diff --git a/2022_Yu_VanDeLoosdrecht_Sicily/2022_Yu_VanDeLoosdrecht_Sicily.bed b/2022_Yu_VanDeLoosdrecht_Sicily/2022_Yu_VanDeLoosdrecht_Sicily.bed deleted file mode 100644 index 20725ae7..00000000 --- a/2022_Yu_VanDeLoosdrecht_Sicily/2022_Yu_VanDeLoosdrecht_Sicily.bed +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:6bade758ba72a25c60f32a4f8f3fbb9cc1ac38a3e40fe2dc350d3a7c1ae62837 -size 4343778 diff --git a/2022_Yu_VanDeLoosdrecht_Sicily/2022_Yu_VanDeLoosdrecht_Sicily.bib b/2022_Yu_VanDeLoosdrecht_Sicily/2022_Yu_VanDeLoosdrecht_Sicily.bib deleted file mode 100644 index 0627c1bd..00000000 --- a/2022_Yu_VanDeLoosdrecht_Sicily/2022_Yu_VanDeLoosdrecht_Sicily.bib +++ /dev/null @@ -1,14 +0,0 @@ -@article{YuiScience2022, - title = {Genomic and dietary discontinuities during the Mesolithic and Neolithic in Sicily}, - volume = {25}, - ISSN = {2589-0042}, - url = {http://dx.doi.org/10.1016/j.isci.2022.104244}, - DOI = {10.1016/j.isci.2022.104244}, - number = {5}, - journal = {iScience}, - publisher = {Elsevier BV}, - author = {Yu, He and van de Loosdrecht, Marieke S. and Mannino, Marcello A. and Talamo, Sahra and Rohrlach, Adam B. and Childebayeva, Ainash and Villalba-Mouco, Vanessa and Aron, Franziska and Brandt, Guido and Burri, Marta and Freund, C\"{a}cilia and Radzeviciute, Rita and Stahl, Raphaela and Wissgott, Antje and Fewlass, Helen and Tagliacozzo, Antonio and Piperno, Marcello and Tusa, Sebastiano and Collina, Carmine and Schimmenti, Vittoria and Di Salvo, Rosaria and Pr\"{u}fer, Kay and Posth, Cosimo and Hublin, Jean-Jacques and Gronenborn, Detlef and Binder, Didier and Jeong, Choongwon and Haak, Wolfgang and Krause, Johannes}, - year = {2022}, - month = may, - pages = {104244} -}i diff --git a/2022_Yu_VanDeLoosdrecht_Sicily/2022_Yu_VanDeLoosdrecht_Sicily.bim b/2022_Yu_VanDeLoosdrecht_Sicily/2022_Yu_VanDeLoosdrecht_Sicily.bim deleted file mode 100644 index 78dd5846..00000000 --- a/2022_Yu_VanDeLoosdrecht_Sicily/2022_Yu_VanDeLoosdrecht_Sicily.bim +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:a2c6797131580548742c3cdc7f3d2e80f832f85159304d6bcd08419cd20c5cc6 -size 30498959 diff --git a/2022_Yu_VanDeLoosdrecht_Sicily/2022_Yu_VanDeLoosdrecht_Sicily.fam b/2022_Yu_VanDeLoosdrecht_Sicily/2022_Yu_VanDeLoosdrecht_Sicily.fam deleted file mode 100644 index 2f072406..00000000 --- a/2022_Yu_VanDeLoosdrecht_Sicily/2022_Yu_VanDeLoosdrecht_Sicily.fam +++ /dev/null @@ -1,20 +0,0 @@ -Sicily_EM UZZ05054 0 0 2 0 -Sicily_LM UZZ04446 0 0 2 0 -Uzzo_exclude UZZ026.cont 0 0 1 0 -Sicily_EN UZZ033 0 0 1 0 -Sicily_EN UZZ034 0 0 2 0 -Sicily_LM UZZ040 0 0 1 0 -Uzzo_EBA UZZ057 0 0 1 0 -Sicily_EN UZZ061 0 0 1 0 -Sicily_LM UZZ069 0 0 2 0 -Sicily_LM UZZ071 0 0 2 0 -Sicily_EN UZZ074 0 0 2 0 -Sicily_EN UZZ075 0 0 2 0 -Sicily_EN UZZ077 0 0 2 0 -Sicily_LM UZZ079 0 0 2 0 -Sicily_LM UZZ080 0 0 2 0 -Sicily_LM UZZ081 0 0 1 0 -Sicily_LM UZZ082 0 0 2 0 -Sicily_EN UZZ087 0 0 2 0 -Sicily_LM UZZ088 0 0 2 0 -Sicily_LM UZZ096 0 0 2 0 diff --git a/2022_Yu_VanDeLoosdrecht_Sicily/2022_Yu_VanDeLoosdrecht_Sicily.janno b/2022_Yu_VanDeLoosdrecht_Sicily/2022_Yu_VanDeLoosdrecht_Sicily.janno deleted file mode 100644 index 520cda66..00000000 --- a/2022_Yu_VanDeLoosdrecht_Sicily/2022_Yu_VanDeLoosdrecht_Sicily.janno +++ /dev/null @@ -1,21 +0,0 @@ -Poseidon_ID Genetic_Sex Group_Name Alternative_IDs Relation_To Relation_Degree Country Country_ISO Location Site Latitude Longitude Date_Type Date_C14_Labnr Date_C14_Uncal_BP Date_C14_Uncal_BP_Err Date_BC_AD_Start Date_BC_AD_Median Date_BC_AD_Stop MT_Haplogroup Y_Haplogroup Source_Tissue Nr_Libraries Capture_Type UDG Library_Built Genotype_Ploidy Nr_SNPs Coverage_on_Target_SNPs Damage Contamination Contamination_Err Contamination_Meas Genetic_Source_Accession_IDs Primary_Contact Publication -UZZ05054 F Sicily_EM R-EVA 1935 n/a n/a Italy IT Sicily Grotta dell'Uzzo 38.11 12.79 C14 MAMS-40710 9436 29 -8800 -8710 -8620 U2'3'4'7'8'9 n/a tooth 13 1240K mixed mixed haploid 704825 3.718 39.2 0.01;0.03 0.01;0.01 Schmutzi;Contamix v1.0.10 PRJEB50762 He Yu YuiScience2022 -UZZ04446 F Sicily_LM R-EVA 1930 n/a n/a Italy IT Sicily Grotta dell'Uzzo 38.11 12.79 C14 MAMS-40709 7713 26 -6480 -6330 -6180 U5b2b n/a tooth;bone_mandible 5 1240K minus ss haploid 484393 1.229 34.8 0.02;0.04 0.01;0.01 Schmutzi;Contamix v1.0.10 PRJEB50762 He Yu YuiScience2022 -UZZ026.cont M Uzzo_exclude R-EVA 1918 n/a n/a Italy IT Sicily Grotta dell'Uzzo 38.11 12.79 C14 MAMS-40708 9436 36 -9040 -8830 -8620 n/a n/a bone_cranial 1 1240K minus ss haploid 52636 0.075 21.1 0.02;0.15 0.01;0.05 Schmutzi;Contamix v1.0.10 PRJEB50762 He Yu YuiScience2022 -UZZ033 M Sicily_EN n/a n/a n/a Italy IT Sicily Grotta dell'Uzzo 38.11 12.79 contextual n/a n/a n/a -5380 -5295 -5210 U8b1b1 H2 tooth 1 1240K minus ss haploid 346153 0.721 28.4 0.01;0.00;0.03 0.01;0.00;0.01 Schmutzi;Contamix v1.0.10;ANGSD v0.910 PRJEB50762 He Yu YuiScience2022 -UZZ034 F Sicily_EN R-EVA 2879 n/a n/a Italy IT Sicily Grotta dell'Uzzo 38.11 12.79 C14 MAMS-40725 6351 24 -5380 -5295 -5210 U8b1b1 n/a tooth 1 1240K minus ss haploid 255340 0.535 27.2 0.01;0.04 0.01;0.01 Schmutzi;Contamix v1.0.10 PRJEB50762 He Yu YuiScience2022 -UZZ040 M Sicily_LM R-EVA 2880 n/a n/a Italy IT Sicily Grotta dell'Uzzo 38.11 12.79 C14 MAMS-40726 7471 26 -6420 -6330 -6240 U4a2f I2a1b tooth 1 1240K minus ss haploid 242290 0.558 45.9 0.01;0.02;0.04 0.01;0.00;0.01 Schmutzi;Contamix v1.0.10;ANGSD v0.910 PRJEB50762 He Yu YuiScience2022 -UZZ057 M Uzzo_EBA R-EVA 2883 n/a n/a Italy IT Sicily Grotta dell'Uzzo 38.11 12.79 C14 MAMS-40727 3708 19 -2200 -2110 -2020 n/a R1b1a1b1a1a2 bone_phalanx 3 1240K minus mixed haploid 170167 0.331 23.3 0.02;0.00;0.01 0.01;0.00;0.01 Schmutzi;Contamix v1.0.10;ANGSD v0.910 PRJEB50762 He Yu YuiScience2022 -UZZ061 M Sicily_EN R-EVA 3521 n/a n/a Italy IT Sicily Grotta dell'Uzzo 38.11 12.79 C14 MAMS-48211 5923 25 -4880 -4795 -4710 K1a2 C1a2b1 bone_phalanx 3 1240K minus mixed haploid 656124 3.653 28.6 0.01;0.03;0.02 0.01;0.02;0.00 Schmutzi;Contamix v1.0.10;ANGSD v0.910 PRJEB50762 He Yu YuiScience2022 -UZZ069 F Sicily_LM R-EVA 1948 n/a n/a Italy IT Sicily Grotta dell'Uzzo 38.11 12.79 C14 MAMS-40711 7848 26 -6590 -6415 -6240 U5b2b n/a bone_mandible 5 1240K minus mixed haploid 620607 2.822 33.8 0.03;0.07 0.01;0.03 Schmutzi;Contamix v1.0.10 PRJEB50762 He Yu YuiScience2022 -UZZ071 F Sicily_LM R-EVA 3522 n/a n/a Italy IT Sicily Grotta dell'Uzzo 38.11 12.79 C14 MAMS-48212 7051 27 -6010 -5925 -5840 U5a2+16294 n/a tooth 3 1240K mixed mixed haploid 519594 1.598 36.8 0.01;0.01 0.01;0.01 Schmutzi;Contamix v1.0.10 PRJEB50762 He Yu YuiScience2022 -UZZ074 F Sicily_EN R-EVA 1953 n/a n/a Italy IT Sicily Grotta dell'Uzzo 38.11 12.79 C14 MAMS-40716 6310 23 -5330 -5270 -5210 N1a1a1 n/a bone_femur 1 1240K minus ss haploid 179591 0.375 46.8 0.02;0.02 0.01;0.02 Schmutzi;Contamix v1.0.10 PRJEB50762 He Yu YuiScience2022 -UZZ075 F Sicily_EN R-EVA 1954 n/a n/a Italy IT Sicily Grotta dell'Uzzo 38.11 12.79 C14 MAMS-40717 6310 23 -5330 -5270 -5210 J1c5 n/a bone_petrous 2 1240K minus ss haploid 756409 5.973 41.3 0.01;0.01 0.01;0.01 Schmutzi;Contamix v1.0.10 PRJEB50762 He Yu YuiScience2022 -UZZ077 F Sicily_EN R-EVA 3523 n/a n/a Italy IT Sicily Grotta dell'Uzzo 38.11 12.79 C14 MAMS-48213 6446 25 -5480 -5420 -5360 H n/a tooth 1 1240K minus ss haploid 155557 0.273 44.5 0.01;0.00 0.01;0.00 Schmutzi;Contamix v1.0.10 PRJEB50762 He Yu YuiScience2022 -UZZ079 F Sicily_LM R-EVA 1957 UZZ081 first Italy IT Sicily Grotta dell'Uzzo 38.11 12.79 C14 MAMS-40719 7809 26 -6570 -6390 -6210 U5b3(d) n/a bone_petrous 2 1240K minus ss haploid 750625 7.271 31.8 0.01;0.02 0.01;0.01 Schmutzi;Contamix v1.0.10 PRJEB50762 He Yu YuiScience2022 -UZZ080 F Sicily_LM R-EVA 1958 n/a n/a Italy IT Sicily Grotta dell'Uzzo 38.11 12.79 C14 MAMS-40720 7809 26 -6570 -6390 -6210 U5b2b1a n/a bone_petrous 3 1240K mixed mixed haploid 796174 9.392 35.8 0.02;0.04 0.01;0.01 Schmutzi;Contamix v1.0.10 PRJEB50762 He Yu YuiScience2022 -UZZ081 M Sicily_LM R-EVA 1959 UZZ079 first Italy IT Sicily Grotta dell'Uzzo 38.11 12.79 C14 MAMS-40721 7807 26 -6570 -6400 -6230 U5b3(d) I2a1b2 bone_petrous 2 1240K mixed mixed haploid 283872 0.675 36 0.01;0.01;0.04 0.01;0.01;0.01 Schmutzi;Contamix v1.0.10;ANGSD v0.910 PRJEB50762 He Yu YuiScience2022 -UZZ082 F Sicily_LM R-EVA 1960 n/a n/a Italy IT Sicily Grotta dell'Uzzo 38.11 12.79 C14 MAMS-40722 7809 26 -6700 -6635 -6570 U5a1 n/a bone_petrous 2 1240K mixed mixed haploid 720058 4.932 42.8 0.01;0.02 0.01;0.00 Schmutzi;Contamix v1.0.10 PRJEB50762 He Yu YuiScience2022 -UZZ087 F Sicily_EN R-EVA 1964 n/a n/a Italy IT Sicily Grotta dell'Uzzo 38.11 12.79 C14 MAMS-40723 6286 24 -5320 -5265 -5210 n/a n/a bone_humerus 1 1240K minus ss haploid 53352 0.087 52.3 0.03 0.01 Schmutzi PRJEB50762 He Yu YuiScience2022 -UZZ088 F Sicily_LM R-EVA 1965 n/a n/a Italy IT Sicily Grotta dell'Uzzo 38.11 12.79 C14 MAMS-40712 7036 25 -6000 -5920 -5840 U5b3(d) n/a bone_phalanx 1 1240K minus ss haploid 556469 1.978 40.7 0.02;0.04 0.01;0.01 Schmutzi;Contamix v1.0.10 PRJEB50762 He Yu YuiScience2022 -UZZ096 F Sicily_LM n/a n/a n/a Italy IT Sicily Grotta dell'Uzzo 38.11 12.79 contextual n/a n/a n/a -8800 -8300 -7800 U2'3'4'7'8'9 n/a tooth_M2 upper right 1 1240K minus ss haploid 67911 0.109 41.7 0.02;0.07 0.01;0.07 Schmutzi;Contamix v1.0.10 PRJEB50762 He Yu YuiScience2022 diff --git a/2022_Yu_VanDeLoosdrecht_Sicily/POSEIDON.yml b/2022_Yu_VanDeLoosdrecht_Sicily/POSEIDON.yml deleted file mode 100644 index ab0107d3..00000000 --- a/2022_Yu_VanDeLoosdrecht_Sicily/POSEIDON.yml +++ /dev/null @@ -1,22 +0,0 @@ -poseidonVersion: 2.7.1 -title: 2022_Yu_VanDeLoosdrecht_Sicily -description: Genotypes of ancient individuals from Grotta dell'Uzzo, excluding SNP sites on CpG islands -contributor: -- name: He Yu - email: yuhe@pku.edu.cn - orcid: 0000-0003-1323-4730 -packageVersion: 1.0.0 -lastModified: 2023-11-23 -genotypeData: - format: PLINK - genoFile: 2022_Yu_VanDeLoosdrecht_Sicily.bed - 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