_N	R16_Central_Ita_N
1.099998951	1.173102975	1703	0.073104024	18	R6_Central_Ita_N	SEC004_Sardinia_LateC
0.628377974	0.714112997	3365	0.085735023	18	R6_Central_Ita_N	SUC002_Sardinia_EBA_Nuragic
0.628397	0.714173019	3313	0.085776031	18	R6_Central_Ita_N	R25_Sardinia_EBA_Nuragic
0.428718001	0.491939992	1457	0.063221991	19	UZZ071_Sicily_LateMesolithic	R6_Central_Ita_N
0.031847	0.123511001	798	0.091664001	19	R6_Central_Ita_N	R18_Central_Ita_N
0.224729002	0.309895992	2822	0.085166991	21	R6_Central_Ita_N	R16_Central_Ita_N
0.224735	0.309881985	2766	0.085146978	21	R6_Central_Ita_N	R16_Central_Ita_N
0.539336	0.620001018	2074	0.080664992	21	R6_Central_Ita_N	RISE486-EBA
0.461008996	0.532106996	2553	0.071098	22	R6_Central_Ita_N	I14677_Sardinia_C_MonteClaro
0.056503	0.164136007	1406	0.107633006	22	NEO828_C_Campania_Gaudo	R6_Central_Ita_N
0.107702	0.197623998	1165	0.089921996	22	R6_Central_Ita_N	C7-R116_Imperial

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