Identifying diagnostic genetic markers for a cryptic invasive agricultural pest: a test case using the apple maggot fly, Rhagoletis pomonella (Diptera: Tephritidae)
Data files
Dec 17, 2020 version files 114 GB
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DoellmanHoodRzeph_popIDs.txt
12.03 KB
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DoellmanHoodRzephL1_1.fq.gz
13.73 GB
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DoellmanHoodRzephL1_2.fq.gz
13.62 GB
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DoellmanHoodRzephL1_barcodes.txt
3.04 KB
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DoellmanHoodRzephL2_1.fq.gz
13.53 GB
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DoellmanHoodRzephL2_2.fq.gz
13.34 GB
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DoellmanHoodRzephL2_barcodes.txt
3.11 KB
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DoellmanHoodRzephL3_1.fq.gz
15.12 GB
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DoellmanHoodRzephL3_2.fq.gz
14.91 GB
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DoellmanHoodRzephL3_barcodes.txt
3.20 KB
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DoellmanHoodRzephL4_1.fq.gz
14.90 GB
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DoellmanHoodRzephL4_2.fq.gz
14.81 GB
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DoellmanHoodRzephL4_barcodes.txt
2.36 KB
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DoellmanHoodRzephSNPs.vcf.gz
41.65 MB
Abstract
Usage notes
Filtered vcf file with genotype probabilities: DoellmanHoodRzephSNPs.vcf.gz
This is a vcf file generated using the GATK unified genotyper, then filtered as describe in the paper. The PL field provides the phred-scaled and normalized genotype probabilities produced using the GATK model.
File mapping individual IDs to host associations: DoellmanHoodRzeph_popIDs.txt
column 1 = sample id (sample id in the vcf file), column 2 = host association
Raw Illumina sequencing data and barcodes for demultiplexing, Lane 1
DoellmanHoodRzephL1_1.fq.gz
Illumina forward reads
DoellmanHoodRzephL1_2.fq.gz
Illumina paired reads
DoellmanHoodRzephL1_barcodes.txt
column 1 = inline barcode (5' end of the forward read), column 2 = sample id (sample id in the vcf file)
Raw Illumina sequencing data and barcodes for demultiplexing, Lane 2
DoellmanHoodRzephL2_1.fq.gz
Illumina forward reads
DoellmanHoodRzephL2_2.fq.gz
Illumina paired reads
DoellmanHoodRzephL2_barcodes.txt
column 1 = inline barcode (5' end of the forward read), column 2 = sample id (sample id in the vcf file)
Raw Illumina sequencing data and barcodes for demultiplexing, Lane 3
DoellmanHoodRzephL3_1.fq.gz
Illumina forward reads
DoellmanHoodRzephL3_2.fq.gz
Illumina paired reads
DoellmanHoodRzephL3_barcodes.txt
column 1 = inline barcode (5' end of the forward read), column 2 = sample id (sample id in the vcf file)
Raw Illumina sequencing data and barcodes for demultiplexing, Lane 4
DoellmanHoodRzephL4_1.fq.gz
Illumina forward reads
DoellmanHoodRzephL4_2.fq.gz
Illumina paired reads
DoellmanHoodRzephL4_barcodes.txt
column 1 = inline barcode (5' end of the forward read), column 2 = sample id (sample id in the vcf file)