Supplementary tables for the manuscript titled "DNA methylation haplotype block signatures responding to S. aureus subclinical mastitis and association with production and health traits".

Supplemental Table S1 Detail information on cows selected for whole genome DNA methylation sequencing. 

Supplemental Table S2 General statistics on whole genome DNA methylation sequencing read statistics

Supplemental Table S3 Comparisons of methylation level between cows with S. aureus subclinical mastitis and healthy control cows at a scope of the whole genome, chromosomes and gene features.

Supplemental Table S4 List of differentially methylated cytosines in the context of CpG

Supplemental Table S5 List of differentially methylated cytosines in the context of CHG and CHH

Supplemental Table S6 Distribution of differentially methylated cytosines among chromosomes and genetic features 

Supplemental Table S7 Count of differentially methylated cytosines (DMCs) in the context of CpG, CHG and CHH in different gene features per gene

Supplemental Table S8 Functional enrichment of differentially expressed genes harboring differentially methylated cytosines at different genomic functional regions 

Supplemental Table S9 Predicted methylation level for LINE-1 and tRNA-derived SINEs and comparisons between cows with S. aureus subclinical mastitis and healthy control cows

Supplemental Table S10 Differential methylation haplotype blocks and their colocation with QTLs related to mastitis and immune capacity

Supplemental Table S11 Differential genes with significant changes in general methylation level of regulatory regions and gene expression changes

Supplemental Table S12 Functional enrichment for differential genes with significant changes in general methylation level of regulatory regions and gene expression changes

Supplemental Table S13 Correlation between dMHBs located at regulatory regions and their overlapped differentially expressed genes

Supplemental Table S14 Motif enrichment and identification in GE-dMHBs

Supplemental Table S15 Functional enrichment for GE-dMHBs (dMHBs overlapped with genes and significantly correlated with the expression of corresponding genes)

Supplemental Table S16 Candidate discriminate signatures selected from GE-dMHBs (pro-GE-dMHBs) and their overlapped genes

Supplemental Table S17 Information about samples and primers used for TBAS and results of seven GE-dMHBs analyzed in 200 cows