####Filename: Medulis_phenotype.txt
Description:
Phenotypic data on resistance to Vibrio splendidus were measured in 2,279 individuals. 
Experimental infections (EI_1, EI_2, EI_3) were conducted using a highly pathogenic strain of V. splendidus (strain 14/053 2T1) on adult mussels with a mean individual weight of approximately 5 g. 
Dead mussels were counted and sampled daily up to 72 hours post-injection, while live mussels were counted at the end of the experiment.

The data comprises a text file containing nine tab-separated columns that indicate:
id (1st column), sire_id (2nd column), dam_id (3rd column), family (4th column), pop (5th column), set (6th column), exp (7th column), phenotype (8th column), replicate(9th column).


pop  (population origins): OLE-PON, WIM, YEU_001 
set (set of crosses): set 1, set 2 
exp (replication of the experimental infection): 1, 2, and 3
Phenotype: dead=1 and alive =2.
replicate(tankreplicate): A, B, C


####Filename: Medulis_genotype.txt
Description:
Genotype data for a hatchery-produced blue mussel population after quality control (n = 644 offspring) with corresponding phenotype data (attached file: Medulis_phenotype.txt).
Trait of interest: Resistance to Vibrio splendidus (coded as dead = 1, alive = 2).
Individual mussels were genotyped using the 60K multi-species medium-density Affymetrix Axiom® Mussel SNP-array (Array Type Name: Axiom_Myt_v1). 
The genotype data are available in text format for markers that passed quality control (QC) filters, as detailed below.
SNP genotypes (.CEL files) were imported into the Axiom Analysis Suite v4.0.3.3 software for QC assessment. 
The default best practice workflow recommended by the manufacturer was followed, with minor threshold modifications. 
These modifications included individual QC and SNP QC analysis with the following criteria:
Dish Quality Control (DQC) ≥ 0.20
QC call rate ≥ 90%
Percentage of passing samples ≥ 98%
Average call rate for passing samples ≥ 92%
Call rate cutoff ≥ 95%
Fisher’s Linear Discriminant ≥ 2.6
Genotypes were generated using the default parameter settings for diploid species. 
Probes from the SNP array were subjected to further QC using PLINK v1.9 software. 
SNP variants with a call rate > 90%, a minor allele frequency (MAF) > 0.01, and Hardy-Weinberg equilibrium (HWE) p-value < 0.0000001 were retained. 
Identity-by-descent (IBS) values exceeding 0.90 were excluded.
Parentage assignment was conducted using the R package APIS, with a mismatch threshold set to 5%. 
A subset of 1,471 SNPs with a call rate > 90% and MAF > 0.01 was used for parentage assignment, and only assigned offspring were retained.
Principal component analysis (PCA) was performed using PLINK v1.9. Three individuals were identified as outliers based on population structure and were subsequently excluded from further analysis.
Genotypes were mapped to the chromosome-level Mytilus edulis genome assembly (xbMytEdul2, GenBank accession number: GCA_963676595.2).
The final dataset comprises 644 samples genotyped at 3,406 genome-wide SNPs.


####Filename: QC_SNPs.txt
Description: List of SNP markers retained after Axiom and PLINK quality control.
Number of SNPs: 3,406


####Filename: mapped_SNPs.txt
Description: List of SNPs retained after quality control and mapped to the Mytilus edulis reference genome (GenBank accession number: GCA_963676595.2).
Number of SNPs: 2,204