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| Unknown GUP001_SG_MNT 0 0 0 0 | ||
| Unknown GUP001_TF_MNT 0 0 0 0 | ||
| Unknown GUP001_MNT 0 0 0 0 | ||
| Unknown GUP001_SG_ss_MNT 0 0 0 0 | ||
| Unknown GUP001_TF_ss_MNT 0 0 0 0 | ||
| Unknown GUP001_ss_MNT 0 0 0 0 |
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| Poseidon_ID Genetic_Sex Group_Name Alternative_IDs Main_ID Relation_To Relation_Degree Relation_Type Relation_Note Collection_ID 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 Date_Note MT_Haplogroup Y_Haplogroup Source_Tissue Nr_Libraries Library_Names Capture_Type UDG Library_Built Genotype_Ploidy Data_Preparation_Pipeline_URL Endogenous Nr_SNPs Coverage_on_Target_SNPs Damage Contamination Contamination_Err Contamination_Meas Contamination_Note Genetic_Source_Accession_IDs Primary_Contact Publication Note Keywords Eager_ID RateX RateY RateErrX RateErrY | ||
| GUP001_SG_MNT U Unknown n/a GUP001_SG n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a 1 GUP001.A0101 n/a n/a n/a n/a n/a n/a 89 n/a 0.29907621247113164 n/a n/a n/a Nr Snps (per library): 0. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded. n/a n/a n/a n/a n/a GUP001_SG 0.9636086526349631 0.0 0.010204199133524001 0.0 | ||
| GUP001_TF_MNT U Unknown n/a GUP001_TF n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a 1 GUP001.A0101 n/a n/a n/a n/a n/a n/a 272453 n/a 0.4671036789297659 0.111878 3.564714e-14 ANGSD[v0.935] Nr Snps (per library): 688. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded. n/a n/a n/a n/a n/a GUP001_TF 0.8070175688796091 0.015203507302283 0.000625416818528 0.00013595636502000002 | ||
| GUP001_MNT U Unknown n/a GUP001 n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a 1 GUP001.A0101 n/a n/a n/a n/a n/a n/a 272731 n/a 0.4636218846261551 0.11128 3.536035e-14 ANGSD[v0.935] Nr Snps (per library): 691. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded. n/a n/a n/a n/a n/a GUP001 0.807350562380271 0.014966276895201 0.0006189713976130001 0.00013347233346400002 | ||
| GUP001_SG_ss_MNT U Unknown n/a GUP001_SG n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a 1 GUP001.A0102 n/a n/a n/a n/a n/a n/a 234 n/a 0.6001231021748051 n/a n/a n/a Nr Snps (per library): 0. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded. n/a n/a n/a n/a n/a GUP001_SG_ss 0.9660581314505241 0.0 0.004707619706178 0.0 | ||
| GUP001_TF_ss_MNT U Unknown n/a GUP001_TF n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a 1 GUP001.A0102 n/a n/a n/a n/a n/a n/a 125634 n/a 0.5882118560276257 0.100717 5.1028e-15 ANGSD[v0.935] Nr Snps (per library): 339. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded. n/a n/a n/a n/a n/a GUP001_TF_ss 0.7869599919082071 0.014694578552265001 0.0008079036163350001 0.000174936775572 | ||
| GUP001_ss_MNT U Unknown n/a GUP001 n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a 1 GUP001.A0102 n/a n/a n/a n/a n/a n/a 134067 n/a 0.5877389065164661 0.097276 3.860919e-15 ANGSD[v0.935] Nr Snps (per library): 345. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded. n/a n/a n/a n/a n/a GUP001_ss 0.52657564310572 0.008035372443371 0.000444473767365 8.758126192708205e-05 | ||
| GUP001_MNT U Unknown n/a GUP001 n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a 1 GUP001.A0101 1240K;Shotgun half ds haploid https://github.com/nf-core/eager/releases/tag/2.4.6 6.762222 272731 n/a 0.4636218846261551 0.11128 3.536035e-14 ANGSD[v0.935] Nr Snps (per library): 691. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded. PRJEB43715;ERS5956814;ERR5490520;ERR5490521;ERR5490522;ERR5490523;ERR5490524;ERR5490525;ERR5490526 n/a n/a n/a n/a GUP001 0.8115348979428191 0.020098725775262002 0.007582631999185001 0.001447150678242 | ||
| GUP001_ss_MNT U Unknown n/a GUP001 n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a 1 GUP001.A0102 1240K;Shotgun minus ss haploid https://github.com/nf-core/eager/releases/tag/2.4.6 13.339985 134067 n/a 0.5877457008717157 0.097276 3.860919e-15 ANGSD[v0.935] Nr Snps (per library): 345. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded. PRJEB43715;ERS5956814;ERR5490527;ERR5490528;ERR5490529 n/a n/a n/a n/a GUP001_ss 0.7711635308594431 0.019378750752398 0.008514648295196001 0.0016382538785210002 |
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| sample_accession study_accession run_accession sample_alias poseidon_IDs udg library_built secondary_sample_accession first_public last_updated instrument_model library_layout library_source instrument_platform library_name library_strategy fastq_aspera fastq_bytes fastq_md5 fastq_ftp read_count submitted_ftp | ||
| SAMEA8270508 PRJEB43715 ERR5490520 GUP001 GUP001_MNT half ds ERS5956814 2021-06-18 2021-06-18 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA GUP001.A0101 Targeted-Capture fasp.sra.ebi.ac.uk:/vol1/fastq/ERR549/000/ERR5490520/ERR5490520.fastq.gz 31485654 842ec55a3a0aff4979dea1b5dc529e7c ftp.sra.ebi.ac.uk/vol1/fastq/ERR549/000/ERR5490520/ERR5490520.fastq.gz 945210 ftp.sra.ebi.ac.uk/vol1/run/ERR549/ERR5490520/GUP001.A0101.MT1.1.fastq.truncated.gz | ||
| SAMEA8270508 PRJEB43715 ERR5490521 GUP001 GUP001_MNT half ds ERS5956814 2021-06-18 2021-06-18 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA GUP001.A0101 Targeted-Capture fasp.sra.ebi.ac.uk:/vol1/fastq/ERR549/001/ERR5490521/ERR5490521.fastq.gz 32643939 e4c9ae3aed81094a383c2c2003dd961f ftp.sra.ebi.ac.uk/vol1/fastq/ERR549/001/ERR5490521/ERR5490521.fastq.gz 1040533 ftp.sra.ebi.ac.uk/vol1/run/ERR549/ERR5490521/GUP001.A0101.MT1.2.fastq.truncated.gz | ||
| SAMEA8270508 PRJEB43715 ERR5490522 GUP001 GUP001_MNT half ds ERS5956814 2021-06-18 2021-06-18 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA GUP001.A0101 Targeted-Capture fasp.sra.ebi.ac.uk:/vol1/fastq/ERR549/002/ERR5490522/ERR5490522.fastq.gz 192243801 a4add9bc886418c913420eab0391297e ftp.sra.ebi.ac.uk/vol1/fastq/ERR549/002/ERR5490522/ERR5490522.fastq.gz 6189559 ftp.sra.ebi.ac.uk/vol1/run/ERR549/ERR5490522/GUP001.A0101.MT1.3.fastq.truncated.gz | ||
| SAMEA8270508 PRJEB43715 ERR5490523 GUP001 GUP001_MNT half ds ERS5956814 2021-06-18 2021-06-18 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA GUP001.A0101 WGS fasp.sra.ebi.ac.uk:/vol1/fastq/ERR549/003/ERR5490523/ERR5490523.fastq.gz 95526960 29a36d22db98919f96d32af631a9422c ftp.sra.ebi.ac.uk/vol1/fastq/ERR549/003/ERR5490523/ERR5490523.fastq.gz 2888875 ftp.sra.ebi.ac.uk/vol1/run/ERR549/ERR5490523/GUP001.A0101.SG1.1.fastq.truncated.gz | ||
| SAMEA8270508 PRJEB43715 ERR5490524 GUP001 GUP001_MNT half ds ERS5956814 2021-06-18 2021-06-18 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA GUP001.A0101 Targeted-Capture fasp.sra.ebi.ac.uk:/vol1/fastq/ERR549/004/ERR5490524/ERR5490524.fastq.gz 562634908 ee58126a3880e12ac25ff3c1adf97aec ftp.sra.ebi.ac.uk/vol1/fastq/ERR549/004/ERR5490524/ERR5490524.fastq.gz 17847250 ftp.sra.ebi.ac.uk/vol1/run/ERR549/ERR5490524/GUP001.A0101.TF1.1.fastq.truncated.gz | ||
| SAMEA8270508 PRJEB43715 ERR5490525 GUP001 GUP001_MNT half ds ERS5956814 2021-06-18 2021-06-18 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA GUP001.A0101 Targeted-Capture fasp.sra.ebi.ac.uk:/vol1/fastq/ERR549/005/ERR5490525/ERR5490525.fastq.gz 1541567827 640a45bc4956b647f5578a66763813d0 ftp.sra.ebi.ac.uk/vol1/fastq/ERR549/005/ERR5490525/ERR5490525.fastq.gz 50108944 ftp.sra.ebi.ac.uk/vol1/run/ERR549/ERR5490525/GUP001.A0101.TF1.2.fastq.truncated.gz | ||
| SAMEA8270508 PRJEB43715 ERR5490526 GUP001 GUP001_MNT half ds ERS5956814 2021-06-18 2021-06-18 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA GUP001.A0101 Targeted-Capture fasp.sra.ebi.ac.uk:/vol1/fastq/ERR549/006/ERR5490526/ERR5490526.fastq.gz 674880719 e58345ddc808d879d255f8d68065050d ftp.sra.ebi.ac.uk/vol1/fastq/ERR549/006/ERR5490526/ERR5490526.fastq.gz 23288459 ftp.sra.ebi.ac.uk/vol1/run/ERR549/ERR5490526/GUP001.A0101.TF1.3.fastq.truncated.gz | ||
| SAMEA8270508 PRJEB43715 ERR5490527 GUP001 GUP001_ss_MNT minus ss ERS5956814 2021-06-18 2021-06-18 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA GUP001.A0102 Targeted-Capture fasp.sra.ebi.ac.uk:/vol1/fastq/ERR549/007/ERR5490527/ERR5490527.fastq.gz 656969967 d16a8f18feef912878f0b56218581717 ftp.sra.ebi.ac.uk/vol1/fastq/ERR549/007/ERR5490527/ERR5490527.fastq.gz 21959304 ftp.sra.ebi.ac.uk/vol1/run/ERR549/ERR5490527/GUP001.A0102.AA1.1.fastq.truncated.gz | ||
| SAMEA8270508 PRJEB43715 ERR5490528 GUP001 GUP001_ss_MNT minus ss ERS5956814 2021-06-18 2021-06-18 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA GUP001.A0102 WGS fasp.sra.ebi.ac.uk:/vol1/fastq/ERR549/008/ERR5490528/ERR5490528.fastq.gz 145599926 e2be513bf56c01591ecdb7dfbe55c5cb ftp.sra.ebi.ac.uk/vol1/fastq/ERR549/008/ERR5490528/ERR5490528.fastq.gz 5086983 ftp.sra.ebi.ac.uk/vol1/run/ERR549/ERR5490528/GUP001.A0102.SG1.1.fastq.truncated.gz | ||
| SAMEA8270508 PRJEB43715 ERR5490529 GUP001 GUP001_ss_MNT minus ss ERS5956814 2021-06-18 2021-06-18 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA GUP001.A0102 Targeted-Capture fasp.sra.ebi.ac.uk:/vol1/fastq/ERR549/009/ERR5490529/ERR5490529.fastq.gz 674885210 189d55160fdfec278ddc8fba5296ad18 ftp.sra.ebi.ac.uk/vol1/fastq/ERR549/009/ERR5490529/ERR5490529.fastq.gz 23288459 ftp.sra.ebi.ac.uk/vol1/run/ERR549/ERR5490529/GUP001.A0102.TF1.1.fastq.truncated.gz |
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@@ -6,18 +6,21 @@ contributor: | |
| email: [email protected] | ||
| orcid: 0000-0002-1825-0097 | ||
| packageVersion: 0.1.1 | ||
| lastModified: 2023-09-13 | ||
| lastModified: 2024-04-03 | ||
| genotypeData: | ||
| format: PLINK | ||
| genoFile: 2021_CarlhoffNature.bed | ||
| genoFileChkSum: 240f4f944f13093abeeec6cb5096b717 | ||
| genoFileChkSum: 079d15ad25a6db3f7e3d1da9e105abc3 | ||
| snpFile: 2021_CarlhoffNature.bim | ||
| snpFileChkSum: 433fa85a23f3123bade02348e4628b75 | ||
| indFile: 2021_CarlhoffNature.fam | ||
| indFileChkSum: 03f67f28a9d7278322b8bdb5b8108842 | ||
| indFileChkSum: 25f3c92e8bb97f3ef155488b3e22e479 | ||
| snpSet: 1240K | ||
| jannoFile: 2021_CarlhoffNature.janno | ||
| jannoFileChkSum: 8a66d20c37652d196022483b340003aa | ||
| jannoFileChkSum: 206ca32937eade1c26fe90c7f5f51d7e | ||
| sequencingSourceFile: 2021_CarlhoffNature.ssf | ||
| sequencingSourceFileChkSum: ac4cec11100b5ab343548313c86c68b2 | ||
| bibFile: 2021_CarlhoffNature.bib | ||
| bibFileChkSum: 9edc4a757f785a8ecb59c54d16c5690a | ||
| readmeFile: README.md | ||
| changelogFile: CHANGELOG.md | ||
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| # 2021_CarlhoffNature | ||
| This package was created on 2024-04-03 and was processed using the following versions: | ||
| - nf-core/eager version: 2.4.6 | ||
| - Minotaur config version: 0.2.1dev | ||
| - CaptureType profile: 1240K | ||
| - CaptureType config version: 0.2.2dev | ||
| - Config template version: 0.3.0dev | ||
| - Package config version: 0.3.0dev | ||
| - Minotaur-packager version: 0.3.0dev | ||
| - populate_janno.py version: 0.3.2dev |