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High quality G-to-A SNPs from the genomes of 96 wild caught three-spine sticklebacks (2019)

Meyer, Britta S ; Heckwolf, Melanie ; Häsler, Robert ; [et al.]

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Publication Date: 2023-01-13

Description: To improve the methylation estimates in our study, we corrected for SNPs, which could have led to a wrong methylation call. The excluded positions were derived with custom written perl scripts from C-to-T and G-to-A-SNPs with genotype quality of 20 and a minimum allele frequency of 0.005 from the 96 wild caught three-spined sticklebacks with a combination of custom written Perl and R-scripts using packages from methylkit and GenomicRanges. This BED-file contains the G-to-A-SNPs, in which the first field is the name of the chromosome; the second describes the start position and the third the end position of the feature in standard chromosomal coordinates.

Keywords: Baltic Sea; BED; Local adaptation; methylation call; population genomics; SNP; three-spined stickleback; Whole genome sequencing

Type: Dataset

Format: application/zip, 5.8 MBytes

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High quality C-to-T SNPs from the genomes of 96 wild caught three-spine sticklebacks (2019)

Meyer, Britta S ; Heckwolf, Melanie ; Häsler, Robert ; [et al.]

PANGAEA

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Publication Date: 2023-01-13

Description: To improve the methylation estimates in our study, we corrected for SNPs, which could have led to a wrong methylation call. The excluded positions were derived with custom written perl scripts from C-to-T and G-to-A-SNPs with genotype quality of 20 and a minimum allele frequency of 0.005 from the 96 wild caught three-spined sticklebacks with a combination of custom written Perl and R-scripts using packages from methylkit and GenomicRanges. This BED-file contains the C-to-T SNPs, in which the first field is the name of the chromosome; the second describes the start position and the third the end position of the feature in standard chromosomal coordinates.

Keywords: Baltic Sea; BED; Local adaptation; methylation call; population genomics; SNP; three-spined stickleback; Whole genome sequencing

Type: Dataset

Format: application/zip, 5.8 MBytes

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Genomic data of three-spined sticklebacks from Kiel (KIE), Germany and Nynäshamn (NYN), Sweden around inducible differentially methylated sites in decreasing salinity (2019)

Meyer, Britta S ; Heckwolf, Melanie ; Häsler, Robert ; [et al.]

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Publication Date: 2023-01-13

Description: This vcf file is generated from genomic data of three-spined sticklebacks from Kiel (KIE), Germany and Nynäshamn (NYN), Sweden. The individuals from Kiel are S3, S4, S19, S20, S33, S34, S47, S48, S49, S50, S63, S64, S77, S78, S89, S90. The individuals from NYN are S5, S6, S21, S22, S35, S36, S37, S38, S51, S52, S65, S66, S79, S80, S85, S86. It contains high quality biallelic positions (GQ=20) and is filtered for minor allele frequencies of maf = 0.05, allows 40 % of missing data (13 individuals) and a read depth of 〉=5. Further this vcf file is subset to the inducible differentially methylated sites (DMS) (198sites) in decreasing PSU (_6PSU) with 5 kilobases (kb) before and after DMS. With this file further calculations were performed to estimate the genetic differentiation (i.e. Fst) between the different populations (see manuscript indicated below).

Keywords: Baltic Sea; Local adaptation; population genomics; three-spined stickleback; VCF; Whole genome sequencing

Type: Dataset

Format: application/zip, 1.6 MBytes

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Genomic data of three-spined sticklebacks from Kiel (KIE) and Sylt (SYL), Germany around inducible differentially methylated sites in increasing salinity (2019)

Meyer, Britta S ; Heckwolf, Melanie ; Häsler, Robert ; [et al.]

PANGAEA

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Publication Date: 2023-01-13

Description: This vcf file is generated from genomic data of three-spined sticklebacks from Kiel (KIE) and Sylt (SYL), Germany. The individuals from Kiel are S3, S4, S19, S20, S33, S34, S47, S48, S49, S50, S63, S64, S77, S78, S89, S90. The individuals from SYL are S9, S10, S17, S18, S31, S32, S45, S46, S59, S60, S61, S62, S73, S74, S87, S88. It contains high quality biallelic positions (GQ=20) and is filtered for minor allele frequencies of maf = 0.05, allows 40 % of missing data (13 individuals) and a read depth of 〉=5. Further this vcf file is subset to the inducible differentially methylated sites (DMS) (148sites) in increasing PSU (_33PSU) with 5 kilobases (kb) before and after DMS. With this file further calculations were performed to estimate the genetic differentiation (i.e. Fst) between the different populations (see manuscript indicated below).

Keywords: Baltic Sea; Local adaptation; population genomics; three-spined stickleback; VCF; Whole genome sequencing

Type: Dataset

Format: application/zip, 1.2 MBytes

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