High-density SNP-based Linkage Mapping reveals Novel QTLs for Noug
Guizotia abyssinica
isolate
Ethiopia
cultivar
Noug
ecotype
Ethiopia
age
2 weeks
dev_stage
vegetative
collection_date
2022-01-05
geo_loc_name
Ethiopia
tissue
leaves
library_id
NGS2778
title
High-density SNP-based Linkage Mapping reveals Novel QTLs for Noug (Guizotia abyssinica).
library_strategy
GBS
library_source
GENOMIC
library_selection
Restriction Digest
library_layout
single
platform
ILLUMINA
instrument_model
NextSeq 500
design_description
GBS clustering, alignment and SNP discovery:Clustering of combined reads with CD-HIT-EST v4.6.1 [4], allowing up to 5% difference (folder Clusters) filtering of the clusters: excluding singletons and clusters created from < 20 readsAlignment of subsampled quality trimmed reads against cluster reference using Bowtie2 v2.2.3 [5] (folder Alignments):one combined alignment for all samples in coordinate-sorted BAM formatVariant discovery and genotyping of samples with Freebayes v1.0.2-16 [6] (folderVariantAnalysis):the following specific parameters were used: - -min-base-quality 10 - -min-supportingalleleqsum 10 - -read-mismatch-limit 3 - -min-coverage 5 - -no-indels - -min-alternatecount 4 - -exclude-unobserved-genotypes - -genotype-qualities - -ploidy 2 or 4 - -nomnps - -nocomplex - -mismatch-base-quality-threshold 10Filtering of variants using a GBS-specific rule set:the read count for a locus must exceed 8 reads (GMCF8 Excel spreadsheets)genotypes must have been observed in at least 10% of samples (MinNS Excel spreadsheets)minimum allele frequency across all samples must exceed 5% (MinAF0.05 Excel spreadsheets)filtering of parental alleles with regard to progenyGenetic distance matrix generation (Kosman/Leonard distance)
filetype
fastq
filename
SRA metadata SUB14889612.tsv
BioSampleModel
Plant